Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:53:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4n_27893/02_2023/8e4n_27893_neut_trim_updated.pdb" } resolution = 3.07 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= 0.040 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 Process input model Symmetric amino acids flipped Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 52736 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 13137 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 21, 'TRANS': 879} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 749 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 394 Chain: "B" Number of atoms: 13137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 13137 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 21, 'TRANS': 879} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 749 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 394 Chain: "C" Number of atoms: 13137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 13137 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 21, 'TRANS': 879} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 749 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 394 Chain: "D" Number of atoms: 13137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 13137 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 21, 'TRANS': 879} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 749 Unresolved non-hydrogen dihedrals: 495 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 394 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.82, per 1000 atoms: 0.38 Number of scatterers: 52736 At special positions: 0 Unit cell: (148.896, 148.896, 147.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 12 15.00 O 4844 8.00 N 4488 7.00 C 17824 6.00 H 25460 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.04 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.04 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.04 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.04 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: 33.17 Conformation dependent library (CDL) restraints added in 3.5 seconds 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 4 sheets defined 67.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 126 through 136 removed outlier: 3.688A pdb=" N HIS A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 371 through 385 Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 455 through 468 removed outlier: 5.029A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) 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 499 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 533 removed outlier: 3.553A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.828A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'A' and resid 608 through 635 Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 656 through 662 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 removed outlier: 3.748A pdb=" N PHE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.695A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 787 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 797 through 817 Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.592A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 889 Proline residue: A 855 - end of helix removed outlier: 3.739A pdb=" N ARG A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 3.848A pdb=" N ILE A 904 " --> pdb=" O PHE A 900 " (cutoff:3.500A) Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 953 through 987 Proline residue: A 958 - end of helix removed outlier: 3.824A pdb=" N GLY A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1006 Processing helix chain 'A' and resid 1013 through 1015 No H-bonds generated for 'chain 'A' and resid 1013 through 1015' Processing helix chain 'A' and resid 1017 through 1024 removed outlier: 3.823A pdb=" N PHE A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1073 removed outlier: 4.232A pdb=" N LYS A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A1072 " --> pdb=" O ASN A1068 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A1073 " --> pdb=" O THR A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1103 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 126 through 136 removed outlier: 3.688A pdb=" N HIS B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 455 through 468 removed outlier: 5.028A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) 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 499 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 533 removed outlier: 3.553A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.828A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 608 through 635 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 656 through 662 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 removed outlier: 3.749A pdb=" N PHE B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.695A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 787 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 797 through 817 Processing helix chain 'B' and resid 822 through 849 removed outlier: 3.592A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 889 Proline residue: B 855 - end of helix removed outlier: 3.739A pdb=" N ARG B 862 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 909 removed outlier: 3.848A pdb=" N ILE B 904 " --> pdb=" O PHE B 900 " (cutoff:3.500A) Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'B' and resid 953 through 987 Proline residue: B 958 - end of helix removed outlier: 3.824A pdb=" N GLY B 984 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 985 " --> pdb=" O TYR B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1006 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1017 through 