Starting phenix.real_space_refine on Thu Dec 7 16:13:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/12_2023/8e4o_27894_neut_trim_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.037 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 112 5.16 5 C 17964 2.51 5 N 4528 2.21 5 O 4856 1.98 5 H 26024 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 53496 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 13333 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 21, 'TRANS': 875} Chain breaks: 10 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 344 Chain: "D" Number of atoms: 13333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 13333 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 21, 'TRANS': 875} Chain breaks: 10 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 344 Chain: "B" Number of atoms: 13333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 13333 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 21, 'TRANS': 875} Chain breaks: 10 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 344 Chain: "C" Number of atoms: 13333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 13333 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 21, 'TRANS': 875} Chain breaks: 10 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 344 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 17.57, per 1000 atoms: 0.33 Number of scatterers: 53496 At special positions: 0 Unit cell: (154.44, 154.44, 144.72, 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 112 16.00 P 12 15.00 O 4856 8.00 N 4528 7.00 C 17964 6.00 H 26024 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=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.03 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: 31.31 Conformation dependent library (CDL) restraints added in 4.2 seconds 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 4 sheets defined 65.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.522A pdb=" N PHE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 455 through 467 removed outlier: 4.685A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.000A 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 521 through 533 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.042A 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 609 through 635 Processing helix chain 'A' and resid 638 through 644 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 Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' 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: 3.518A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 889 removed outlier: 4.248A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 911 Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 953 through 987 removed outlier: 3.616A pdb=" N ILE A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) Proline residue: A 958 - end of helix removed outlier: 4.233A pdb=" N VAL A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1006 removed outlier: 3.927A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 4.817A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1073 removed outlier: 4.281A pdb=" N LYS A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A1072 " --> pdb=" O ASN A1068 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1073 " --> pdb=" O THR A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1103 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 159 through 175 removed outlier: 3.522A pdb=" N PHE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 310 through 322 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 365 through 368 No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 371 through 386 Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 455 through 467 removed outlier: 4.686A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.999A 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 521 through 533 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 4.041A 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 609 through 635 Processing helix chain 'D' and resid 638 through 644 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 Processing helix chain 'D' and resid 702 through 704 No H-bonds generated for 'chain 'D' and resid 702 through 704' 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: 3.518A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 889 removed outlier: 4.248A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP D 866 " --> pdb=" O ARG D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 911 Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 953 through 987 removed outlier: 3.616A pdb=" N ILE D 957 " --> pdb=" O GLU D 953 " (cutoff:3.500A) Proline residue: D 958 - end of helix removed outlier: 4.234A pdb=" N VAL D 983 " --> pdb=" O PHE D 979 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY D 984 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 985 " --> pdb=" O TYR D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1006 removed outlier: 3.927A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D1005 " --> pdb=" O LEU