Starting phenix.real_space_refine on Tue Jun 24 13:54:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvg_34126/06_2025/7yvg_34126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvg_34126/06_2025/7yvg_34126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvg_34126/06_2025/7yvg_34126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvg_34126/06_2025/7yvg_34126.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvg_34126/06_2025/7yvg_34126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvg_34126/06_2025/7yvg_34126.cif" } resolution = 3.4 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= -0.000 sd= 0.043 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 129 5.16 5 C 18192 2.51 5 N 4692 2.21 5 O 5466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 201 residue(s): 1.72s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7634 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 248 Chain: "B" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7643 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7649 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 237 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 18.29, per 1000 atoms: 0.64 Number of scatterers: 28479 At special positions: 0 Unit cell: (143.5, 147.6, 225.5, 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 129 16.00 O 5466 8.00 N 4692 7.00 C 18192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.02 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=2.04 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=2.06 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 7.33 Conformation dependent library (CDL) restraints added in 3.7 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 21.1% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.858A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.775A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.522A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.077A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.525A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.199A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.813A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.778A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.595A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.524A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.012A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.988A 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 337 through 344 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.904A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.533A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.162A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.789A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.030A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.092A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.002A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 86 through 90 removed outlier: 4.046A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.122A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.714A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.649A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.865A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.656A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.182A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.616A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.837A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.870A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.690A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.690A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.081A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.634A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.829A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.978A 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 removed outlier: 3.764A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.064A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 327 removed outlier: 5.672A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.538A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.909A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.614A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.614A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.369A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.527A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.522A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.935A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.077A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.669A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.669A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.521A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.620A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.811A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.658A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.911A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.747A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.989A