1024 removed outlier: 3.823A pdb=" N PHE B1021 " --> pdb=" O VAL B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1073 removed outlier: 4.231A pdb=" N LYS B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN B1072 " --> pdb=" O ASN B1068 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP B1073 " --> pdb=" O THR B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1103 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 126 through 136 removed outlier: 3.689A pdb=" N HIS C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 455 through 468 removed outlier: 5.029A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) 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 499 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 533 removed outlier: 3.553A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.829A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 602 Processing helix chain 'C' and resid 608 through 635 Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 656 through 662 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 removed outlier: 3.748A pdb=" N PHE C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.695A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 787 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 797 through 817 Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.593A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 889 Proline residue: C 855 - end of helix removed outlier: 3.739A pdb=" N ARG C 862 " --> pdb=" O ILE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 909 removed outlier: 3.848A pdb=" N ILE C 904 " --> pdb=" O PHE C 900 " (cutoff:3.500A) Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'C' and resid 953 through 987 Proline residue: C 958 - end of helix removed outlier: 3.824A pdb=" N GLY C 984 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 985 " --> pdb=" O TYR C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1006 Processing helix chain 'C' and resid 1013 through 1015 No H-bonds generated for 'chain 'C' and resid 1013 through 1015' Processing helix chain 'C' and resid 1017 through 1024 removed outlier: 3.824A pdb=" N PHE C1021 " --> pdb=" O VAL C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1073 removed outlier: 4.231A pdb=" N LYS C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN C1072 " --> pdb=" O ASN C1068 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP C1073 " --> pdb=" O THR C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1103 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 126 through 136 removed outlier: 3.689A pdb=" N HIS D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 175 Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 427 through 436 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 455 through 468 removed outlier: 5.028A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) 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 499 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 533 removed outlier: 3.553A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.829A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 602 Processing helix chain 'D' and resid 608 through 635 Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 656 through 662 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 removed outlier: 3.749A pdb=" N PHE D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.695A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 787 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 797 through 817 Processing helix chain 'D' and resid 822 through 849 removed outlier: 3.592A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 889 Proline residue: D 855 - end of helix removed outlier: 3.738A pdb=" N ARG D 862 " --> pdb=" O ILE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 909 removed outlier: 3.848A pdb=" N ILE D 904 " --> pdb=" O PHE D 900 " (cutoff:3.500A) Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 916 through 920 Processing helix chain 'D' and resid 953 through 987 Proline residue: D 958 - end of helix removed outlier: 3.825A pdb=" N GLY D 984 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 985 " --> pdb=" O TYR D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1006 Processing helix chain 'D' and resid 1013 through 1015 No H-bonds generated for 'chain 'D' and resid 1013 through 1015' Processing helix chain 'D' and resid 1017 through 1024 removed outlier: 3.823A pdb=" N PHE D1021 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1073 removed outlier: 4.232A pdb=" N LYS D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN D1072 " --> pdb=" O ASN D1068 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP D1073 " --> pdb=" O THR D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 120 removed outlier: 8.474A pdb=" N ILE A 146 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 302 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR A 392 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 116 through 120 removed outlier: 8.474A pdb=" N ILE B 146 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 302 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR B 392 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 116 through 120 removed outlier: 8.474A pdb=" N ILE C 146 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 302 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 392 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 116 through 120 removed outlier: 8.474A pdb=" N ILE D 146 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 302 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR D 392 " --> pdb=" O VAL D 328 " (cutoff:3.500A) 1696 hydrogen bonds defined for protein. 5052 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: 16.49 Time building geometry restraints manager: 34.