D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1024 removed outlier: 4.818A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1073 removed outlier: 4.281A pdb=" N LYS D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN D1072 " --> pdb=" O ASN D1068 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP D1073 " --> pdb=" O THR D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1103 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 159 through 175 removed outlier: 3.522A pdb=" N PHE B 165 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 365 through 368 No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 371 through 386 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 455 through 467 removed outlier: 4.686A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.001A 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 521 through 533 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 4.042A 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 609 through 635 Processing helix chain 'B' and resid 638 through 644 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 Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' 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: 3.517A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 889 removed outlier: 4.248A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP B 866 " --> pdb=" O ARG B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 911 Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 953 through 987 removed outlier: 3.616A pdb=" N ILE B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) Proline residue: B 958 - end of helix removed outlier: 4.233A pdb=" N VAL B 983 " --> pdb=" O PHE B 979 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 984 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 985 " --> pdb=" O TYR B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1006 removed outlier: 3.927A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1024 removed outlier: 4.816A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1073 removed outlier: 4.282A pdb=" N LYS B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B1072 " --> pdb=" O ASN B1068 " (cutoff:3.500A) removed outlier: 3.533A 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 135 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.522A pdb=" N PHE C 165 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 310 through 322 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 365 through 368 No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 371 through 386 Processing helix chain 'C' and resid 404 through 417 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 455 through 467 removed outlier: 4.686A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.000A 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 521 through 533 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 4.042A 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 609 through 635 Processing helix chain 'C' and resid 638 through 644 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 Processing helix chain 'C' and resid 702 through 704 No H-bonds generated for 'chain 'C' and resid 702 through 704' 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: 3.518A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 889 removed outlier: 4.249A pdb=" N ILE C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP C 866 " --> pdb=" O ARG C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 911 Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 953 through 987 removed outlier: 3.616A pdb=" N ILE C 957 " --> pdb=" O GLU C 953 " (cutoff:3.500A) Proline residue: C 958 - end of helix removed outlier: 4.233A pdb=" N VAL C 983 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 984 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 985 " --> pdb=" O TYR C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1006 removed outlier: 3.927A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1024 removed outlier: 4.817A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1073 removed outlier: 4.282A pdb=" N LYS C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA C1071 " --> pdb=" O ILE C1067 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN C1072 " --> pdb=" O ASN C1068 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C1073 " --> pdb=" O THR C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 259 through 263 removed outlier: 8.285A pdb=" N ILE A 146 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 302 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL A 148 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE A 304 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA A 305 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 327 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 392 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 259 through 263 removed outlier: 8.287A pdb=" N ILE D 146 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 302 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL D 148 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE D 