pdb=" N LEU J 11 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.972A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.768A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.620A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.151A pdb=" N GLY M 10 " --> pdb=" O THR M 115 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3255 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: 13.33 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6885 1.33 - 1.47: 10791 1.47 - 1.62: 11293 1.62 - 1.76: 50 1.76 - 1.91: 116 Bond restraints: 29135 Sorted by residual: bond pdb=" CG LEU I 4 " pdb=" CD2 LEU I 4 " ideal model delta sigma weight residual 1.521 1.730 -0.209 3.30e-02 9.18e+02 4.00e+01 bond pdb=" CB TRP B 886 " pdb=" CG TRP B 886 " ideal model delta sigma weight residual 1.498 1.346 0.152 3.10e-02 1.04e+03 2.41e+01 bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.190 0.051 1.12e-02 7.97e+03 2.04e+01 bond pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 1.808 1.667 0.141 3.30e-02 9.18e+02 1.82e+01 bond pdb=" C PRO A 863 " pdb=" O PRO A 863 " ideal model delta sigma weight residual 1.232 1.182 0.050 1.20e-02 6.94e+03 1.77e+01 ... (remaining 29130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 38572 3.35 - 6.71: 1093 6.71 - 10.06: 101 10.06 - 13.41: 26 13.41 - 16.77: 3 Bond angle restraints: 39795 Sorted by residual: angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 131.17 -16.77 2.30e+00 1.89e-01 5.31e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 129.51 -15.11 2.30e+00 1.89e-01 4.32e+01 angle pdb=" C SER H 30 " pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta sigma weight residual 122.14 111.20 10.94 1.67e+00 3.59e-01 4.29e+01 angle pdb=" C SER A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta sigma weight residual 121.54 133.94 -12.40 1.91e+00 2.74e-01 4.21e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 111.81 106.48 5.33 8.60e-01 1.35e+00 3.84e+01 ... (remaining 39790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 16589 22.37 - 44.74: 856 44.74 - 67.11: 141 67.11 - 89.48: 49 89.48 - 111.85: 3 Dihedral angle restraints: 17638 sinusoidal: 6784 harmonic: 10854 Sorted by residual: dihedral pdb=" CA PRO J 95 " pdb=" C PRO J 95 " pdb=" N PRO J 96 " pdb=" CA PRO J 96 " ideal model delta harmonic sigma weight residual -180.00 -68.15 -111.85 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA PRO H 95 " pdb=" C PRO H 95 " pdb=" N PRO H 96 " pdb=" CA PRO H 96 " ideal model delta harmonic sigma weight residual -180.00 -68.58 -111.42 0 5.00e+00 4.00e-02 4.97e+02 dihedral pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual -180.00 -69.01 -110.99 0 5.00e+00 4.00e-02 4.93e+02 ... (remaining 17635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3790 0.099 - 0.197: 785 0.197 - 0.296: 78 0.296 - 0.394: 11 0.394 - 0.493: 6 Chirality restraints: 4670 Sorted by residual: chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA CYS A 166 " pdb=" N CYS A 166 " pdb=" C CYS A 166 " pdb=" CB CYS A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 4667 not shown) Planarity restraints: 5097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.032 2.00e-02 2.50e+03 3.07e-02 2.35e+01 pdb=" CG TRP A 886 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 38 " 0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLN L 38 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN L 38 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS L 39 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 576 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C VAL B 576 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL B 576 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG B 577 " -0.024 2.00e-02 2.50e+03 ... (remaining 5094 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 545 2.63 - 3.20: 26794 3.20 - 3.77: 41289 3.77 - 4.33: 55666 4.33 - 4.90: 94357 Nonbonded interactions: 218651 Sorted by model distance: nonbonded pdb=" O SER L 77 " pdb=" NE2 GLN L 79 " model vdw 2.068 3.120 nonbonded pdb=" O THR I 28 " pdb=" ND2 ASN I 32 " model vdw 2.127 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.149 3.120 nonbonded pdb=" OD1 ASN A 657 " pdb=" O6 NAG A1301 " model vdw 2.160 3.040 nonbonded pdb=" O LEU A 752 " pdb=" NE2 GLN A 755 " model vdw 2.161 3.120 ... (remaining 218646 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 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 532 or (resid 533 and (name N o \ r name CA or name C or name O or name CB )) or resid 534 through 1146 or resid 1 \ 301 through 1311)) selection = (chain 'C' and (resid 27 through 327 or (resid 328 through 329 and (name N or na \ me CA or name C or name O or name CB )) or resid 330 through 532 or (resid 533 a \ nd (name N or name CA or name C or name O or name CB )) or resid 534 through 114 \ 6 or resid 1301 through 1311)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 114.520 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 69.810 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.150 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.017 