Starting phenix.real_space_refine on Fri Aug 9 06:48:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0a_13742/08_2024/7q0a_13742_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0a_13742/08_2024/7q0a_13742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0a_13742/08_2024/7q0a_13742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0a_13742/08_2024/7q0a_13742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0a_13742/08_2024/7q0a_13742_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q0a_13742/08_2024/7q0a_13742_neut.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 16009 2.51 5 N 4117 2.21 5 O 4886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25125 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7628 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 49, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 7530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7530 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 48, 'TRANS': 935} Chain breaks: 10 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ASN:plan1': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 7582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7582 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "Y" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 884 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "Z" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.41, per 1000 atoms: 0.57 Number of scatterers: 25125 At special positions: 0 Unit cell: (126.28, 134.48, 218.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 4886 8.00 N 4117 7.00 C 16009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 95 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1401 " - " ASN A 282 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 616 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 234 " " NAG B1403 " - " ASN B 282 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B 717 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 282 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 616 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1074 " " NAG C1408 " - " ASN C1134 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " Time building additional restraints: 10.46 Conformation dependent library (CDL) restraints added in 4.7 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5966 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 50 sheets defined 26.3% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.990A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.661A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.766A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.505A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.707A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.428A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.025A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.541A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.267A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.699A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.561A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.337A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.701A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.598A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.658A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.235A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.546A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.737A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.096A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 86 through 90 Processing helix chain 