304 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA D 305 " --> pdb=" O PRO D 325 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 327 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR D 392 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 259 through 263 removed outlier: 8.286A pdb=" N ILE B 146 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 302 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL B 148 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 304 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA B 305 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 327 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR B 392 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 259 through 263 removed outlier: 8.286A pdb=" N ILE C 146 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 302 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL C 148 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 304 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA C 305 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 327 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR C 392 " --> pdb=" O VAL C 328 " (cutoff:3.500A) 1644 hydrogen bonds defined for protein. 4812 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: 16.52 Time building geometry restraints manager: 33.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 25984 1.02 - 1.22: 48 1.22 - 1.42: 11948 1.42 - 1.62: 15944 1.62 - 1.82: 188 Bond restraints: 54112 Sorted by residual: bond pdb=" C5A PIO D1201 " pdb=" C6A PIO D1201 " ideal model delta sigma weight residual 1.528 1.578 -0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" C5A PIO A1201 " pdb=" C6A PIO A1201 " ideal model delta sigma weight residual 1.528 1.578 -0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" C5A PIO B1201 " pdb=" C6A PIO B1201 " ideal model delta sigma weight residual 1.528 1.577 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C5A PIO C1201 " pdb=" C6A PIO C1201 " ideal model delta sigma weight residual 1.528 1.577 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" C2A PIO A1201 " pdb=" C3A PIO A1201 " ideal model delta sigma weight residual 1.530 1.570 -0.040 2.00e-02 2.50e+03 4.03e+00 ... (remaining 54107 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.81: 653 106.81 - 113.62: 61955 113.62 - 120.43: 18955 120.43 - 127.24: 15433 127.24 - 134.05: 320 Bond angle restraints: 97316 Sorted by residual: angle pdb=" CA TRP B 877 " pdb=" CB TRP B 877 " pdb=" CG TRP B 877 " ideal model delta sigma weight residual 113.60 120.66 -7.06 1.90e+00 2.77e-01 1.38e+01 angle pdb=" CA TRP C 877 " pdb=" CB TRP C 877 " pdb=" CG TRP C 877 " ideal model delta sigma weight residual 113.60 120.64 -7.04 1.90e+00 2.77e-01 1.37e+01 angle pdb=" CA TRP D 877 " pdb=" CB TRP D 877 " pdb=" CG TRP D 877 " ideal model delta sigma weight residual 113.60 120.62 -7.02 1.90e+00 2.77e-01 1.37e+01 angle pdb=" CA TRP A 877 " pdb=" CB TRP A 877 " pdb=" CG TRP A 877 " ideal model delta sigma weight residual 113.60 120.61 -7.01 1.90e+00 2.77e-01 1.36e+01 angle pdb=" CD GLN D 992 " pdb=" NE2 GLN D 992 " pdb="HE21 GLN D 992 " ideal model delta sigma weight residual 120.00 111.79 8.21 3.00e+00 1.11e-01 7.48e+00 ... (remaining 97311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.58: 24524 25.58 - 51.17: 601 51.17 - 76.75: 55 76.75 - 102.34: 8 102.34 - 127.92: 4 Dihedral angle restraints: 25192 sinusoidal: 12400 harmonic: 12792 Sorted by residual: dihedral pdb=" C3B PIO C1201 " pdb=" C1B PIO C1201 " pdb=" C2B PIO C1201 " pdb=" O3C PIO C1201 " ideal model delta sinusoidal sigma weight residual 150.54 22.62 127.92 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C3B PIO D1201 " pdb=" C1B PIO D1201 " pdb=" C2B PIO D1201 " pdb=" O3C PIO D1201 " ideal model delta sinusoidal sigma weight residual 150.54 22.63 127.91 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C3B PIO A1201 " pdb=" C1B PIO A1201 " pdb=" C2B PIO A1201 " pdb=" O3C PIO A1201 " ideal model delta sinusoidal sigma weight residual 150.54 22.67 127.87 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 25189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3174 0.028 - 0.056: 803 0.056 - 0.084: 305 0.084 - 0.112: 141 0.112 - 0.140: 37 Chirality restraints: 4460 Sorted by residual: chirality pdb=" CA ILE C1011 " pdb=" N ILE C1011 " pdb=" C ILE C1011 " pdb=" CB ILE C1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE D1011 " pdb=" N ILE D1011 " pdb=" C ILE D1011 " pdb=" CB ILE D1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B 299 " pdb=" N ILE B 299 " pdb=" C ILE B 299 " pdb=" CB ILE B 299 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 4457 not shown) Planarity restraints: 8188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PIO B1201 " -0.520 2.00e-02 2.50e+03 4.81e-01 6.95e+03 pdb=" C2 PIO B1201 " -0.155 2.00e-02 2.50e+03 pdb=" C3 PIO B1201 " -0.517 2.00e-02 2.50e+03 pdb=" C4 PIO B1201 " 0.150 2.00e-02 2.50e+03 pdb=" C5 PIO B1201 " -0.143 2.00e-02 2.50e+03 pdb=" C6 PIO B1201 " 0.161 2.00e-02 2.50e+03 pdb=" O1 PIO B1201 " -0.129 2.00e-02 2.50e+03 pdb=" O2 PIO B1201 " 1.224 2.00e-02 2.50e+03 pdb=" O3 PIO B1201 " -0.100 2.00e-02 2.50e+03 pdb=" O4 PIO B1201 " -0.328 2.00e-02 2.50e+03 pdb=" O5 PIO B1201 " 0.654 2.00e-02 2.50e+03 pdb=" O6 PIO B1201 " -0.297 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO A1201 " 0.520 2.00e-02 2.50e+03 4.81e-01 6.95e+03 pdb=" C2 PIO A1201 " 0.155 2.00e-02 2.50e+03 pdb=" C3 PIO A1201 " 0.517 2.00e-02 2.50e+03 pdb=" C4 PIO A1201 " -0.150 2.00e-02 2.50e+03 pdb=" C5 PIO A1201 " 0.143 2.00e-02 2.50e+03 pdb=" C6 PIO A1201 " -0.161 2.00e-02 2.50e+03 pdb=" O1 PIO A1201 " 0.129 2.00e-02 2.50e+03 pdb=" O2 PIO A1201 " -1.224 2.00e-02 2.50e+03 pdb=" O3 PIO A1201 " 0.100 2.00e-02 2.50e+03 pdb=" O4 PIO A1201 " 0.328 2.00e-02 2.50e+03 pdb=" O5 PIO A1201 " -0.654 2.00e-02 2.50e+03 pdb=" O6 PIO A1201 " 0.297 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO C1201 " -0.520 2.00e-02 2.50e+03 4.81e-01 6.94e+03 pdb=" C2 PIO C1201 " -0.156 2.00e-02 2.50e+03 pdb=" C3 PIO C1201 " -0.517 2.00e-02 2.50e+03 pdb=" C4 PIO C1201 " 0.151 2.00e-02 2.50e+03 pdb=" C5 PIO C1201 " -0.143 2.00e-02 2.50e+03 pdb=" C6 PIO C1201 " 0.161 2.00e-02 2.50e+03 pdb=" O1 PIO C1201 " -0.129 2.00e-02 2.50e+03 pdb=" O2 PIO C1201 " 1.224 2.00e-02 2.50e+03 pdb=" O3 PIO C1201 " -0.100 2.00e-02 2.50e+03 pdb=" O4 PIO C1201 " -0.328 2.00e-02 2.50e+03 pdb=" O5 PIO C1201 " 0.654 2.00e-02 2.50e+03 pdb=" O6 PIO C1201 " -0.296 2.00e-02 2.50e+03 ... (remaining 8185 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1865 2.16 - 2.77: 101369 2.77 - 3.38: 146787 3.38 - 3.99: 175903 3.99 - 4.60: 283955 Nonbonded interactions: 709879 Sorted by model distance: nonbonded pdb=" O GLU A1076 " pdb=" HD1 HIS A1080 " model vdw 1.555 1.850 nonbonded pdb=" O GLU B1076 " pdb=" HD1 HIS B1080 " model vdw 1.555 1.850 nonbonded pdb=" O GLU D1076 " pdb=" HD1 HIS D1080 " model vdw 1.555 1.850 nonbonded pdb=" O GLU C1076 " pdb=" HD1 HIS C1080 " model vdw 1.555 1.850 nonbonded pdb=" HG1 THR B 494 " pdb=" O PHE B 531 " model vdw 1.571 1.850 ... (remaining 709874 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 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: 1.140 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: 0.590 Extract box with map and model: 8.180 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 124.940 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.002 0.050 28088 Z= 0.152 Angle : 0.443 7.058 38264 Z= 0.239 Chirality : 0.034 0.140 4460 Planarity : 0.014 0.481 4728 Dihedral : 11.665 127.919 9516 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.45 % Allowed : 4.93 % Favored : 94.62 % 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: 2.99 (0.14), residues: 3500 helix: 2.86 (0.10), residues: 2516 sheet: 1.10 (0.41), residues: 192 loop : -0.85 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 877 HIS 0.002 0.000 HIS D 136 PHE 0.010 0.001 PHE A1000 TYR 0.009 0.001 TYR A 999 ARG 0.002 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 384 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 372 time to evaluate : 3.262 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 383 average time/residue: 0.6652 time to fit residues: 407.8555 Evaluate side-chains 237 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5691 time to fit residues: 11.6258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 107 optimal weight: 0.0170 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 323 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN D 279 ASN D 671 GLN B 279 ASN B 671 GLN C 279 ASN C 671 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28088 Z= 0.319 Angle : 0.726 16.778 38264 Z= 0.343 Chirality : 0.037 0.232 4460 Planarity : 0.004 0.043 4728 Dihedral : 8.129 111.322 3936 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.01 % Allowed : 9.98 % Favored : 89.01 % 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: 2.89 (0.14), residues: 3500 helix: 2.86 (0.10), residues: 2508 sheet: 0.26 (0.41), residues: 192 loop : -0.89 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 877 HIS 0.004 0.001 HIS A 136 PHE 0.010 0.001 PHE D 629 TYR 0.015 0.001 TYR D 295 ARG 0.009 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 3.156 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 revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 255 average time/residue: 0.7294 time to fit residues: 299.1899 Evaluate side-chains 234 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 3.193 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.6958 time to fit residues: 28.4705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 269 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28088 Z= 0.261 Angle : 0.664 13.405 38264 Z= 0.306 Chirality : 0.035 0.142 4460 Planarity : 0.004 0.056 4728 Dihedral : 7.595 89.529 3936 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.08 % Allowed : 10.72 % Favored : 88.19 % 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: 2.81 (0.14), residues: 3500 helix: 2.84 (0.10), residues: 2512 sheet: -0.11 (0.41), residues: 192 loop : -1.00 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 877 HIS 0.004 0.001 HIS A 136 PHE 0.011 0.001 PHE D 