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25408 1.02 - 1.22: 72 1.22 - 1.42: 11832 1.42 - 1.62: 15840 1.62 - 1.82: 180 Bond restraints: 53332 Sorted by residual: bond pdb=" SG CYS D 632 " pdb=" HG CYS D 632 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" SG CYS B 632 " pdb=" HG CYS B 632 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" SG CYS C 632 " pdb=" HG CYS C 632 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" SG CYS A 632 " pdb=" HG CYS A 632 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C5A PIO D1201 " pdb=" C6A PIO D1201 " ideal model delta sigma weight residual 1.528 1.577 -0.049 2.00e-02 2.50e+03 6.04e+00 ... (remaining 53327 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.29: 503 106.29 - 113.25: 60406 113.25 - 120.21: 17575 120.21 - 127.18: 16976 127.18 - 134.14: 316 Bond angle restraints: 95776 Sorted by residual: angle pdb=" N VAL C 876 " pdb=" CA VAL C 876 " pdb=" C VAL C 876 " ideal model delta sigma weight residual 110.30 113.81 -3.51 9.70e-01 1.06e+00 1.31e+01 angle pdb=" N VAL A 876 " pdb=" CA VAL A 876 " pdb=" C VAL A 876 " ideal model delta sigma weight residual 110.30 113.81 -3.51 9.70e-01 1.06e+00 1.31e+01 angle pdb=" N VAL D 876 " pdb=" CA VAL D 876 " pdb=" C VAL D 876 " ideal model delta sigma weight residual 110.30 113.81 -3.51 9.70e-01 1.06e+00 1.31e+01 angle pdb=" N VAL B 876 " pdb=" CA VAL B 876 " pdb=" C VAL B 876 " ideal model delta sigma weight residual 110.30 113.78 -3.48 9.70e-01 1.06e+00 1.29e+01 angle pdb=" N VAL B 879 " pdb=" CA VAL B 879 " pdb=" C VAL B 879 " ideal model delta sigma weight residual 110.72 107.13 3.59 1.01e+00 9.80e-01 1.26e+01 ... (remaining 95771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 20158 16.32 - 32.64: 1218 32.64 - 48.97: 304 48.97 - 65.29: 64 65.29 - 81.61: 12 Dihedral angle restraints: 21756 sinusoidal: 8972 harmonic: 12784 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 326 " pdb=" CB CYS B 326 " ideal model delta sinusoidal sigma weight residual -86.00 -51.57 -34.43 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CB CYS A 303 " pdb=" SG CYS A 303 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -51.60 -34.40 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CB CYS C 303 " pdb=" SG CYS C 303 " pdb=" SG CYS C 326 " pdb=" CB CYS C 326 " ideal model delta sinusoidal sigma weight residual -86.00 -51.61 -34.39 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 21753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3975 0.060 - 0.119: 473 0.119 - 0.179: 12 0.179 - 0.239: 4 0.239 - 0.299: 4 Chirality restraints: 4468 Sorted by residual: chirality pdb=" CA TRP A 877 " pdb=" N TRP A 877 " pdb=" C TRP A 877 " pdb=" CB TRP A 877 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA TRP C 877 " pdb=" N TRP C 877 " pdb=" C TRP C 877 " pdb=" CB TRP C 877 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA TRP D 877 " pdb=" N TRP D 877 " pdb=" C TRP D 877 " pdb=" CB TRP D 877 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4465 not shown) Planarity restraints: 8180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PIO C1201 " -0.537 2.00e-02 2.50e+03 4.66e-01 6.52e+03 pdb=" C2 PIO C1201 " -0.211 2.00e-02 2.50e+03 pdb=" C3 PIO C1201 " -0.500 2.00e-02 2.50e+03 pdb=" C4 PIO C1201 " 0.150 2.00e-02 2.50e+03 pdb=" C5 PIO C1201 " -0.139 2.00e-02 2.50e+03 pdb=" C6 PIO C1201 " 0.176 2.00e-02 2.50e+03 pdb=" O1 PIO C1201 " -0.124 2.00e-02 2.50e+03 pdb=" O2 PIO C1201 " 1.146 2.00e-02 2.50e+03 pdb=" O3 PIO C1201 " -0.005 2.00e-02 2.50e+03 pdb=" O4 PIO C1201 " -0.362 2.00e-02 2.50e+03 pdb=" O5 PIO C1201 " 0.657 2.00e-02 2.50e+03 pdb=" O6 PIO C1201 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO D1201 " 0.537 2.00e-02 2.50e+03 4.66e-01 6.52e+03 pdb=" C2 PIO D1201 " 0.211 2.00e-02 2.50e+03 pdb=" C3 PIO D1201 " 0.500 2.00e-02 2.50e+03 pdb=" C4 PIO D1201 " -0.150 2.00e-02 2.50e+03 pdb=" C5 PIO D1201 " 0.140 2.00e-02 2.50e+03 pdb=" C6 PIO D1201 " -0.176 2.00e-02 2.50e+03 pdb=" O1 PIO D1201 " 0.124 2.00e-02 2.50e+03 pdb=" O2 PIO D1201 " -1.146 2.00e-02 2.50e+03 pdb=" O3 PIO D1201 " 0.006 2.00e-02 2.50e+03 pdb=" O4 PIO D1201 " 0.361 2.00e-02 2.50e+03 pdb=" O5 PIO D1201 " -0.656 2.00e-02 2.50e+03 pdb=" O6 PIO D1201 " 0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO B1201 " -0.537 2.00e-02 2.50e+03 4.66e-01 6.52e+03 pdb=" C2 PIO B1201 " -0.211 2.00e-02 2.50e+03 pdb=" C3 PIO B1201 " -0.500 2.00e-02 2.50e+03 pdb=" C4 PIO B1201 " 0.150 2.00e-02 2.50e+03 pdb=" C5 PIO B1201 " -0.139 2.00e-02 2.50e+03 pdb=" C6 PIO B1201 " 0.176 2.00e-02 2.50e+03 pdb=" O1 PIO B1201 " -0.124 2.00e-02 2.50e+03 pdb=" O2 PIO B1201 " 1.146 2.00e-02 2.50e+03 pdb=" O3 PIO B1201 " -0.006 2.00e-02 2.50e+03 pdb=" O4 PIO B1201 " -0.361 2.00e-02 2.50e+03 pdb=" O5 PIO B1201 " 0.656 2.00e-02 2.50e+03 pdb=" O6 PIO B1201 " -0.250 2.00e-02 2.50e+03 ... (remaining 8177 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1744 2.15 - 2.76: 98477 2.76 - 3.38: 148333 3.38 - 3.99: 178069 3.99 - 4.60: 288469 Nonbonded interactions: 715092 Sorted by model distance: nonbonded pdb=" HE ARG A 688 " pdb=" O52 PIO A1201 " model vdw 1.539 1.850 nonbonded pdb=" HE ARG D 688 " pdb=" O52 PIO D1201 " model vdw 1.539 1.850 nonbonded pdb=" HE ARG C 688 " pdb=" O52 PIO C1201 " model vdw 1.539 1.850 nonbonded pdb=" HE ARG B 688 " pdb=" O52 PIO B1201 " model vdw 1.539 1.850 nonbonded pdb=" O PRO A 952 " pdb=" HG1 THR A 956 " model vdw 1.597 1.850 ... (remaining 715087 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 108 5.16 5 C 17824 2.51 5 N 4488 2.21 5 O 4844 1.98 5 H 25460 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 individual isotropic 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: 1.690 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: 0.620 Extract box with map and model: 10.300 Check model