'Z' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.752A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.648A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.547A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.660A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.729A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.996A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.103A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.587A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.032A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.618A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.406A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.892A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.296A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.567A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.995A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.912A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.834A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.948A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.507A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.192A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.106A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.798A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.339A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'Y' and resid 11 through 12 removed outlier: 6.794A pdb=" N MET Y 34 " --> pdb=" O VAL Y 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'Z' and resid 4 through 7 removed outlier: 4.002A pdb=" N ASP Z 70 " --> pdb=" O SER Z 67 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER Z 67 " --> pdb=" O ASP Z 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 10 through 14 removed outlier: 6.701A pdb=" N LEU Z 11 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS Z 107 " --> pdb=" O LEU Z 11 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA Z 13 " --> pdb=" O LYS Z 107 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN Z 37 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU Z 46 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 10 through 14 removed outlier: 6.701A pdb=" N LEU Z 11 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS Z 107 " --> pdb=" O LEU Z 11 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA Z 13 " --> pdb=" O LYS Z 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR Z 97 " --> pdb=" O GLN Z 90 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2952 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: 11.01 Time building geometry restraints manager: 11.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7984 1.34 - 1.46: 6379 1.46 - 1.58: 11167 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 25672 Sorted by residual: bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.22e-02 6.72e+03 9.01e+00 bond pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.20e-02 6.94e+03 7.45e+00 bond pdb=" N THR B 333 " pdb=" CA THR B 333 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.23e-02 6.61e+03 6.52e+00 bond pdb=" N ASN B 121 " pdb=" CA ASN B 121 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.25e-02 6.40e+03 5.93e+00 ... (remaining 25667 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 712 106.59 - 113.44: 14193 113.44 - 120.29: 8635 120.29 - 127.14: 11230 127.14 - 133.99: 218 Bond angle restraints: 34988 Sorted by residual: angle pdb=" N THR A 124 " pdb=" CA THR A 124 " pdb=" C THR A 124 " ideal model delta sigma weight residual 114.75 110.00 4.75 1.26e+00 6.30e-01 1.42e+01 angle pdb=" N PRO Y 102 " pdb=" CA PRO Y 102 " pdb=" C PRO Y 102 " ideal model delta sigma weight residual 112.47 118.98 -6.51 2.06e+00 2.36e-01 9.98e+00 angle pdb=" CA CYS C 738 " pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 114.40 107.19 7.21 2.30e+00 1.89e-01 9.83e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 126.10 -9.80 3.50e+00 8.16e-02 7.84e+00 angle pdb=" C CYS C 738 " pdb=" CA CYS C 738 " pdb=" CB CYS C 738 " ideal model delta sigma weight residual 110.79 106.25 4.54 1.66e+00 3.63e-01 7.49e+00 ... (remaining 34983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14980 17.91 - 35.82: 659 35.82 - 53.74: 144 53.74 - 71.65: 41 71.65 - 89.56: 26 Dihedral angle restraints: 15850 sinusoidal: 6579 harmonic: 9271 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -159.51 73.51 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.41 72.41 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.20 72.20 1 1.00e+01 1.00e-02 6.67e+01 ... (remaining 15847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3214 