979 TYR 0.012 0.001 TYR A 295 ARG 0.005 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 246 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 217 time to evaluate : 3.250 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 outliers start: 29 outliers final: 9 residues processed: 235 average time/residue: 0.6769 time to fit residues: 260.1153 Evaluate side-chains 219 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5759 time to fit residues: 12.8380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 344 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7435 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 28088 Z= 0.240 Angle : 0.646 13.802 38264 Z= 0.295 Chirality : 0.034 0.138 4460 Planarity : 0.003 0.053 4728 Dihedral : 7.289 73.287 3936 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.16 % Allowed : 10.76 % Favored : 88.08 % 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: 2.77 (0.14), residues: 3500 helix: 2.86 (0.10), residues: 2488 sheet: -0.39 (0.39), residues: 192 loop : -1.02 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 877 HIS 0.003 0.001 HIS D 136 PHE 0.010 0.001 PHE A 629 TYR 0.012 0.001 TYR D 295 ARG 0.006 0.000 ARG D 862 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 247 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 3.223 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 outliers start: 31 outliers final: 13 residues processed: 229 average time/residue: 0.6998 time to fit residues: 262.8746 Evaluate side-chains 213 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5188 time to fit residues: 16.2492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 237 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 ASN B 990 ASN C 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 28088 Z= 0.151 Angle : 0.620 12.911 38264 Z= 0.274 Chirality : 0.034 0.140 4460 Planarity : 0.003 0.028 4728 Dihedral : 6.856 59.086 3936 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.41 % Allowed : 11.96 % Favored : 87.63 % 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: 3.05 (0.15), residues: 3500 helix: 3.05 (0.10), residues: 2488 sheet: -0.08 (0.39), residues: 192 loop : -0.90 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 877 HIS 0.002 0.000 HIS D 136 PHE 0.010 0.001 PHE D1000 TYR 0.011 0.001 TYR A 999 ARG 0.004 0.000 ARG B 862 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 219 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 3.214 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 outliers start: 11 outliers final: 2 residues processed: 212 average time/residue: 0.6353 time to fit residues: 225.5915 Evaluate side-chains 205 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4483 time to fit residues: 5.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 202 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28088 Z= 0.273 Angle : 0.651 12.193 38264 Z= 0.299 Chirality : 0.035 0.137 4460 Planarity : 0.003 0.031 4728 Dihedral : 6.497 47.435 3936 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.49 % Allowed : 12.48 % Favored : 87.03 % 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: 2.78 (0.14), residues: 3500 helix: 2.87 (0.10), residues: 2484 sheet: -0.14 (0.40), residues: 184 loop : -1.06 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 954 HIS 0.003 0.001 HIS A 136 PHE 0.012 0.001 PHE D 629 TYR 0.015 0.001 TYR C 295 ARG 0.002 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 217 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 3.227 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 outliers start: 13 outliers final: 7 residues processed: 211 average time/residue: 0.6451 time to fit residues: 225.7456 Evaluate side-chains 214 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 3.221 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4907 time to fit residues: 10.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 251 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28088 Z= 0.248 Angle : 0.660 11.988 38264 Z= 0.303 Chirality : 0.035 0.179 4460 Planarity : 0.003 0.034 4728 Dihedral : 6.316 53.202 3936 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.64 % Allowed : 12.44 % Favored : 86.92 % 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: 2.74 (0.14), residues: 3500 helix: 2.87 (0.10), residues: 2484 sheet: -0.48 (0.40), residues: 184 loop : -1.11 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 877 HIS 0.003 0.001 HIS A 136 PHE 0.011 0.001 PHE D1000 TYR 0.011 0.001 TYR A 999 ARG 0.001 0.000 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 3.250 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: 17 outliers final: 10 residues processed: 223 average time/residue: 0.7087 time to fit residues: 256.7691 Evaluate side-chains 217 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5742 time to fit residues: 13.9156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.7470 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28088 Z= 0.340 Angle : 0.679 11.729 38264 Z= 0.319 Chirality : 0.036 0.156 4460 Planarity : 0.004 0.044 4728 Dihedral : 6.296 56.504 3936 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.60 % Allowed : 12.74 % Favored : 86.66 % 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: 2.41 (0.15), residues: 3500 helix: 2.66 (0.10), residues: 2484 sheet: -0.79 (0.41), residues: 184 loop : -1.26 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 877 HIS 0.003 0.001 HIS A 136 PHE 0.012 0.001 PHE D 979 TYR 0.015 0.001 TYR A 295 ARG 0.002 0.000 ARG C 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 224 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 3.211 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: 212 average time/residue: 0.6478 time to fit residues: 227.9924 Evaluate side-chains 217 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 3.282 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5617 time to fit residues: 14.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 2.9990 chunk 328 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 318 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7431 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28088 Z= 0.167 Angle : 0.637 11.983 38264 Z= 0.285 Chirality : 0.034 0.155 4460 Planarity : 0.003 0.036 4728 Dihedral : 6.045 59.597 3936 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.37 % Allowed : 12.93 % Favored : 86.70 % 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: 2.77 (0.15), residues: 3500 helix: 2.92 (0.10), residues: 2480 sheet: -0.72 (0.40), residues: 184 loop : -1.05 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 877 HIS 0.002 0.001 HIS D 136 PHE 0.012 0.001 PHE C1000 TYR 0.012 0.001 TYR C 999 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 224 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 216 average time/residue: 0.6516 time to fit residues: 233.3803 Evaluate side-chains 218 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 210 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5560 time to fit residues: 11.6522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.7980 chunk 338 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 chunk 282 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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: 0.7445 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28088 Z= 0.223 Angle : 0.648 11.787 38264 Z= 0.294 Chirality : 0.034 0.153 4460 Planarity : 0.003 0.038 4728 Dihedral : 5.918 57.089 3936 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.15 % Allowed : 13.71 % Favored : 86.14 % 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: 2.70 (0.15), residues: 3500 helix: 2.86 (0.10), residues: 2480 sheet: -0.81 (0.41), residues: 184 loop : -1.06 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 896 HIS 0.005 0.001 HIS A 259 PHE 0.010 0.001 PHE B1000 TYR 0.011 0.001 TYR A 295 ARG 0.003 0.000 ARG C 842 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 SER 121 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue 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 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 MET 219 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 LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue VAL 273 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 357 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 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 VAL 763 is missing expected H atoms. Skipping. Residue LEU 769 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 LEU 797 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 ILE 813 is missing expected H atoms. Skipping. Residue VAL 814 is missing expected H atoms. Skipping. Residue LEU 817 is missing expected H atoms. Skipping. Residue ILE 904 is missing expected H atoms. Skipping. Residue SER 917 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 220 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 3.508 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 outliers start: 4 outliers final: 4 residues processed: 220 average time/residue: 0.6897 time to fit residues: 248.8311 Evaluate side-chains 216 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 3.227 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5923 time to fit residues: 8.7391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.114699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083343 restraints weight = 197950.496| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.85 r_work: 0.3143 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28088 Z= 0.208 Angle : 0.648 11.848 38264 Z= 0.292 Chirality : 0.034 0.154 4460 Planarity : 0.003 0.037 4728 Dihedral : 5.811 54.858 3936 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % 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: 2.74 (0.15), residues: 3500 helix: 2.88 (0.10), residues: 2480 sheet: -0.80 (0.41), residues: 184 loop : -1.01 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 896 HIS 0.002 0.001 HIS A 259 PHE 0.010 0.001 PHE C1000 TYR 0.011 0.001 TYR A 999 ARG 0.003 0.000 ARG D 842 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7487.40 seconds wall clock time: 131 minutes 20.69 seconds (7880.69 seconds total)