Starting phenix.real_space_refine (version: dev) on Thu Dec 22 21:53:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/12_2022/8e4p_27895_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/12_2022/8e4p_27895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/12_2022/8e4p_27895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/12_2022/8e4p_27895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/12_2022/8e4p_27895_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4p_27895/12_2022/8e4p_27895_trim_updated.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 616": "OE1" <-> "OE2" Residue "A TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1056": "OE1" <-> "OE2" Residue "C GLU 616": "OE1" <-> "OE2" Residue "C TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1056": "OE1" <-> "OE2" Residue "D GLU 616": "OE1" <-> "OE2" Residue "D TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1056": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 12733 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 19, 'TRANS': 879} Chain breaks: 10 Unresolved non-hydrogen bonds: 729 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 452 Chain: "B" Number of atoms: 12733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 12733 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 19, 'TRANS': 879} Chain breaks: 10 Unresolved non-hydrogen bonds: 729 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 452 Chain: "C" Number of atoms: 12733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 12733 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 19, 'TRANS': 879} Chain breaks: 10 Unresolved non-hydrogen bonds: 729 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 452 Chain: "D" Number of atoms: 12733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 12733 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 19, 'TRANS': 879} Chain breaks: 10 Unresolved non-hydrogen bonds: 729 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 30, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 452 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 26.57, per 1000 atoms: 0.52 Number of scatterers: 51336 At special positions: 0 Unit cell: (152.28, 152.28, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 4692 8.00 N 4396 7.00 C 17736 6.00 H 24392 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.56 Conformation dependent library (CDL) restraints added in 4.6 seconds 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 8 sheets defined 66.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 371 through 385 Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.742A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.680A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.588A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 588 through 603 Processing helix chain 'A' and resid 608 through 635 Processing helix chain 'A' and resid 638 through 645 removed outlier: 3.650A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 734 through 757 removed outlier: 3.587A pdb=" N LEU A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 789 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 797 through 817 removed outlier: 3.629A pdb=" N ILE A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 811 " --> pdb=" O PHE A 807 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 812 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 851 removed outlier: 3.897A pdb=" N ILE A 837 " --> pdb=" O CYS A 833 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 889 removed outlier: 4.152A pdb=" N ALA A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 912 removed outlier: 3.606A pdb=" N GLU A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 955 through 978 Processing helix chain 'A' and resid 980 through 984 removed outlier: 4.257A pdb=" N GLY A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 980 through 984' Processing helix chain 'A' and resid 990 through 1007 removed outlier: 3.526A pdb=" N TRP A 994 " --> pdb=" O ASN A 990 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 995 " --> pdb=" O ASP A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 4.679A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1074 removed outlier: 3.606A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A1072 " --> pdb=" O ASN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1103 removed outlier: 3.565A pdb=" N ILE A1103 " --> pdb=" O ILE A1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 159 through 175 Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.742A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.679A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.588A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 588 through 603 Processing helix chain 'B' and resid 608 through 635 Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.650A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 734 through 757 removed outlier: 3.587A pdb=" N LEU B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 789 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 797 through 817 removed outlier: 3.629A pdb=" N ILE B 810 " --> pdb=" O LEU B 806 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 811 " --> pdb=" O PHE B 807 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 812 " --> pdb=" O TYR B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 851 removed outlier: 3.897A pdb=" N ILE B 837 " --> pdb=" O CYS B 833 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 889 removed outlier: 4.152A pdb=" N ALA B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 