0.209 29180 Z= 0.693 Angle : 1.366 16.767 39885 Z= 0.745 Chirality : 0.080 0.493 4670 Planarity : 0.007 0.087 5097 Dihedral : 13.676 111.854 10537 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.52 % Favored : 94.02 % Rotamer: Outliers : 0.89 % Allowed : 7.39 % Favored : 91.72 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -2.43 (0.12), residues: 3693 helix: 0.21 (0.20), residues: 647 sheet: -1.30 (0.14), residues: 979 loop : -2.46 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.005 TRP A 886 HIS 0.020 0.003 HIS B1058 PHE 0.062 0.006 PHE A 565 TYR 0.054 0.004 TYR B 756 ARG 0.022 0.002 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.14573 ( 1176) hydrogen bonds : angle 7.28604 ( 3255) SS BOND : bond 0.01190 ( 45) SS BOND : angle 5.47469 ( 90) covalent geometry : bond 0.01715 (29135) covalent geometry : angle 1.34303 (39795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8271 (m-80) cc_final: 0.8010 (m-80) REVERT: A 394 ASN cc_start: 0.6944 (t0) cc_final: 0.6541 (p0) REVERT: A 765 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7494 (mtm-85) REVERT: A 774 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8276 (mp10) REVERT: B 135 PHE cc_start: 0.7033 (m-80) cc_final: 0.6669 (m-80) REVERT: B 957 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 140 PHE cc_start: 0.5203 (p90) cc_final: 0.4578 (p90) REVERT: C 754 LEU cc_start: 0.8792 (mm) cc_final: 0.8581 (mt) REVERT: C 979 ASP cc_start: 0.8801 (t70) cc_final: 0.8341 (t0) REVERT: C 984 LEU cc_start: 0.7919 (tp) cc_final: 0.7669 (mt) REVERT: J 94 TRP cc_start: 0.7006 (t-100) cc_final: 0.6584 (t-100) REVERT: M 34 MET cc_start: 0.4437 (mmt) cc_final: 0.3765 (tpt) REVERT: M 82 MET cc_start: 0.1521 (ptp) cc_final: -0.0605 (ttt) outliers start: 26 outliers final: 8 residues processed: 327 average time/residue: 0.4053 time to fit residues: 210.2693 Evaluate side-chains 202 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 7.9990 chunk 279 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 343 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 801 ASN A 954 HIS A 955 ASN A 978 ASN A1074 ASN A1098 ASN B 354 ASN B 388 ASN B 394 ASN B 409 GLN B 506 GLN B 657 ASN B 856 ASN B 955 ASN B1010 GLN B1088 HIS C 99 ASN C 165 ASN C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 506 GLN C 540 ASN C 544 ASN C 657 ASN C 856 ASN C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1134 ASN H 90 GLN I 3 GLN J 79 GLN M 3 GLN M 81 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109586 restraints weight = 49938.788| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.76 r_work: 0.3035 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 29180 Z= 0.258 Angle : 0.772 12.648 39885 Z= 0.402 Chirality : 0.050 0.280 4670 Planarity : 0.006 0.115 5097 Dihedral : 7.193 59.756 4758 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 2.41 % Allowed : 11.79 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3693 helix: 1.22 (0.20), residues: 660 sheet: -0.61 (0.15), residues: 1000 loop : -2.03 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 64 HIS 0.006 0.001 HIS B1058 PHE 0.027 0.002 PHE A 970 TYR 0.022 0.002 TYR H 98 ARG 0.010 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.06396 ( 1176) hydrogen bonds : angle 6.07335 ( 3255) SS BOND : bond 0.00626 ( 45) SS BOND : angle 3.03226 ( 90) covalent geometry : bond 0.00636 (29135) covalent geometry : angle 0.75970 (39795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8861 (m-80) cc_final: 0.8446 (m-80) REVERT: A 269 TYR cc_start: 0.7518 (m-80) cc_final: 0.6999 (m-80) REVERT: A 530 SER cc_start: 0.7165 (p) cc_final: 0.6809 (t) REVERT: A 574 ASP cc_start: 0.8579 (t70) cc_final: 0.8175 (t0) REVERT: A 964 LYS cc_start: 0.8642 (tppp) cc_final: 0.8111 (tmtt) REVERT: B 432 CYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6654 (m) REVERT: B 762 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: C 106 PHE cc_start: 0.7726 (m-80) cc_final: 0.7476 (m-80) REVERT: C 140 PHE cc_start: 0.6026 (p90) cc_final: 0.4982 (p90) REVERT: C 314 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8208 (tm-30) REVERT: C 856 ASN cc_start: 0.9374 (OUTLIER) cc_final: 0.8583 (t0) REVERT: C 969 LYS cc_start: 0.9438 (mtpp) cc_final: 0.9221 (mmmm) REVERT: J 46 LEU cc_start: 0.5903 (tp) cc_final: 0.5659 (tp) REVERT: K 34 MET cc_start: 0.6440 (mmm) cc_final: 0.6085 (mmm) REVERT: M 34 MET cc_start: 0.4033 (mmt) cc_final: 0.3637 (tpt) REVERT: M 82 MET cc_start: 0.1047 (ptp) cc_final: -0.0377 (ttt) outliers start: 70 outliers final: 32 residues processed: 279 average time/residue: 0.3598 time to fit residues: 166.7342 Evaluate side-chains 218 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 166 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 113 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A1098 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.185131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114037 restraints weight = 50059.405| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 5.28 r_work: 0.3068 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29180 Z= 0.134 Angle : 