Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:42:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_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_27894/02_2023/8e4o_27894_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4o_27894/02_2023/8e4o_27894_neut_trim_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 18.24, per 1000 atoms: 0.34 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: 33.15 Conformation dependent library (CDL) restraints added in 3.4 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: 3.40 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: 17.08 Time building geometry restraints manager: 35.02 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: 21400 25.58 - 51.17: 561 51.17 - 76.75: 47 76.75 - 102.34: 8 102.34 - 127.92: 4 Dihedral angle restraints: 22020 sinusoidal: 9228 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 22017 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 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. 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.600 Extract box with map and model: 10.340 Check model and map are aligned: 0.590 Process input model: 121.310 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.370 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 % 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 *********************** 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 : 3.179 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: 0.6717 time to fit residues: 412.7744 Evaluate side-chains 237 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 3.237 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5607 time to fit residues: 11.5373 ------------------------------------------------------------------------------- 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: 9.9990 chunk 92 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 B 279 ASN C 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 28088 Z= 0.371 Angle : 0.748 15.880 38264 Z= 0.359 Chirality : 0.038 0.247 4460 Planarity : 0.004 0.043 4728 Dihedral : 8.239 110.190 3936 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.14), residues: 3500 helix: 2.69 (0.10), residues: 2512 sheet: -0.02 (0.41), residues: 192 loop : -1.01 (0.20), residues: 796 *********************** 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 255 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 3.252 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 outliers start: 30 outliers final: 28 residues processed: 247 average time/residue: 0.7141 time to fit residues: 282.3969 Evaluate side-chains 236 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 3.252 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6423 time to fit residues: 33.3921 ------------------------------------------------------------------------------- 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: 10.0000 chunk 100 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 321 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 GLN D 671 GLN B 671 GLN C 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 28088 Z= 0.256 Angle : 0.668 13.687 38264 Z= 0.309 Chirality : 0.035 0.167 4460 Planarity : 0.004 0.048 4728 Dihedral : 7.674 90.066 3936 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.72 (0.14), residues: 3500 helix: 2.81 (0.10), residues: 2488 sheet: -0.25 (0.42), residues: 192 loop : -1.03 (0.20), residues: 820 *********************** 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 248 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 3.792 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: 32 outliers final: 8 residues processed: 233 average time/residue: 0.6658 time to fit residues: 254.6713 Evaluate side-chains 219 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 3.247 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5867 time to fit residues: 12.5835 ------------------------------------------------------------------------------- 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: 7.9990 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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: 0.7443 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 28088 Z= 0.282 Angle : 0.666 14.008 38264 Z= 0.309 Chirality : 0.035 0.148 4460 Planarity : 0.003 0.055 4728 Dihedral : 7.519 74.017 3936 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.08 % 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: 2.53 (0.14), residues: 3500 helix: 2.72 (0.10), residues: 2488 sheet: -0.51 (0.42), residues: 184 loop : -1.19 (0.19), residues: 828 *********************** 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 241 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 3.273 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: 29 outliers final: 11 residues processed: 226 average time/residue: 0.6592 time to fit residues: 244.3899 Evaluate side-chains 210 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5198 time to fit residues: 14.0617 ------------------------------------------------------------------------------- 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: 0.5980 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 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: 0.6980 chunk 308 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7400 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 28088 Z= 0.135 Angle : 0.627 13.183 38264 Z= 0.276 Chirality : 0.034 0.141 4460 Planarity : 0.003 0.036 4728 Dihedral : 7.039 59.008 3936 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.14), residues: 3500 helix: 3.03 (0.10), residues: 2484 sheet: -0.16 (0.41), residues: 180 loop : -0.99 (0.20), residues: 836 *********************** 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 226 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 3.253 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 outliers start: 12 outliers final: 6 residues processed: 217 average time/residue: 0.6381 