912 removed outlier: 3.606A pdb=" N GLU B 906 " --> pdb=" O SER B 902 " (cutoff:3.500A) Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 955 through 978 Processing helix chain 'B' and resid 980 through 984 removed outlier: 4.258A pdb=" N GLY B 984 " --> pdb=" O GLY B 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 980 through 984' Processing helix chain 'B' and resid 990 through 1007 removed outlier: 3.526A pdb=" N TRP B 994 " --> pdb=" O ASN B 990 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 995 " --> pdb=" O ASP B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1028 removed outlier: 4.680A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1074 removed outlier: 3.605A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B1072 " --> pdb=" O ASN B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1103 removed outlier: 3.566A pdb=" N ILE B1103 " --> pdb=" O ILE B1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 175 Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.741A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.680A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 532 removed outlier: 3.588A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 588 through 603 Processing helix chain 'C' and resid 608 through 635 Processing helix chain 'C' and resid 638 through 645 removed outlier: 3.650A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 666 through 669 No H-bonds generated for 'chain 'C' and resid 666 through 669' Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 734 through 757 removed outlier: 3.587A pdb=" N LEU C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 789 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 797 through 817 removed outlier: 3.629A pdb=" N ILE C 810 " --> pdb=" O LEU C 806 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 811 " --> pdb=" O PHE C 807 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 812 " --> pdb=" O TYR C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 851 removed outlier: 3.898A pdb=" N ILE C 837 " --> pdb=" O CYS C 833 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 889 removed outlier: 4.152A pdb=" N ALA C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 912 removed outlier: 3.606A pdb=" N GLU C 906 " --> pdb=" O SER C 902 " (cutoff:3.500A) Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 955 through 978 Processing helix chain 'C' and resid 980 through 984 removed outlier: 4.258A pdb=" N GLY C 984 " --> pdb=" O GLY C 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 980 through 984' Processing helix chain 'C' and resid 990 through 1007 removed outlier: 3.526A pdb=" N TRP C 994 " --> pdb=" O ASN C 990 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 995 " --> pdb=" O ASP C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1028 removed outlier: 4.680A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1074 removed outlier: 3.605A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C1072 " --> pdb=" O ASN C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1103 removed outlier: 3.566A pdb=" N ILE C1103 " --> pdb=" O ILE C1099 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 49 Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 351 through 359 Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.742A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 removed outlier: 3.680A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 532 removed outlier: 3.588A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 571 Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 588 through 603 Processing helix chain 'D' and resid 608 through 635 Processing helix chain 'D' and resid 638 through 645 removed outlier: 3.650A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'D' and resid 723 through 732 Processing helix chain 'D' and resid 734 through 757 removed outlier: 3.586A pdb=" N LEU D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 789 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 797 through 817 removed outlier: 3.630A pdb=" N ILE D 810 " --> pdb=" O LEU D 806 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 811 " --> pdb=" O PHE D 807 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 812 " --> pdb=" O TYR D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 851 removed outlier: 3.897A pdb=" N ILE D 837 " --> pdb=" O CYS D 833 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 889 removed outlier: 4.153A pdb=" N ALA D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 912 removed outlier: 3.606A pdb=" N GLU D 906 " --> pdb=" O SER D 902 " (cutoff:3.500A) Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 955 through 978 Processing helix chain 'D' and resid 980 through 984 removed outlier: 4.258A pdb=" N GLY D 984 " --> pdb=" O GLY D 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 980 through 984' Processing helix chain 'D' and resid 990 through 1007 removed outlier: 3.526A pdb=" N TRP D 994 " --> pdb=" O ASN D 990 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS D 995 " --> pdb=" O ASP D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 removed outlier: 4.680A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1074 removed outlier: 3.606A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D1072 " --> pdb=" O ASN D1068 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1103 removed outlier: 3.565A pdb=" N ILE D1103 " --> pdb=" O ILE D1099 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 300 through 304 removed outlier: 3.837A pdb=" N LEU A 144 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP A 178 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER A 147 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 180 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 210 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR A 181 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 212 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N HIS A 259 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA A 215 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 261 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= C, first strand: chain 'B' and resid 300 through 304 removed outlier: 3.837A pdb=" N LEU B 144 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TRP B 178 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER B 147 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 180 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 210 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR B 181 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE B 212 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS B 259 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA B 215 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 261 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= E, first strand: chain 'C' and resid 300 through 304 removed outlier: 3.838A pdb=" N LEU C 144 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP C 178 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER C 147 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 180 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 210 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR C 181 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE C 212 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS C 259 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA C 215 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU C 261 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= G, first strand: chain 'D' and resid 300 through 304 removed outlier: 3.838A pdb=" N LEU D 144 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP D 178 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER D 147 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 180 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D 210 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR D 181 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 212 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS D 259 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA D 215 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 261 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 327 through 329 1640 hydrogen bonds defined for protein. 4716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.76 Time building geometry restraints manager: 43.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 24332 1.03 - 1.23: 97 1.23 - 1.42: 11631 1.42 - 1.62: 15724 1.62 - 1.81: 180 Bond restraints: 51964 Sorted by residual: bond pdb=" CAY Y01 D1202 " pdb=" OAW Y01 D1202 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CAY Y01 C1202 " pdb=" OAW Y01 C1202 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" CAY Y01 B1203 " pdb=" OAW Y01 B1203 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" CAY Y01 C1203 " pdb=" OAW Y01 C1203 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" CAY Y01 A1202 " pdb=" OAW Y01 A1202 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 51959 not shown) Histogram of bond angle deviations from ideal: 93.45 - 101.57: 55 101.57 - 109.70: 34977 109.70 - 117.83: 32183 117.83 - 125.95: 25307 125.95 - 134.08: 582 Bond angle restraints: 93104 Sorted by residual: angle pdb=" CAT Y01 A1201 " pdb=" CBH Y01 A1201 " pdb=" CBF Y01 A1201 " ideal model delta sigma weight residual 108.46 93.45 15.01 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CAT Y01 D1201 " pdb=" CBH Y01 D1201 " pdb=" CBF Y01 D1201 " ideal model delta sigma weight residual 108.46 93.46 15.00 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CAT Y01 B1201 " pdb=" CBH Y01 B1201 " pdb=" CBF Y01 B1201 " ideal model delta sigma weight residual 108.46 93.47 14.99 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CAT Y01 C1201 " pdb=" CBH Y01 C1201 " pdb=" CBF Y01 C1201 " ideal model delta sigma weight residual 108.46 93.50 14.96 3.00e+00 1.11e-01 2.49e+01 angle pdb=" CAT Y01 A1203 " pdb=" CBH Y01 A1203 " pdb=" CBF Y01 A1203 " ideal model delta sigma weight residual 108.46 93.52 14.94 3.00e+00 1.11e-01 2.48e+01 ... (remaining 93099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 19152 16.39 - 32.78: 1588 32.78 - 49.17: 284 49.17 - 65.57: 60 65.57 - 81.96: 12 Dihedral angle restraints: 21096 sinusoidal: 8344 harmonic: 12752 Sorted by residual: dihedral pdb=" CA LYS D 856 " pdb=" C LYS D 856 " pdb=" N ILE D 857 " pdb=" CA ILE D 857 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS A 856 " pdb=" C LYS A 856 " pdb=" N ILE A 857 " pdb=" CA ILE A 857 " ideal model delta harmonic sigma weight residual -180.00 -164.04 -15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS B 856 " pdb=" C LYS B 856 " pdb=" N ILE B 857 " pdb=" CA ILE B 857 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4303 0.089 - 0.178: 129 0.178 - 0.267: 24 0.267 - 0.356: 12 0.356 - 0.445: 24 Chirality restraints: 4492 Sorted by residual: chirality pdb=" CBF Y01 B1202 " pdb=" CAS Y01 B1202 " pdb=" CBD Y01 B1202 " pdb=" CBH Y01 B1202 " both_signs ideal model delta sigma weight residual False -2.45 -2.89 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CBF Y01 A1202 " pdb=" CAS Y01 A1202 " pdb=" CBD Y01 A1202 " pdb=" CBH