0.049 - 0.099: 711 0.099 - 0.148: 241 0.148 - 0.197: 11 0.197 - 0.247: 2 Chirality restraints: 4179 Sorted by residual: chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO Y 102 " pdb=" N PRO Y 102 " pdb=" C PRO Y 102 " pdb=" CB PRO Y 102 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 4176 not shown) Planarity restraints: 4491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.024 2.00e-02 2.50e+03 2.63e-02 8.68e+00 pdb=" CG ASN B 343 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 122 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ASN A 122 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 122 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 123 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C ASN C 122 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.014 2.00e-02 2.50e+03 ... (remaining 4488 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2485 2.75 - 3.29: 24595 3.29 - 3.83: 40967 3.83 - 4.36: 48322 4.36 - 4.90: 84455 Nonbonded interactions: 200824 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.216 3.040 nonbonded pdb=" O ILE C 742 " pdb=" NH1 ARG C1000 " model vdw 2.262 3.120 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.263 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.269 3.040 ... (remaining 200819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 52 or (resid 53 and ( \ name N or name CA or name C or name O or name CB )) or resid 54 through 66 or re \ sid 82 through 87 or (resid 88 and (name N or name CA or name C or name O or nam \ e CB )) or resid 89 through 95 or (resid 96 through 97 and (name N or name CA or \ name C or name O or name CB )) or resid 98 through 109 or (resid 110 and (name \ N or name CA or name C or name O or name CB )) or resid 111 or (resid 112 throug \ h 113 and (name N or name CA or name C or name O or name CB )) or resid 116 thro \ ugh 124 or (resid 125 and (name N or name CA or name C or name O or name CB )) o \ r resid 126 through 131 or (resid 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 or (resid 134 through 138 and (name N or name CA or \ name C or name O or name CB )) or resid 139 through 140 or resid 166 through 168 \ or (resid 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 171 or (resid 172 through 188 and (name N or name CA or name C or n \ ame O or name CB )) or resid 189 through 196 or resid 200 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB )) or (resid 215 and ( \ name N or name CA or name C or name O or name CB )) or resid 216 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 \ through 223 or (resid 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 263 or resid 265 through 308 or (resid 309 and (name N \ or name CA or name C or name O or name CB )) or resid 310 through 323 or (resid \ 324 and (name N or name CA or name C or name O or name CB )) or resid 325 throug \ h 332 or (resid 333 through 334 and (name N or name CA or name C or name O or na \ me CB )) or resid 335 through 457 or (resid 458 and (name N or name CA or name C \ or name O or name CB )) or resid 459 through 516 or resid 522 through 528 or (r \ esid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 t \ hrough 536 or (resid 537 and (name N or name CA or name C or name O or name CB ) \ ) or resid 538 through 747 or (resid 748 and (name N or name CA or name C or nam \ e O or name CB )) or resid 749 through 793 or (resid 794 and (name N or name CA \ or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name \ CA or name C or name O or name CB )) or resid 797 through 827 or (resid 854 thr \ ough 855 and (name N or name CA or name C or name O or name CB )) or resid 856 t \ hrough 867 or (resid 868 and (name N or name CA or name C or name O or name CB ) \ ) or resid 869 through 939 or (resid 940 and (name N or name CA or name C or nam \ e O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA \ or name C or name O or name CB )) or resid 986 through 987 or (resid 988 through \ 989 and (name N or name CA or name C or name O or name CB )) or resid 990 throu \ gh 1141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) \ or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 or resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 109 or (resid 110 and (name N or name CA or name C or name O or n \ ame CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 39 through 140 or resid 166 through 190 or (resid 191 and (name N or name CA or \ name C or name O or name CB )) or resid 192 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 200 through 205 or (resi \ d 206 and (name N or name CA or name C or name O or name CB )) or resid 207 thro \ ugh 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) o \ r resid 238 through 241 or (resid 242 through 263 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or \ name CA or name C or name O or name CB )) or resid 282 through 297 or (resid 29 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 299 through \ 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or re \ sid 325 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 457 or (resid 458 and (name N or name CA or name \ C or name O or name CB )) or resid 459 through 567 or (resid 568 and (name N or \ name CA or name C or name O or name CB )) or resid 569 through 570 or (resid 57 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 572 through \ 579 or (resid 580 and (name N or name CA or name C or name O or name CB )) or re \ sid 581 or (resid 582 through 583 and (name N or name CA or name C or name O or \ name CB )) or resid 584 through 613 or (resid 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 827 or (resid 854 through 855 and (name N or name CA or \ name C or name O or name CB )) or resid 856 through 867 or (resid 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 939 or (res \ id 940 and (name N or name CA or name C or name O or name CB )) or resid 941 thr \ ough 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) \ or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or nam \ e C or name O or name CB )) or resid 990 through 1143 or (resid 1144 through 114 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 1147 or resi \ d 1401 through 1408)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 113 or resid 116 through 134 or (resid 135 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 66 through 172 or (resid 188 and (name N or name CA or name C or name O or name \ CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 205 or (resid 206 and (name N or name \ CA or name C or name O or name CB )) or resid 207 through 209 or (resid 210 and \ (name N or name CA or name C or name O or name CB )) or resid 215 through 217 o \ r (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 19 through 223 or (resid 224 and (name N or name CA or name C or name O or name \ CB )) or resid 225 through 236 or (resid 237 and (name N or name CA or name C or \ name O or name CB )) or resid 238 through 297 or (resid 298 and (name N or name \ CA or name C or name O or name CB )) or resid 299 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 332 o \ r (resid 333 through 334 and (name N or name CA or name C or name O or name CB ) \ ) or resid 335 through 388 or (resid 389 and (name N or name CA or name C or nam \ e O or name CB )) or resid 390 through 516 or resid 522 through 527 or (resid 52 \ 8 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 536 or (resid 537 and (name N or name CA or name C or name O or name \ CB )) or resid 538 through 553 or (resid 554 and (name N or name CA or name C o \ r name O or name CB )) or resid 555 through 557 or (resid 558 and (name N or nam \ e CA or name C or name O or name CB )) or resid 559 through 567 or (resid 568 an \ d (name N or name CA or name C or name O or name CB )) or resid 569 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 579 or (resid 580 and (name N or name CA or name C or name O or name \ CB )) or resid 581 or (resid 582 through 583 and (name N or name CA or name C o \ r name O or name CB )) or resid 584 through 618 or (resid 619 and (name N or nam \ e CA or name C or name O or name CB )) or resid 620 through 645 or (resid 646 th \ rough 647 and (name N or name CA or name C or