time to fit residues: 230.3791 Evaluate side-chains 210 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 3.262 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4899 time to fit residues: 9.2897 ------------------------------------------------------------------------------- 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: 5.9990 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 344 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 28088 Z= 0.210 Angle : 0.636 12.628 38264 Z= 0.286 Chirality : 0.034 0.138 4460 Planarity : 0.003 0.057 4728 Dihedral : 6.657 47.837 3936 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.14), residues: 3500 helix: 2.99 (0.10), residues: 2484 sheet: -0.31 (0.41), residues: 180 loop : -1.06 (0.19), residues: 836 *********************** 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 222 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 3.279 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: 12 outliers final: 7 residues processed: 218 average time/residue: 0.6541 time to fit residues: 234.4634 Evaluate side-chains 215 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6030 time to fit residues: 11.0652 ------------------------------------------------------------------------------- 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: 20.0000 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 0.0980 chunk 251 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 289 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 28088 Z= 0.318 Angle : 0.678 12.214 38264 Z= 0.317 Chirality : 0.036 0.221 4460 Planarity : 0.003 0.037 4728 Dihedral : 6.575 47.811 3936 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.57 (0.14), residues: 3500 helix: 2.81 (0.10), residues: 2484 sheet: -0.94 (0.41), residues: 184 loop : -1.26 (0.19), residues: 832 *********************** 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 218 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 213 average time/residue: 0.6816 time to fit residues: 237.8521 Evaluate side-chains 211 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5565 time to fit residues: 12.5911 ------------------------------------------------------------------------------- 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: 1.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.7422 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28088 Z= 0.185 Angle : 0.638 12.005 38264 Z= 0.285 Chirality : 0.034 0.142 4460 Planarity : 0.003 0.031 4728 Dihedral : 6.260 54.857 3936 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.41 % 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: 2.95 (0.10), residues: 2484 sheet: -0.73 (0.42), residues: 180 loop : -1.19 (0.19), residues: 836 *********************** 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 225 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 3.237 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: 11 outliers final: 8 residues processed: 218 average time/residue: 0.6344 time to fit residues: 230.8318 Evaluate side-chains 214 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 3.242 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5427 time to fit residues: 11.5944 ------------------------------------------------------------------------------- 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: 2.9990 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.7426 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28088 Z= 0.200 Angle : 0.639 11.811 38264 Z= 0.287 Chirality : 0.034 0.142 4460 Planarity : 0.003 0.030 4728 Dihedral : 6.065 59.889 3936 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.15), residues: 3500 helix: 2.97 (0.10), residues: 2480 sheet: -0.77 (0.42), residues: 180 loop : -1.12 (0.20), residues: 840 *********************** 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 : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 221 average time/residue: 0.6848 time to fit residues: 248.7849 Evaluate side-chains 214 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5847 time to fit residues: 11.0048 ------------------------------------------------------------------------------- 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: 0.6980 chunk 338 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 354 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7420 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 28088 Z= 0.176 Angle : 0.640 12.350 38264 Z= 0.285 Chirality : 0.034 0.144 4460 Planarity : 0.003 0.030 4728 Dihedral : 5.907 57.872 3936 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.15 % 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 (0.15), residues: 3500 helix: 3.02 (0.10), residues: 2480 sheet: -0.78 (0.42), residues: 180 loop : -1.07 (0.20), residues: 840 ********************** 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 219 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 219 average time/residue: 0.6476 time to fit residues: 236.5126 Evaluate side-chains 215 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 3.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5517 time to fit residues: 6.8680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.3980 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 290 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.084160 restraints weight = 196938.736| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.88 r_work: 0.3160 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 28088 Z= 0.185 Angle : 0.641 11.920 38264 Z= 0.286 Chirality : 0.034 0.141 4460 Planarity : 0.003 0.031 4728 Dihedral : 5.744 54.488 3936 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.15), residues: 3500 helix: 3.04 (0.10), residues: 2480 sheet: -0.82 (0.42), residues: 180 loop : -1.06 (0.20), residues: 840 =============================================================================== Job complete usr+sys time: 7081.05 seconds wall clock time: 124 minutes 32.72 seconds (7472.72 seconds total)