Y01 A1202 " both_signs ideal model delta sigma weight residual False -2.45 -2.89 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CBF Y01 C1202 " pdb=" CAS Y01 C1202 " pdb=" CBD Y01 C1202 " pdb=" CBH Y01 C1202 " both_signs ideal model delta sigma weight residual False -2.45 -2.89 0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 4489 not shown) Planarity restraints: 8108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 324 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO C 325 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 862 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C ARG B 862 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG B 862 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 863 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 324 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 325 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " 0.023 5.00e-02 4.00e+02 ... (remaining 8105 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 3303 2.21 - 2.81: 101529 2.81 - 3.41: 134144 3.41 - 4.00: 164708 4.00 - 4.60: 258558 Nonbonded interactions: 662242 Sorted by model distance: nonbonded pdb=" O ASN D 821 " pdb=" HG SER D 824 " model vdw 1.615 1.850 nonbonded pdb=" O ASN A 821 " pdb=" HG SER A 824 " model vdw 1.616 1.850 nonbonded pdb=" O ASN C 821 " pdb=" HG SER C 824 " model vdw 1.617 1.850 nonbonded pdb=" O ASN B 821 " pdb=" HG SER B 824 " model vdw 1.617 1.850 nonbonded pdb=" O GLY D 183 " pdb=" H ASP D 254 " model vdw 1.633 1.850 ... (remaining 662237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 17736 2.51 5 N 4396 2.21 5 O 4692 1.98 5 H 24392 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.850 Extract box with map and model: 11.330 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.380 Process input model: 155.690 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 27572 Z= 0.238 Angle : 0.752 15.011 37712 Z= 0.310 Chirality : 0.051 0.445 4492 Planarity : 0.003 0.041 4632 Dihedral : 13.135 81.958 8912 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.15), residues: 3508 helix: 2.89 (0.11), residues: 2472 sheet: 0.08 (0.41), residues: 184 loop : -0.76 (0.19), residues: 852 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 4.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.7838 time to fit residues: 284.5621 Evaluate side-chains 205 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 323 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 483 ASN B 255 ASN B 429 GLN B 483 ASN C 483 ASN D 483 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 27572 Z= 0.266 Angle : 0.529 5.170 37712 Z= 0.279 Chirality : 0.035 0.137 4492 Planarity : 0.003 0.033 4632 Dihedral : 5.475 58.327 3928 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.14), residues: 3508 helix: 2.85 (0.10), residues: 2492 sheet: -0.13 (0.40), residues: 176 loop : -0.60 (0.20), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 208 average time/residue: 0.7209 time to fit residues: 252.6861 Evaluate side-chains 179 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 4.042 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5159 time to fit residues: 12.8621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 323 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 321 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 27572 Z= 0.201 Angle : 0.464 4.751 37712 Z= 0.247 Chirality : 0.034 0.135 4492 Planarity : 0.003 0.035 4632 Dihedral : 5.123 56.640 3928 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.14), residues: 3508 helix: 2.98 (0.10), residues: 2484 sheet: -0.25 (0.40), residues: 176 loop : -0.62 (0.19), residues: 848 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 4.635 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 188 average time/residue: 0.7591 time to fit residues: 239.8726 Evaluate side-chains 167 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5059 time to fit residues: 9.2753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 325 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 308 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN B 429 GLN C 429 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 27572 Z= 0.293 Angle : 0.490 5.177 37712 Z= 0.270 Chirality : 0.035 0.133 4492 Planarity : 0.003 0.031 4632 Dihedral : 5.142 56.873 3928 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.14), residues: 3508 helix: 2.77 (0.10), residues: 2492 sheet: -0.51 (0.39), residues: 176 loop : -0.62 (0.20), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 177 average time/residue: 0.7252 time to fit residues: 214.4420 Evaluate side-chains 168 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 4.106 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4958 time to fit residues: 10.6618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 27572 Z= 0.201 Angle : 0.452 4.649 37712 Z= 0.244 Chirality : 0.034 0.134 4492 Planarity : 0.003 0.034 4632 Dihedral : 4.993 56.430 3928 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.14), residues: 3508 helix: 2.89 (0.10), residues: 2468 sheet: -0.59 (0.39), residues: 176 loop : -0.66 (0.19), residues: 864 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 165 average time/residue: 0.6803 time to fit residues: 195.5271 Evaluate side-chains 162 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 4.351 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5273 time to fit residues: 12.3707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 8.9990 chunk 309 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 27572 Z= 0.262 Angle : 0.481 4.728 37712 Z= 0.265 Chirality : 0.034 0.134 4492 Planarity : 0.003 0.031 4632 Dihedral : 5.123 55.502 3928 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.14), residues: 3508 helix: 2.61 (0.10), residues: 2496 sheet: -0.80 (0.39), residues: 176 loop : -0.99 (0.19), residues: 836 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 3.