0.636 10.143 39885 Z= 0.331 Chirality : 0.045 0.257 4670 Planarity : 0.005 0.062 5097 Dihedral : 6.339 59.930 4747 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 2.44 % Allowed : 13.51 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.90 (0.13), residues: 3693 helix: 1.89 (0.21), residues: 656 sheet: -0.21 (0.15), residues: 1003 loop : -1.72 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 35 HIS 0.006 0.001 HIS A 207 PHE 0.035 0.001 PHE A 970 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 1176) hydrogen bonds : angle 5.58265 ( 3255) SS BOND : bond 0.00628 ( 45) SS BOND : angle 2.36464 ( 90) covalent geometry : bond 0.00303 (29135) covalent geometry : angle 0.62657 (39795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 204 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8108 (mmt180) cc_final: 0.7758 (mmt180) REVERT: A 200 TYR cc_start: 0.8787 (m-80) cc_final: 0.8517 (m-80) REVERT: A 269 TYR cc_start: 0.7191 (m-80) cc_final: 0.6870 (m-80) REVERT: A 530 SER cc_start: 0.6862 (p) cc_final: 0.6508 (t) REVERT: A 574 ASP cc_start: 0.8420 (t70) cc_final: 0.8066 (t0) REVERT: A 754 LEU cc_start: 0.9411 (mm) cc_final: 0.8924 (pp) REVERT: A 964 LYS cc_start: 0.8532 (tppp) cc_final: 0.8055 (tmtt) REVERT: B 140 PHE cc_start: 0.6250 (p90) cc_final: 0.4538 (p90) REVERT: B 169 GLU cc_start: 0.8398 (pm20) cc_final: 0.8191 (tm-30) REVERT: B 200 TYR cc_start: 0.8779 (m-80) cc_final: 0.8462 (m-80) REVERT: B 432 CYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6792 (m) REVERT: B 957 GLN cc_start: 0.8244 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 30 ASN cc_start: 0.6901 (p0) cc_final: 0.6584 (m-40) REVERT: C 140 PHE cc_start: 0.5984 (p90) cc_final: 0.4909 (p90) REVERT: C 314 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 546 LEU cc_start: 0.8039 (tp) cc_final: 0.7790 (mt) REVERT: C 969 LYS cc_start: 0.9404 (mtpp) cc_final: 0.9140 (mmmm) REVERT: J 46 LEU cc_start: 0.6278 (tp) cc_final: 0.5470 (tp) REVERT: K 34 MET cc_start: 0.6508 (mmm) cc_final: 0.6159 (mmm) REVERT: M 34 MET cc_start: 0.4384 (mmt) cc_final: 0.3802 (tpp) REVERT: M 82 MET cc_start: 0.0987 (ptp) cc_final: -0.0377 (ttt) outliers start: 71 outliers final: 35 residues processed: 264 average time/residue: 0.3513 time to fit residues: 156.4265 Evaluate side-chains 212 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain K residue 101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 171 optimal weight: 0.0670 chunk 229 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 345 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 320 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN J 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.182326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110388 restraints weight = 49856.193| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.68 r_work: 0.3040 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29180 Z= 0.216 Angle : 0.681 18.923 39885 Z= 0.353 Chirality : 0.047 0.353 4670 Planarity : 0.005 0.062 5097 Dihedral : 6.286 59.360 4747 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 3.75 % Allowed : 14.13 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.85 (0.13), residues: 3693 helix: 1.84 (0.21), residues: 654 sheet: -0.11 (0.15), residues: 995 loop : -1.69 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 35 HIS 0.004 0.001 HIS B1058 PHE 0.020 0.002 PHE B 329 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 1176) hydrogen bonds : angle 5.60389 ( 3255) SS BOND : bond 0.00692 ( 45) SS BOND : angle 2.73601 ( 90) covalent geometry : bond 0.00532 (29135) covalent geometry : angle 0.66893 (39795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 187 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7814 (mmt180) REVERT: A 200 TYR cc_start: 0.8866 (m-80) cc_final: 0.8572 (m-80) REVERT: A 269 TYR cc_start: 0.7416 (m-80) cc_final: 0.7027 (m-80) REVERT: A 530 SER cc_start: 0.7141 (p) cc_final: 0.6849 (t) REVERT: A 574 ASP cc_start: 0.8569 (t70) cc_final: 0.8233 (t0) REVERT: A 754 LEU cc_start: 0.9418 (mm) cc_final: 0.8977 (pp) REVERT: A 950 ASP cc_start: 0.8225 (m-30) cc_final: 0.7991 (m-30) REVERT: B 88 ASP cc_start: 0.8319 (m-30) cc_final: 0.8094 (m-30) REVERT: B 169 GLU cc_start: 0.8439 (pm20) cc_final: 0.8125 (mp0) REVERT: B 200 TYR cc_start: 0.8801 (m-80) cc_final: 0.8496 (m-80) REVERT: B 432 CYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6611 (m) REVERT: B 957 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 140 PHE cc_start: 0.5926 (p90) cc_final: 0.4759 (p90) REVERT: C 314 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8264 (tm-30) REVERT: C 365 TYR cc_start: 0.7773 (m-80) cc_final: 0.7569 (m-80) REVERT: C 480 CYS cc_start: 0.4242 (OUTLIER) cc_final: 0.3980 (p) REVERT: C 546 LEU cc_start: 0.8283 (tp) cc_final: 0.7826 (pp) REVERT: C 969 LYS cc_start: 0.9378 (mtpp) cc_final: 0.9038 (mmmm) REVERT: C 994 ASP cc_start: 0.7717 (m-30) cc_final: 0.7472 (m-30) REVERT: H 104 THR cc_start: -0.1682 (OUTLIER) cc_final: -0.1961 (t) REVERT: J 29 VAL cc_start: 0.5119 (t) cc_final: 0.4918 (m) REVERT: J 102 GLN cc_start: 0.6920 (tp40) cc_final: 0.6446 (mp10) REVERT: K 34 MET cc_start: 0.6501 (mmm) cc_final: 0.6128 (mmm) REVERT: M 34 MET cc_start: 0.4536 (mmt) cc_final: 0.3942 (tpp) REVERT: M 82 MET cc_start: 0.1063 (ptp) cc_final: -0.0369 (ttt) outliers start: 109 outliers final: 70 residues processed: 276 average time/residue: 0.3701 time to fit residues: 175.3376 Evaluate side-chains 250 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 330 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 30.0000 chunk 185 optimal weight: 0.7980 chunk 346 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN B 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.185691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115391 restraints weight = 49654.159| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.92 r_work: 0.3092 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29180 Z= 0.126 Angle : 0.607 16.502 39885 Z= 0.315 Chirality : 0.045 0.365 4670 Planarity : 0.004 0.057 5097 Dihedral : 5.684 59.994 4747 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 3.58 % Allowed : 15.02 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.62 (0.14), residues: 3693 helix: 2.19 (0.21), residues: 649 sheet: 0.08 (0.15), residues: 987 loop : -1.60 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 35 HIS 0.004 0.001 HIS A1088 PHE 0.025 0.001 PHE B 168 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 1176) hydrogen bonds : angle 5.25994 ( 3255) SS BOND : bond 0.00577 ( 45) SS BOND : angle 2.69844 ( 90) covalent geometry : bond 0.00289 (29135) covalent geometry : angle 0.59383 (39795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 196 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8179 (mmt180) cc_final: 0.7757 (mmt180) REVERT: A 200 TYR cc_start: 0.8799 (m-80) cc_final: 0.8579 (m-80) REVERT: A 269 TYR cc_start: 0.7271 (m-80) cc_final: 0.6954 (m-80) REVERT: A 530 SER cc_start: 0.6950 (p) cc_final: 0.6674 (t) REVERT: A 553 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8764 (p) REVERT: A 574 ASP cc_start: 0.8503 (t70) cc_final: 0.8188 (t0) REVERT: A 754 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8984 (pp) REVERT: B 88 ASP cc_start: 0.8292 (m-30) cc_final: 0.8085 (m-30) REVERT: B 200 TYR cc_start: 0.8723 (m-80) cc_final: 0.8420 (m-80) REVERT: B 432 CYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6856 (m) REVERT: B 957 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 140 PHE cc_start: 0.6007 (p90) cc_final: 0.4808 (p90) REVERT: C 314 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 480 CYS cc_start: 0.4188 (OUTLIER) cc_final: 0.3920 (p) REVERT: C 546 LEU cc_start: 0.8260 (tp) cc_final: 0.7873 (pp) REVERT: C 969 LYS cc_start: 0.9382 (mtpp) cc_final: 0.9060 (mmmm) REVERT: H 4 MET cc_start: 0.4506 (ttt) cc_final: -0.0182 (pmm) REVERT: H 104 THR cc_start: -0.1611 (OUTLIER) cc_final: -0.1937 (t) REVERT: J 102 GLN cc_start: 0.6819 (tp40) cc_final: 0.6371 (mp10) REVERT: K 34 MET cc_start: 0.6515 (mmm) cc_final: 0.6204 (mmm) REVERT: M 34 MET cc_start: 0.4685 (mmt) cc_final: 0.4142 (tpp) REVERT: M 82 MET cc_start: 0.1180 (ptp) cc_final: -0.0111 (ttt) outliers start: 104 outliers final: 67 residues processed: 282 average time/residue: 0.4194 time to fit residues: 203.3151 Evaluate side-chains 243 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 265 optimal weight: 0.6980 chunk 309 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 136 optimal weight: 0.0370 chunk 351 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 314 optimal weight: 6.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 751 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.188477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118289 restraints weight = 48705.419| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.77 r_work: 0.3075 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29180 Z= 0.130 Angle : 0.595 11.450 39885 Z= 0.308 Chirality : 0.044 0.294 4670 Planarity : 0.004 0.054 5097 Dihedral : 5.472 59.950 4747 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 3.68 % Allowed : 15.74 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.51 (0.14), residues: 3693 helix: 2.30 (0.21), residues: 649 sheet: 0.17 (0.16), residues: 981 loop : -1.55 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 35 HIS 0.003 0.001 HIS A1088 PHE 0.025 0.001 PHE B 168 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 1176) hydrogen bonds : angle 5.18120 ( 3255) SS BOND : bond 0.00490 ( 45) SS BOND : angle 2.42093 ( 90) covalent geometry : bond 0.00302 (29135) covalent geometry : angle 0.58474 (39795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 177 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7764 (mmt180) REVERT: A 200 TYR cc_start: 0.8821 (m-80) cc_final: 0.8621 (m-80) REVERT: A 239 GLN cc_start: 0.8348 (mt0) cc_final: 0.8077 (mm110) REVERT: A 269 TYR cc_start: 0.7275 (m-80) cc_final: 0.6928 (m-80) REVERT: A 553 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 574 ASP cc_start: 0.8527 (t70) cc_final: 0.8203 (t0) REVERT: A 582 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7435 (mt) REVERT: A 754 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9023 (pp) REVERT: A 1017 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8654 (tt0) REVERT: B 88 ASP cc_start: 0.8239 (m-30) cc_final: 0.8012 (m-30) REVERT: B 170 TYR cc_start: 0.7541 (t80) cc_final: 0.7215 (t80) REVERT: B 200 TYR cc_start: 0.8703 (m-80) cc_final: 0.8388 (m-80) REVERT: B 432 CYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6600 (m) REVERT: B 957 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 140 PHE cc_start: 0.5806 (p90) cc_final: 0.4590 (p90) REVERT: C 314 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8237 (tm-30) REVERT: C 440 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8374 (mmmt) REVERT: C 480 CYS cc_start: 0.4213 (OUTLIER) cc_final: 0.3944 (p) REVERT: C 546 LEU cc_start: 0.8282 (tp) cc_final: 0.7868 (pp) REVERT: C 969 LYS cc_start: 0.9360 (mtpp) cc_final: 0.9011 (mmmm) REVERT: H 4 MET cc_start: 0.3527 (ttt) cc_final: -0.0343 (pmm) REVERT: H 104 THR cc_start: -0.1871 (OUTLIER) cc_final: -0.2160 (t) REVERT: K 34 MET cc_start: 0.6454 (mmm) cc_final: 0.6146 (mmm) REVERT: M 34 MET cc_start: 0.4712 (mmt) cc_final: 0.4122 (tpp) REVERT: M 82 MET cc_start: 0.1027 (ptp) cc_final: -0.0359 (ttt) outliers start: 107 outliers final: 78 residues processed: 262 average time/residue: 0.3492 time to fit residues: 154.8747 Evaluate side-chains 257 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 173 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 201 optimal weight: 0.3980 chunk 155 optimal weight: 4.9990 chunk 275 optimal weight: 0.0170 chunk 94 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 chunk 190 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 73 optimal weight: 0.0040 overall best weight: 0.5432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 422 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.184082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112163 restraints weight = 49877.626| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.50 r_work: 0.3092 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29180 Z= 0.112 Angle : 0.584 22.353 39885 Z= 0.302 Chirality : 0.044 0.330 4670 Planarity : 0.004 0.054 5097 Dihedral : 5.242 59.320 4747 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 3.23 % Allowed : 16.64 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.38 (0.14), residues: 3693 helix: 2.40 (0.21), residues: 651 sheet: 0.24 (0.16), residues: 976 loop : -1.46 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 35 HIS 0.003 0.001 HIS A1088 PHE 0.024 0.001 PHE B 168 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1176) hydrogen bonds : angle 5.05713 ( 3255) SS BOND : bond 0.00530 ( 45) SS BOND : angle 2.37716 ( 90) covalent geometry : bond 0.00252 (29135) covalent geometry : angle 0.57350 (39795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 186 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8175 (mmt180) cc_final: 0.7706 (mmt180) REVERT: A 269 TYR cc_start: 0.7205 (m-80) cc_final: 0.6885 (m-80) REVERT: A 390 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6674 (mt) REVERT: A 544 ASN cc_start: 0.8949 (m-40) cc_final: 0.8307 (t0) REVERT: A 553 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8738 (p) REVERT: A 574 ASP cc_start: 0.8412 (t70) cc_final: 0.8095 (t0) REVERT: A 582 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7497 (mt) REVERT: A 754 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9049 (pp) REVERT: B 88 ASP cc_start: 0.8282 (m-30) cc_final: 0.8071 (m-30) REVERT: B 200 TYR cc_start: 0.8639 (m-80) cc_final: 0.8334 (m-80) REVERT: B 432 CYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6733 (m) REVERT: B 957 GLN cc_start: 0.8282 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 30 ASN cc_start: 0.7214 (p0) cc_final: 0.6672 (m-40) REVERT: C 140 PHE cc_start: 0.5760 (p90) cc_final: 0.4539 (p90) REVERT: C 314 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8258 (tm-30) REVERT: C 440 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8367 (mmmt) REVERT: C 480 CYS cc_start: 0.4064 (OUTLIER) cc_final: 0.3785 (p) REVERT: C 546 LEU cc_start: 0.8245 (tp) cc_final: 0.7851 (pp) REVERT: C 969 LYS cc_start: 0.9358 (mtpp) cc_final: 0.9009 (mmmm) REVERT: H 104 THR cc_start: -0.1888 (OUTLIER) cc_final: -0.2187 (t) REVERT: K 34 MET cc_start: 0.6459 (mmm) cc_final: 0.6198 (mmm) REVERT: M 34 MET cc_start: 0.4694 (mmt) cc_final: 0.4103 (tpp) REVERT: M 82 MET cc_start: 0.1019 (ptp) cc_final: -0.0339 (ttt) outliers start: 94 outliers final: 70 residues processed: 258 average time/residue: 0.3518 time to fit residues: 155.7176 Evaluate side-chains 252 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 175 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 190 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 0.0030 chunk 212 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.180963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107818 restraints weight = 49244.133| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.02 r_work: 0.3007 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29180 Z= 0.154 