name O or name CB )) or resid 648 \ through 795 or (resid 796 and (name N or name CA or name C or name O or name CB \ )) or resid 797 through 1141 or (resid 1142 and (name N or name CA or name C or \ name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or na \ me CA or name C or name O or name CB )) or resid 1147 or resid 1401 through 1408 \ )) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 72.150 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25672 Z= 0.215 Angle : 0.577 9.801 34988 Z= 0.297 Chirality : 0.046 0.247 4179 Planarity : 0.004 0.046 4453 Dihedral : 11.425 89.559 9761 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 0.34 % Allowed : 4.17 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.52 (0.15), residues: 3133 helix: 1.35 (0.21), residues: 637 sheet: -0.45 (0.17), residues: 794 loop : -0.93 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 PHE 0.013 0.001 PHE A 318 TYR 0.019 0.001 TYR A 904 ARG 0.005 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 534 time to evaluate : 3.574 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.9000 (t) cc_final: 0.8761 (p) REVERT: A 772 VAL cc_start: 0.9238 (t) cc_final: 0.8790 (p) REVERT: A 782 PHE cc_start: 0.8962 (m-80) cc_final: 0.8667 (m-10) REVERT: A 806 LEU cc_start: 0.8861 (mt) cc_final: 0.8414 (tt) REVERT: A 916 LEU cc_start: 0.9311 (tp) cc_final: 0.9061 (tp) REVERT: A 1063 LEU cc_start: 0.9304 (mt) cc_final: 0.9093 (mm) REVERT: A 1064 HIS cc_start: 0.8164 (m-70) cc_final: 0.7438 (m170) REVERT: B 54 LEU cc_start: 0.9321 (mt) cc_final: 0.8928 (tp) REVERT: B 135 PHE cc_start: 0.5532 (m-80) cc_final: 0.4727 (m-80) REVERT: B 266 TYR cc_start: 0.6888 (m-80) cc_final: 0.5921 (m-80) REVERT: B 276 LEU cc_start: 0.9052 (tp) cc_final: 0.8843 (mm) REVERT: B 279 TYR cc_start: 0.8486 (m-80) cc_final: 0.8209 (m-10) REVERT: B 712 ILE cc_start: 0.9386 (tt) cc_final: 0.8999 (mt) REVERT: B 763 LEU cc_start: 0.9046 (mt) cc_final: 0.8753 (mt) REVERT: B 770 ILE cc_start: 0.8776 (mt) cc_final: 0.8481 (tt) REVERT: B 777 ASN cc_start: 0.8493 (m-40) cc_final: 0.7906 (m110) REVERT: B 802 PHE cc_start: 0.8776 (m-80) cc_final: 0.8540 (m-80) REVERT: B 902 MET cc_start: 0.8809 (mmm) cc_final: 0.8267 (mmm) REVERT: B 906 PHE cc_start: 0.8415 (m-80) cc_final: 0.7938 (m-10) REVERT: B 948 LEU cc_start: 0.9603 (mt) cc_final: 0.9321 (mp) REVERT: B 1001 LEU cc_start: 0.9323 (tp) cc_final: 0.9046 (pp) REVERT: B 1004 LEU cc_start: 0.8949 (mt) cc_final: 0.8735 (tp) REVERT: B 1017 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6636 (tt0) REVERT: B 1018 ILE cc_start: 0.9201 (mm) cc_final: 0.8893 (tp) REVERT: B 1036 GLN cc_start: 0.8326 (tt0) cc_final: 0.7822 (tp-100) REVERT: B 1063 LEU cc_start: 0.8660 (mt) cc_final: 0.8446 (mp) REVERT: C 104 TRP cc_start: 0.6802 (m-90) cc_final: 0.6203 (m-90) REVERT: C 194 PHE cc_start: 0.7796 (m-80) cc_final: 0.7438 (m-80) REVERT: C 718 PHE cc_start: 0.8779 (p90) cc_final: 0.7592 (p90) REVERT: C 733 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7426 (mtmm) REVERT: C 742 ILE cc_start: 0.8328 (mt) cc_final: 0.7899 (tt) REVERT: C 759 PHE cc_start: 0.7483 (m-80) cc_final: 0.7192 (m-80) REVERT: C 983 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7685 (ptm-80) REVERT: C 1018 ILE cc_start: 0.9778 (mm) cc_final: 0.9230 (tp) REVERT: C 1042 PHE cc_start: 0.8604 (t80) cc_final: 0.8145 (t80) REVERT: Y 104 MET cc_start: -0.3017 (ptm) cc_final: -0.4208 (mtt) outliers start: 9 outliers final: 3 residues processed: 539 average time/residue: 0.3705 time to fit residues: 312.1193 Evaluate side-chains 310 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 306 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1058 HIS B1071 GLN C 613 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 25672 Z= 0.400 Angle : 0.748 14.545 34988 Z= 0.396 Chirality : 0.047 0.209 4179 Planarity : 0.005 0.062 4453 Dihedral : 6.428 59.724 4434 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.56 (0.14), residues: 3133 helix: 0.69 (0.19), residues: 662 sheet: -0.25 (0.18), residues: 790 loop : -0.83 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.013 0.002 HIS A1048 