and map are aligned: 0.770 Process input model: 124.110 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.370 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:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.003 0.049 27872 Z= 0.227 Angle : 0.470 5.146 38004 Z= 0.265 Chirality : 0.037 0.299 4468 Planarity : 0.014 0.466 4704 Dihedral : 11.075 81.612 9340 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 3.01 (0.14), residues: 3516 helix: 3.02 (0.10), residues: 2476 sheet: 0.12 (0.37), residues: 184 loop : -0.83 (0.19), residues: 856 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 398 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 3.293 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 revert: symmetry clash 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: 0 outliers final: 0 residues processed: 398 average time/residue: 0.7030 time to fit residues: 453.6296 Evaluate side-chains 233 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.0570 chunk 282 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 997 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN C 997 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 27872 Z= 0.278 Angle : 0.677 13.494 38004 Z= 0.313 Chirality : 0.036 0.141 4468 Planarity : 0.004 0.058 4704 Dihedral : 6.121 54.214 3972 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.27 % 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: 2.86 (0.14), residues: 3516 helix: 2.88 (0.10), residues: 2520 sheet: -0.39 (0.38), residues: 184 loop : -0.88 (0.19), residues: 812 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 3.375 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 273 average time/residue: 0.6403 time to fit residues: 286.2678 Evaluate side-chains 262 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4349 time to fit residues: 23.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 0.2980 chunk 353 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 799 ASN B 317 ASN C 317 ASN D 317 ASN D 799 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 27872 Z= 0.357 Angle : 0.687 14.186 38004 Z= 0.321 Chirality : 0.037 0.137 4468 Planarity : 0.004 0.061 4704 Dihedral : 6.083 58.873 3972 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.96 % 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: 3516 helix: 2.64 (0.10), residues: 2520 sheet: -0.47 (0.37), residues: 184 loop : -1.24 (0.18), residues: 812 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 251 time to evaluate : 3.461 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 267 average time/residue: 0.6385 time to fit residues: 280.5219 Evaluate side-chains 244 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 3.330 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5444 time to fit residues: 19.1691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN B 799 ASN C 799 ASN D 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 27872 Z= 0.233 Angle : 0.651 14.216 38004 Z= 0.296 Chirality : 0.035 0.141 4468 Planarity : 0.003 0.047 4704 Dihedral : 6.036 59.983 3972 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.00 % 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: 2.58 (0.14), residues: 3516 helix: 2.72 (0.10), residues: 2516 sheet: -0.62 (0.37), residues: 184 loop : -1.10 (0.18), residues: 816 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 235 time to evaluate : 3.356 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 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: 26 outliers final: 12 residues processed: 253 average time/residue: 0.6094 time to fit residues: 257.4790 Evaluate side-chains 235 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 223 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4382 time to fit residues: 14.0003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 799 ASN C 799 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.044 27872 Z= 0.500 Angle : 0.730 14.274 38004 Z= 0.351 Chirality : 0.040 0.166 4468 Planarity : 0.004 0.058 4704 Dihedral : 6.335 58.717 3972 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.73 % 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: 1.74 (0.14), residues: 3516 helix: 2.13 (0.10), residues: 2516 sheet: -0.81 (0.36), residues: 192 loop : -1.58 (0.18), residues: 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 3.388 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: 45 outliers final: 19 residues processed: 264 average time/residue: 0.6859 time to fit residues: 303.8406 Evaluate side-chains 236 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 3.340 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5487 time to fit residues: 22.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 9.9990 chunk 313 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 27872 Z= 0.353 Angle : 0.688 14.272 38004 Z= 0.322 Chirality : 0.037 0.139 4468 Planarity : 0.004 0.052 4704 Dihedral : 6.189 58.989 3972 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.85 % 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: 1.86 (0.14), residues: 3516 helix: 2.28 (0.10), residues: 2492 sheet: -1.04 (0.36), residues: 184 loop : -1.55 (0.18), residues: 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 3.382 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: 22 outliers final: 15 residues processed: 252 average time/residue: 0.6463 time to fit residues: 270.5233 Evaluate side-chains 238 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 3.376 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4399 time to fit residues: 16.5943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 293 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 346 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 27872 Z= 0.186 Angle : 0.657 14.160 38004 Z= 0.296 Chirality : 0.035 0.141 4468 Planarity : 0.003 0.046 4704 Dihedral : 5.926 58.017 3972 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % 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: 2.23 (0.14), residues: 3516 helix: 2.53 (0.10), residues: 2540 sheet: -1.03 (0.36), residues: 184 loop : -1.54 (0.19), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 3.450 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: 16 outliers final: 11 residues processed: 234 average time/residue: 0.7197 time to fit residues: 278.6500 Evaluate side-chains 228 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5964 time to fit residues: 15.