Angle : 0.606 15.888 39885 Z= 0.315 Chirality : 0.045 0.328 4670 Planarity : 0.004 0.051 5097 Dihedral : 5.307 57.607 4747 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer: Outliers : 3.47 % Allowed : 16.88 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.41 (0.14), residues: 3693 helix: 2.35 (0.21), residues: 650 sheet: 0.30 (0.16), residues: 974 loop : -1.51 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 35 HIS 0.003 0.001 HIS A1088 PHE 0.019 0.001 PHE B 168 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 1176) hydrogen bonds : angle 5.12346 ( 3255) SS BOND : bond 0.00509 ( 45) SS BOND : angle 2.45734 ( 90) covalent geometry : bond 0.00369 (29135) covalent geometry : angle 0.59505 (39795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 180 time to evaluate : 3.107 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: A 190 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7594 (mmt180) REVERT: A 269 TYR cc_start: 0.7105 (m-80) cc_final: 0.6584 (m-80) REVERT: A 390 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6773 (mt) REVERT: A 544 ASN cc_start: 0.8956 (m-40) cc_final: 0.8324 (t0) REVERT: A 553 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 574 ASP cc_start: 0.8306 (t70) cc_final: 0.7967 (t0) REVERT: A 582 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7592 (mt) REVERT: A 754 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9080 (pp) REVERT: A 970 PHE cc_start: 0.8334 (m-80) cc_final: 0.8053 (m-10) REVERT: B 88 ASP cc_start: 0.8157 (m-30) cc_final: 0.7945 (m-30) REVERT: B 135 PHE cc_start: 0.7642 (m-80) cc_final: 0.6947 (m-80) REVERT: B 200 TYR cc_start: 0.8719 (m-80) cc_final: 0.8405 (m-80) REVERT: B 432 CYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6734 (m) REVERT: B 957 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 140 PHE cc_start: 0.5764 (p90) cc_final: 0.4483 (p90) REVERT: C 314 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 380 TYR cc_start: 0.4575 (OUTLIER) cc_final: 0.2312 (m-80) REVERT: C 440 LYS cc_start: 0.8851 (tmtt) cc_final: 0.8366 (mmmt) REVERT: C 480 CYS cc_start: 0.3927 (OUTLIER) cc_final: 0.3663 (p) REVERT: C 546 LEU cc_start: 0.8261 (tp) cc_final: 0.7770 (pp) REVERT: H 4 MET cc_start: 0.2582 (ttt) cc_final: -0.0766 (pmm) REVERT: H 104 THR cc_start: -0.1928 (OUTLIER) cc_final: -0.2218 (t) REVERT: M 34 MET cc_start: 0.4666 (mmt) cc_final: 0.4103 (tpp) REVERT: M 82 MET cc_start: 0.0961 (ptp) cc_final: -0.0381 (ttt) outliers start: 101 outliers final: 79 residues processed: 258 average time/residue: 0.3457 time to fit residues: 153.1977 Evaluate side-chains 257 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 170 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 317 optimal weight: 40.0000 chunk 321 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 285 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 327 optimal weight: 40.0000 chunk 99 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 232 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112693 restraints weight = 50280.177| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 5.58 r_work: 0.3094 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29180 Z= 0.123 Angle : 0.580 13.268 39885 Z= 0.301 Chirality : 0.044 0.307 4670 Planarity : 0.004 0.053 5097 Dihedral : 5.111 54.261 4747 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 3.47 % Allowed : 17.33 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.29 (0.14), residues: 3693 helix: 2.47 (0.21), residues: 652 sheet: 0.36 (0.16), residues: 980 loop : -1.43 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 35 HIS 0.003 0.001 HIS A1088 PHE 0.019 0.001 PHE B 168 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 1176) hydrogen bonds : angle 4.99707 ( 3255) SS BOND : bond 0.00488 ( 45) SS BOND : angle 2.27131 ( 90) covalent geometry : bond 0.00287 (29135) covalent geometry : angle 0.57102 (39795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 180 time to evaluate : 3.132 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: A 190 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7617 (mmt180) REVERT: A 269 TYR cc_start: 0.7067 (m-80) cc_final: 0.6663 (m-80) REVERT: A 390 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6829 (mt) REVERT: A 544 ASN cc_start: 0.8956 (m-40) cc_final: 0.8411 (t0) REVERT: A 553 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8775 (p) REVERT: A 574 ASP cc_start: 0.8302 (t70) cc_final: 0.8040 (t0) REVERT: A 582 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7692 (mt) REVERT: B 200 TYR cc_start: 0.8643 (m-80) cc_final: 0.8351 (m-80) REVERT: B 432 CYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6894 (m) REVERT: B 957 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 1141 LEU cc_start: 0.8851 (tp) cc_final: 0.8594 (tt) REVERT: C 129 LYS cc_start: 0.8256 (tttm) cc_final: 0.7962 (tmtt) REVERT: C 140 PHE cc_start: 0.5534 (p90) cc_final: 0.4290 (p90) REVERT: C 314 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8253 (tm-30) REVERT: C 440 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8331 (mmmt) REVERT: C 480 CYS