PHE 0.029 0.003 PHE A 759 TYR 0.025 0.002 TYR B 369 ARG 0.023 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 292 time to evaluate : 2.638 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.9233 (t) cc_final: 0.9028 (p) REVERT: A 900 MET cc_start: 0.8840 (mmt) cc_final: 0.8334 (mmt) REVERT: A 968 SER cc_start: 0.9572 (m) cc_final: 0.8911 (p) REVERT: A 980 ILE cc_start: 0.9111 (mt) cc_final: 0.8909 (pt) REVERT: A 1006 THR cc_start: 0.9124 (m) cc_final: 0.8534 (m) REVERT: A 1063 LEU cc_start: 0.9263 (mt) cc_final: 0.8914 (mm) REVERT: B 54 LEU cc_start: 0.9356 (mt) cc_final: 0.8890 (pt) REVERT: B 91 TYR cc_start: 0.8326 (t80) cc_final: 0.7816 (t80) REVERT: B 266 TYR cc_start: 0.6824 (m-80) cc_final: 0.5988 (m-80) REVERT: B 279 TYR cc_start: 0.8745 (m-80) cc_final: 0.8418 (m-80) REVERT: B 312 ILE cc_start: 0.8965 (tt) cc_final: 0.8356 (pt) REVERT: B 753 LEU cc_start: 0.8903 (pp) cc_final: 0.8668 (pp) REVERT: B 1036 GLN cc_start: 0.8681 (tt0) cc_final: 0.8348 (tp40) REVERT: C 36 VAL cc_start: 0.7920 (m) cc_final: 0.7409 (m) REVERT: C 56 LEU cc_start: 0.8166 (mt) cc_final: 0.7654 (tp) REVERT: C 238 PHE cc_start: 0.8313 (p90) cc_final: 0.8039 (p90) REVERT: C 415 THR cc_start: 0.7538 (p) cc_final: 0.7291 (p) REVERT: C 733 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7545 (mtmm) REVERT: C 781 VAL cc_start: 0.9503 (t) cc_final: 0.9159 (m) REVERT: C 1018 ILE cc_start: 0.9419 (mm) cc_final: 0.9094 (mm) REVERT: Y 104 MET cc_start: -0.1896 (ptm) cc_final: -0.3540 (mtt) REVERT: Y 112 MET cc_start: -0.2672 (tpt) cc_final: -0.2899 (tpt) outliers start: 2 outliers final: 0 residues processed: 294 average time/residue: 0.3753 time to fit residues: 174.4702 Evaluate side-chains 200 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 0.0020 chunk 89 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 231 optimal weight: 0.1980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN A 935 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1083 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 607 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Z 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25672 Z= 0.187 Angle : 0.570 11.095 34988 Z= 0.298 Chirality : 0.045 0.248 4179 Planarity : 0.004 0.078 4453 Dihedral : 5.630 53.820 4434 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.10 (0.14), residues: 3133 helix: 1.33 (0.19), residues: 673 sheet: -0.06 (0.18), residues: 775 loop : -0.61 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.005 0.001 HIS B1048 PHE 0.024 0.001 PHE B 201 TYR 0.018 0.001 TYR B 369 ARG 0.007 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 269 time to evaluate : 2.741 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: A 83 VAL cc_start: 0.9204 (t) cc_final: 0.8982 (p) REVERT: A 194 PHE cc_start: 0.7824 (m-10) cc_final: 0.7272 (m-10) REVERT: A 195 LYS cc_start: 0.8992 (pttm) cc_final: 0.8222 (ttpp) REVERT: A 611 LEU cc_start: 0.8575 (mm) cc_final: 0.8155 (mm) REVERT: A 651 ILE cc_start: 0.8168 (mt) cc_final: 0.7343 (mm) REVERT: A 740 MET cc_start: 0.8235 (tpt) cc_final: 0.7518 (tpp) REVERT: A 968 SER cc_start: 0.9450 (m) cc_final: 0.8766 (p) REVERT: A 1006 THR cc_start: 0.9215 (m) cc_final: 0.9002 (m) REVERT: A 1064 HIS cc_start: 0.8837 (m-70) cc_final: 0.7820 (m-70) REVERT: B 54 LEU cc_start: 0.9239 (mt) cc_final: 0.8672 (pt) REVERT: B 266 TYR cc_start: 0.6553 (m-80) cc_final: 0.5776 (m-80) REVERT: B 276 LEU cc_start: 0.9147 (tt) cc_final: 0.8794 (tp) REVERT: B 279 TYR cc_start: 0.8414 (m-80) cc_final: 0.8176 (m-80) REVERT: B 770 ILE cc_start: 0.9212 (mm) cc_final: 0.8774 (mm) REVERT: B 902 MET cc_start: 0.8388 (mmm) cc_final: 0.7338 (mmm) REVERT: B 979 ASP cc_start: 0.8126 (t0) cc_final: 0.7747 (t0) REVERT: B 1018 ILE cc_start: 0.8770 (mm) cc_final: 0.8513 (mt) REVERT: B 1036 GLN cc_start: 0.8532 (tt0) cc_final: 0.8041 (tp40) REVERT: B 1108 ASN cc_start: 0.8809 (t0) cc_final: 0.8380 (t0) REVERT: C 740 MET cc_start: 0.8485 (tmm) cc_final: 0.8235 (tmm) REVERT: C 781 VAL cc_start: 0.9537 (t) cc_final: 0.9050 (m) REVERT: C 788 ILE cc_start: 0.8240 (pt) cc_final: 0.7733 (mp) REVERT: C 973 ILE