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 272 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 799 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 27872 Z= 0.241 Angle : 0.666 14.106 38004 Z= 0.304 Chirality : 0.035 0.153 4468 Planarity : 0.003 0.048 4704 Dihedral : 5.819 56.612 3972 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer Outliers : 0.50 % 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: 2.33 (0.14), residues: 3516 helix: 2.65 (0.10), residues: 2492 sheet: -1.08 (0.36), residues: 184 loop : -1.38 (0.18), residues: 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 3.515 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: 13 outliers final: 6 residues processed: 234 average time/residue: 0.6531 time to fit residues: 253.6120 Evaluate side-chains 222 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 216 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4791 time to fit residues: 9.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 305 optimal weight: 0.9980 chunk 322 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN B 799 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 27872 Z= 0.186 Angle : 0.669 15.047 38004 Z= 0.302 Chirality : 0.035 0.154 4468 Planarity : 0.003 0.045 4704 Dihedral : 5.717 55.733 3972 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer Outliers : 0.19 % 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: 2.47 (0.14), residues: 3516 helix: 2.75 (0.10), residues: 2492 sheet: -1.01 (0.36), residues: 184 loop : -1.33 (0.18), residues: 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 3.346 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: 5 outliers final: 5 residues processed: 218 average time/residue: 0.6617 time to fit residues: 238.4361 Evaluate side-chains 224 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 3.407 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6815 time to fit residues: 9.6277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.2980 chunk 341 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 358 optimal weight: 20.0000 chunk 330 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 27872 Z= 0.240 Angle : 0.669 13.996 38004 Z= 0.305 Chirality : 0.035 0.163 4468 Planarity : 0.003 0.045 4704 Dihedral : 5.676 54.705 3972 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % 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: 2.46 (0.14), residues: 3516 helix: 2.74 (0.10), residues: 2492 sheet: -1.04 (0.35), residues: 184 loop : -1.33 (0.19), residues: 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 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 TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue THR 128 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 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 MET 161 is missing expected H atoms. Skipping. Residue LYS 163 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 ILE 201 is missing expected H atoms. Skipping. Residue LEU 226 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 VAL 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue LYS 298 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 VAL 343 is missing expected H atoms. Skipping. Residue SER 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 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 THR 557 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue VAL 705 is missing expected H atoms. Skipping. Residue LEU 769 is missing expected H atoms. Skipping. Residue MET 788 is missing expected H atoms. Skipping. Residue VAL 791 is missing expected H atoms. Skipping. Residue THR 795 is missing expected H atoms. Skipping. Residue VAL 800 is missing expected H atoms. Skipping. Residue LEU 804 is missing expected H atoms. Skipping. Residue TYR 905 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue SER 921 is missing expected H atoms. Skipping. Residue ILE 955 is missing expected H atoms. Skipping. Residue ILE 985 is missing expected H atoms. Skipping. Residue LEU 1001 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 3.374 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: 1 outliers final: 0 residues processed: 227 average time/residue: 0.6795 time to fit residues: 257.2364 Evaluate side-chains 218 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 263 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.126004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088008 restraints weight = 191979.543| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.84 r_work: 0.3250 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 27872 Z= 0.162 Angle : 0.652 13.964 38004 Z= 0.291 Chirality : 0.034 0.144 4468 Planarity : 0.003 0.044 4704 Dihedral : 5.536 53.354 3972 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % Rotamer Outliers : 0.38 % 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: 3516 helix: 2.86 (0.10), residues: 2492 sheet: -0.98 (0.35), residues: 184 loop : -1.27 (0.19), residues: 840 =============================================================================== Job complete usr+sys time: 7790.25 seconds wall clock time: 136 minutes 25.18 seconds (8185.18 seconds total)