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 183 average time/residue: 0.6474 time to fit residues: 205.8241 Evaluate side-chains 171 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5368 time to fit residues: 20.8122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 289 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27572 Z= 0.201 Angle : 0.454 4.679 37712 Z= 0.247 Chirality : 0.034 0.135 4492 Planarity : 0.003 0.034 4632 Dihedral : 5.041 55.665 3928 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.14), residues: 3508 helix: 2.70 (0.10), residues: 2496 sheet: -0.82 (0.39), residues: 176 loop : -1.05 (0.19), residues: 836 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 165 average time/residue: 0.6352 time to fit residues: 183.5658 Evaluate side-chains 149 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5201 time to fit residues: 5.9969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 269 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 27572 Z= 0.175 Angle : 0.439 4.729 37712 Z= 0.238 Chirality : 0.034 0.134 4492 Planarity : 0.003 0.032 4632 Dihedral : 4.935 55.437 3928 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.14), residues: 3508 helix: 2.77 (0.10), residues: 2492 sheet: -0.73 (0.40), residues: 176 loop : -1.06 (0.19), residues: 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 162 average time/residue: 0.6495 time to fit residues: 183.1840 Evaluate side-chains 150 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 3.983 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6054 time to fit residues: 7.1106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 2.9990 chunk 328 optimal weight: 0.7980 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 27572 Z= 0.190 Angle : 0.442 4.795 37712 Z= 0.240 Chirality : 0.034 0.134 4492 Planarity : 0.003 0.034 4632 Dihedral : 4.924 55.279 3928 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.14), residues: 3508 helix: 2.79 (0.10), residues: 2484 sheet: -0.84 (0.39), residues: 176 loop : -1.12 (0.19), residues: 848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 152 average time/residue: 0.6608 time to fit residues: 177.5719 Evaluate side-chains 154 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 4.172 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5126 time to fit residues: 8.9285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 354 optimal weight: 0.7980 chunk 326 optimal weight: 3.9990 chunk 282 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 27572 Z= 0.224 Angle : 0.458 4.789 37712 Z= 0.251 Chirality : 0.034 0.136 4492 Planarity : 0.003 0.031 4632 Dihedral : 5.008 55.159 3928 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3508 helix: 2.67 (0.10), residues: 2496 sheet: -1.05 (0.38), residues: 176 loop : -1.10 (0.19), residues: 836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7016 Ramachandran restraints generated. 3508 Oldfield, 0 Emsley, 3508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue ILE 45 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue THR 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 141 is missing expected H atoms. Skipping. Residue ILE 146 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue ILE 324 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LEU 381 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue ILE 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LEU 412 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 733 is missing expected H atoms. Skipping. Residue SER 762 is missing expected H atoms. Skipping. Residue VAL 763 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue MET 801 is missing expected H atoms. Skipping. Residue SER 819 is missing expected H atoms. Skipping. Residue LYS 822 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue VAL 986 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1030 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue SER 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 152 average time/residue: 0.6439 time to fit residues: 171.4602 Evaluate side-chains 151 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.956 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5119 time to fit residues: 5.6048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 260 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 290 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.104670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081996 restraints weight = 207150.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085527 restraints weight = 89069.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087845 restraints weight = 53299.596| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 27572 Z= 0.140 Angle : 0.431 4.815 37712 Z= 0.230 Chirality : 0.033 0.135 4492 Planarity : 0.002 0.035 4632 Dihedral : 4.822 55.339 3928 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.14), residues: 3508 helix: 2.87 (0.10), residues: 2484 sheet: -0.82 (0.39), residues: 176 loop : -1.13 (0.19), residues: 848 =============================================================================== Job complete usr+sys time: 6263.45 seconds wall clock time: 112 minutes 18.73 seconds (6738.73 seconds total)