cc_start: 0.9091 (pt) cc_final: 0.8877 (tp) REVERT: C 1018 ILE cc_start: 0.9345 (mm) cc_final: 0.8964 (tp) REVERT: Y 104 MET cc_start: -0.1618 (ptm) cc_final: -0.2773 (mtt) REVERT: Y 112 MET cc_start: -0.2198 (tpt) cc_final: -0.2454 (tpt) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.3591 time to fit residues: 154.4803 Evaluate side-chains 194 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 137 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25672 Z= 0.225 Angle : 0.573 10.215 34988 Z= 0.302 Chirality : 0.044 0.187 4179 Planarity : 0.004 0.054 4453 Dihedral : 5.159 43.025 4434 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.01 (0.14), residues: 3133 helix: 1.30 (0.20), residues: 676 sheet: 0.14 (0.18), residues: 741 loop : -0.56 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.010 0.001 HIS A1048 PHE 0.024 0.001 PHE B 201 TYR 0.017 0.001 TYR B 369 ARG 0.003 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.960 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: A 83 VAL cc_start: 0.9134 (t) cc_final: 0.8897 (p) REVERT: A 193 VAL cc_start: 0.8746 (t) cc_final: 0.8420 (p) REVERT: A 194 PHE cc_start: 0.7661 (m-10) cc_final: 0.6953 (m-10) REVERT: A 338 PHE cc_start: 0.8644 (m-10) cc_final: 0.8383 (m-80) REVERT: A 651 ILE cc_start: 0.8096 (mt) cc_final: 0.7405 (mm) REVERT: A 740 MET cc_start: 0.8283 (tpt) cc_final: 0.7904 (tpt) REVERT: A 900 MET cc_start: 0.8655 (mmt) cc_final: 0.8023 (mmt) REVERT: A 955 ASN cc_start: 0.8679 (m110) cc_final: 0.8447 (m110) REVERT: A 968 SER cc_start: 0.9399 (m) cc_final: 0.8883 (p) REVERT: A 993 ILE cc_start: 0.9261 (mt) cc_final: 0.9009 (mm) REVERT: B 54 LEU cc_start: 0.9230 (mt) cc_final: 0.8631 (pt) REVERT: B 238 PHE cc_start: 0.8156 (p90) cc_final: 0.7805 (p90) REVERT: B 266 TYR cc_start: 0.6683 (m-80) cc_final: 0.5901 (m-80) REVERT: B 275 PHE cc_start: 0.7288 (m-80) cc_final: 0.6538 (m-80) REVERT: B 279 TYR cc_start: 0.8457 (m-80) cc_final: 0.8245 (m-80) REVERT: B 979 ASP cc_start: 0.8435 (t0) cc_final: 0.7776 (t0) REVERT: B 1018 ILE cc_start: 0.8928 (mm) cc_final: 0.8613 (mt) REVERT: B 1050 MET cc_start: 0.9045 (pmm) cc_final: 0.8491 (pmm) REVERT: B 1108 ASN cc_start: 0.9304 (t0) cc_final: 0.8537 (t0) REVERT: C 781 VAL cc_start: 0.9537 (t) cc_final: 0.9116 (m) REVERT: C 1018 ILE cc_start: 0.9296 (mm) cc_final: 0.9035 (tp) REVERT: Y 104 MET cc_start: -0.1676 (ptm) cc_final: -0.2441 (mtt) REVERT: Y 112 MET cc_start: -0.2072 (tpt) cc_final: -0.2366 (tpt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.3493 time to fit residues: 143.3093 Evaluate side-chains 180 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25672 Z= 0.183 Angle : 0.552 11.521 34988 Z= 0.288 Chirality : 0.044 0.239 4179 Planarity : 0.004 0.077 4453 Dihedral : 4.849 30.150 4434 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 0.12 (0.15), residues: 3133 helix: 1.53 (0.20), residues: 667 sheet: 0.26 (0.18), residues: 739 loop : -0.56 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.014 0.001 HIS B1048 PHE 0.023 0.001 PHE B 201 TYR 0.016 0.001 TYR B 204 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.078 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 REVERT: A 83 VAL cc_start: 0.9109 (t) cc_final: 0.8901 (p) REVERT: A 193 VAL cc_start: 0.8762 (t) cc_final: 0.8488 (p) REVERT: A 194 PHE cc_start: 0.7680 (m-10) cc_final: 0.6811 (m-10) REVERT: A 338 PHE cc_start: 0.8643 (m-10) cc_final: 0.8372 (m-80) REVERT: A 611 LEU cc_start: 0.8650 (mm) cc_final: 0.8228 (mm) REVERT: A 651 ILE cc_start: 0.8050 (mt) cc_final: 0.7443 (mm) REVERT: A 740 MET cc_start: 0.8294 (tpt) cc_final: 0.7829 (tpt) REVERT: A 878 LEU cc_start: 0.9381 (mt) cc_final: 0.9179 (mt) REVERT: A 950 ASP cc_start: 0.7930 (t70) cc_final: 0.7482 (t0) REVERT: A 968 SER cc_start: 0.9392 (m) cc_final: 0.8876 (p) REVERT: A 993 ILE cc_start: 0.9241 (mt) cc_final: 0.9000 (mm) REVERT: A 1067 TYR cc_start: 0.8325 (t80) cc_final: 0.8121 (t80) REVERT: B 54 LEU cc_start: 0.9271 (mt) cc_final: 0.8794 (pt) REVERT: B 238 PHE cc_start: 0.8010 (p90) cc_final: 0.7400 (p90) REVERT: B 266 TYR cc_start: 0.6626 (m-80) cc_final: 0.5889 (m-80) REVERT: B 