cc_start: 0.3784 (OUTLIER) cc_final: 0.3518 (p) REVERT: C 546 LEU cc_start: 0.8279 (tp) cc_final: 0.7863 (pp) REVERT: H 4 MET cc_start: 0.2972 (ttt) cc_final: -0.0456 (pmm) REVERT: H 104 THR cc_start: -0.1784 (OUTLIER) cc_final: -0.2104 (t) REVERT: K 52 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4292 (t80) REVERT: M 34 MET cc_start: 0.4687 (mmt) cc_final: 0.4140 (tpp) REVERT: M 82 MET cc_start: 0.1023 (ptp) cc_final: -0.0217 (ttt) outliers start: 101 outliers final: 81 residues processed: 259 average time/residue: 0.3476 time to fit residues: 154.0787 Evaluate side-chains 266 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 178 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 200 optimal weight: 0.4980 chunk 268 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 290 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 255 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 405 ASN C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.183772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112998 restraints weight = 50404.751| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 5.47 r_work: 0.3107 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29180 Z= 0.113 Angle : 0.575 12.808 39885 Z= 0.298 Chirality : 0.044 0.298 4670 Planarity : 0.004 0.052 5097 Dihedral : 4.914 53.967 4747 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 3.06 % Allowed : 17.84 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.19 (0.14), residues: 3693 helix: 2.61 (0.21), residues: 646 sheet: 0.38 (0.16), residues: 987 loop : -1.36 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 35 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE B 168 TYR 0.021 0.001 TYR C 170 ARG 0.015 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1176) hydrogen bonds : angle 4.89915 ( 3255) SS BOND : bond 0.00462 ( 45) SS BOND : angle 2.22364 ( 90) covalent geometry : bond 0.00257 (29135) covalent geometry : angle 0.56604 (39795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 186 time to evaluate : 3.104 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: A 190 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7739 (mmt180) REVERT: A 269 TYR cc_start: 0.7234 (m-80) cc_final: 0.6788 (m-80) REVERT: A 390 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6805 (mt) REVERT: A 544 ASN cc_start: 0.9033 (m-40) cc_final: 0.8476 (t0) REVERT: A 553 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8794 (p) REVERT: A 574 ASP cc_start: 0.8619 (t70) cc_final: 0.8322 (t0) REVERT: B 200 TYR cc_start: 0.8647 (m-80) cc_final: 0.8342 (m-80) REVERT: B 957 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 129 LYS cc_start: 0.8240 (tttm) cc_final: 0.7923 (tmtt) REVERT: C 140 PHE cc_start: 0.5707 (p90) cc_final: 0.4389 (p90) REVERT: C 314 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8434 (tm-30) REVERT: C 380 TYR cc_start: 0.4498 (OUTLIER) cc_final: 0.2938 (m-80) REVERT: C 440 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8328 (mmmt) REVERT: C 480 CYS cc_start: 0.3861 (OUTLIER) cc_final: 0.3583 (p) REVERT: C 546 LEU cc_start: 0.8367 (tp) cc_final: 0.7954 (pp) REVERT: H 4 MET cc_start: 0.2800 (ttt) cc_final: -0.0554 (pmm) REVERT: H 104 THR cc_start: -0.1804 (OUTLIER) cc_final: -0.2112 (t) REVERT: K 52 PHE cc_start: 0.5111 (OUTLIER) cc_final: 0.4330 (t80) REVERT: M 34 MET cc_start: 0.4842 (mmt) cc_final: 0.4289 (tpp) REVERT: M 82 MET cc_start: 0.1012 (ptp) cc_final: -0.0261 (ttt) outliers start: 89 outliers final: 78 residues processed: 259 average time/residue: 0.3498 time to fit residues: 154.3247 Evaluate side-chains 262 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 178 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 337 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 160 optimal weight: 0.3980 chunk 241 optimal weight: 7.9990 chunk 336 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 330 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.184398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113667 restraints weight = 50275.372| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.92 r_work: 0.3123 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 29180 Z= 0.179 Angle : 0.774 59.200 39885 Z= 0.443 Chirality : 0.048 1.057 4670 Planarity : 0.005 0.161 5097 Dihedral : 4.917 53.977 4747 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 2.92 % Allowed : 17.88 % Favored : 79.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.20 (0.14), residues: 3693 helix: 2.57 (0.21), residues: 646 sheet: 0.39 (0.16), residues: 987 loop : -1.37 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 35 HIS 0.003 0.001 HIS A1088 PHE 0.017 0.001 PHE B 168 TYR 0.020 0.001 TYR B1067 ARG 0.014 0.000 ARG A 983 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1176) hydrogen bonds : angle 4.90622 ( 3255) SS BOND : bond 0.00459 ( 45) SS BOND : angle 2.19985 ( 90) covalent geometry : bond 0.00397 (29135) covalent geometry : angle 0.76802 (39795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21683.92 seconds wall clock time: 375 minutes 30.93 seconds (22530.93 seconds total)