276 LEU cc_start: 0.9122 (tt) cc_final: 0.8882 (tp) REVERT: B 770 ILE cc_start: 0.9194 (mm) cc_final: 0.8643 (mm) REVERT: B 773 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 902 MET cc_start: 0.8320 (mmp) cc_final: 0.7679 (mmp) REVERT: B 906 PHE cc_start: 0.7482 (m-10) cc_final: 0.7078 (m-80) REVERT: B 979 ASP cc_start: 0.8396 (t0) cc_final: 0.7813 (t0) REVERT: B 1018 ILE cc_start: 0.8901 (mm) cc_final: 0.8630 (mt) REVERT: B 1050 MET cc_start: 0.8732 (pmm) cc_final: 0.8307 (pmm) REVERT: B 1108 ASN cc_start: 0.8886 (t0) cc_final: 0.8634 (t0) REVERT: C 238 PHE cc_start: 0.8148 (p90) cc_final: 0.7755 (p90) REVERT: C 781 VAL cc_start: 0.9531 (t) cc_final: 0.9066 (m) REVERT: C 902 MET cc_start: 0.8192 (tpt) cc_final: 0.7806 (tpp) REVERT: C 1018 ILE cc_start: 0.9257 (mm) cc_final: 0.9027 (tp) REVERT: Y 104 MET cc_start: -0.1583 (ptm) cc_final: -0.2227 (mtt) REVERT: Y 112 MET cc_start: -0.2033 (tpt) cc_final: -0.2310 (tpt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3656 time to fit residues: 148.3714 Evaluate side-chains 191 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 10.0000 chunk 275 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 306 optimal weight: 50.0000 chunk 254 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25672 Z= 0.183 Angle : 0.549 7.447 34988 Z= 0.288 Chirality : 0.044 0.193 4179 Planarity : 0.004 0.067 4453 Dihedral : 4.682 29.320 4434 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.04 % Allowed : 1.39 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 0.15 (0.15), residues: 3133 helix: 1.50 (0.20), residues: 666 sheet: 0.30 (0.18), residues: 744 loop : -0.52 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.013 0.001 HIS B1048 PHE 0.043 0.001 PHE B 906 TYR 0.019 0.001 TYR B 741 ARG 0.008 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 3.016 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 revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.9009 (t) cc_final: 0.8788 (p) REVERT: A 193 VAL cc_start: 0.8791 (t) cc_final: 0.8581 (p) REVERT: A 194 PHE cc_start: 0.7603 (m-10) cc_final: 0.6669 (m-10) REVERT: A 338 PHE cc_start: 0.8581 (m-10) cc_final: 0.8201 (m-80) REVERT: A 611 LEU cc_start: 0.8727 (mm) cc_final: 0.8469 (mm) REVERT: A 651 ILE cc_start: 0.8155 (mt) cc_final: 0.7446 (mm) REVERT: A 740 MET cc_start: 0.8288 (tpt) cc_final: 0.7735 (tpt) REVERT: A 900 MET cc_start: 0.8672 (mmt) cc_final: 0.8014 (mmt) REVERT: A 950 ASP cc_start: 0.8037 (t70) cc_final: 0.7502 (t0) REVERT: A 968 SER cc_start: 0.9417 (m) cc_final: 0.8900 (p) REVERT: A 993 ILE cc_start: 0.9199 (mt) cc_final: 0.8963 (mm) REVERT: A 1019 ARG cc_start: 0.8579 (ttp-170) cc_final: 0.8196 (ttp-110) REVERT: A 1067 TYR cc_start: 0.8101 (t80) cc_final: 0.7879 (t80) REVERT: B 54 LEU cc_start: 0.9279 (mt) cc_final: 0.8750 (pt) REVERT: B 238 PHE cc_start: 0.7923 (p90) cc_final: 0.7300 (p90) REVERT: B 266 TYR cc_start: 0.6646 (m-80) cc_final: 0.5918 (m-80) REVERT: B 276 LEU cc_start: 0.9222 (tt) cc_final: 0.8747 (tp) REVERT: B 611 LEU cc_start: 0.9194 (tp) cc_final: 0.8975 (tp) REVERT: B 770 ILE cc_start: 0.9146 (mm) cc_final: 0.8474 (mm) REVERT: B 773 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 902 MET cc_start: 0.7822 (mmp) cc_final: 0.7497 (mmp) REVERT: B 979 ASP cc_start: 0.8211 (t0) cc_final: 0.7879 (t0) REVERT: B 1018 ILE cc_start: 0.8927 (mm) cc_final: 0.8622 (mt) REVERT: B 1050 MET cc_start: 0.8965 (pmm) cc_final: 0.8431 (pmm) REVERT: B 1108 ASN cc_start: 0.9243 (t0) cc_final: 0.8604 (t0) REVERT: C 758 SER cc_start: 0.8911 (t) cc_final: 0.8151 (t) REVERT: C 781 VAL cc_start: 0.9545 (t) cc_final: 0.9095 (m) REVERT: C 900 MET cc_start: 0.7859 (mmt) cc_final: 0.7626 (mmt) REVERT: C 1018 ILE cc_start: 0.9262 (mm) cc_final: 0.9017 (tp) REVERT: Y 112 MET cc_start: -0.1258 (tpt) cc_final: -0.1571 (tpt) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.3604 time to fit residues: 143.7012 Evaluate side-chains 189 residues out of total 2786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 258 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 305 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: