Starting phenix.real_space_refine on Sun Jul 5 14:26:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvg_34126/07_2026/7yvg_34126.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 4, 'ARG:plan': 10, 'TYR:plan': 4} 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: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 10, 'TYR:plan': 4} 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: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 9, 'TYR:plan': 4} 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 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 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 chiralities: 13 Time building chain proxies: 6.41, per 1000 atoms: 0.23 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 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: 1.28 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: 9.46 Time building geometry restraints manager: 3.56 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: 15937 22.37 - 44.74: 799 44.74 - 67.11: 94 67.11 - 89.48: 49 89.48 - 111.85: 3 Dihedral angle restraints: 16882 sinusoidal: 6028 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 16879 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 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 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 131 \ 1)) } 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: 0.010 Normalize map: mean=0, sd=1: 11.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.780 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 13.411 111.854 9781 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.022 0.002 ARG M 86 TYR 0.054 0.004 TYR B 756 PHE 0.062 0.006 PHE A 565 TRP 0.072 0.005 TRP A 886 HIS 0.020 0.003 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.01715 / 0.69 (29135) covalent geometry : angle 1.34303 / 0.74 (39795) SS BOND : bond 0.01190 / 0.78 ( 45) SS BOND : angle 5.47469 / 3.73 ( 90) hydrogen bonds : bond 0.14573 / 9.78 ( 1176) hydrogen bonds : angle 7.28604 / 5.04 ( 3255) *********************** 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 : 1.142 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: 0.6540 (p0) REVERT: A 765 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7448 (ttp-170) REVERT: A 774 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8281 (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: 0.8580 (mt) REVERT: C 979 ASP cc_start: 0.8801 (t70) cc_final: 0.8337 (t0) REVERT: C 984 LEU cc_start: 0.7919 (tp) cc_final: 0.7668 (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: 0.3777 (tpt) REVERT: M 82 MET cc_start: 0.1521 (ptp) cc_final: -0.0602 (ttt) outliers start: 26 outliers final: 8 residues processed: 327 average time/residue: 0.1848 time to fit residues: 96.6417 Evaluate side-chains 199 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 343 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 506 GLN 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 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 C1113 GLN C1134 ASN H 90 GLN I 3 GLN J 79 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4391 r_free = 0.4391 target = 0.184096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112652 restraints weight = 50389.457| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.70 r_work: 0.3102 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29180 Z= 0.158 Angle : 0.701 12.195 39885 Z= 0.363 Chirality : 0.047 0.257 4670 Planarity : 0.005 0.107 5097 Dihedral : 5.021 42.432 4002 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 1.93 % Allowed : 11.52 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 3693 helix: 1.41 (0.21), residues: 660 sheet: -0.53 (0.15), residues: 992 loop : -1.92 (0.12), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 346 TYR 0.021 0.001 TYR H 98 PHE 0.025 0.002 PHE B 92 TRP 0.012 0.002 TRP B 436 HIS 0.008 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (29135) covalent geometry : angle 0.68976 / 0.36 (39795) SS BOND : bond 0.00542 / 0.36 ( 45) SS BOND : angle 2.68809 / 1.77 ( 90) hydrogen bonds : bond 0.05427 / 3.67 ( 1176) hydrogen bonds : angle 5.86908 / 4.04 ( 3255) *********************** 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 297 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8774 (m-80) cc_final: 0.8416 (m-80) REVERT: A 218 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7748 (mm-40) REVERT: A 269 TYR cc_start: 0.7397 (m-80) cc_final: 0.6945 (m-80) REVERT: A 394 ASN cc_start: 0.7351 (t0) cc_final: 0.7117 (p0) REVERT: A 530 SER cc_start: 0.6915 (p) cc_final: 0.6557 (t) REVERT: A 574 ASP cc_start: 0.8531 (t70) cc_final: 0.8111 (t0) REVERT: A 754 LEU cc_start: 0.9427 (mm) cc_final: 0.8828 (pp) REVERT: A 964 LYS cc_start: 0.8585 (tppp) cc_final: 0.8033 (tmtt) REVERT: B 88 ASP cc_start: 0.8354 (m-30) cc_final: 0.8072 (m-30) REVERT: B 432 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6575 (m) REVERT: B 762 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: B 957 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 30 ASN cc_start: 0.7308 (p0) cc_final: 0.6856 (m-40) REVERT: C 140 PHE cc_start: 0.5907 (p90) cc_final: 0.4873 (p90) REVERT: C 170 TYR cc_start: 0.7817 (t80) cc_final: 0.7473 (t80) REVERT: C 969 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9092 (mmmm) REVERT: J 46 LEU cc_start: 0.5954 (tp) cc_final: 0.5689 (tp) REVERT: K 34 MET cc_start: 0.6531 (mmm) cc_final: 0.6160 (mmm) REVERT: M 34 MET cc_start: 0.4141 (mmt) cc_final: 0.3706 (tpt) REVERT: M 82 MET cc_start: 0.0924 (ptp) cc_final: -0.0404 (ttt) outliers start: 56 outliers final: 21 residues processed: 285 average time/residue: 0.1652 time to fit residues: 78.7754 Evaluate side-chains 204 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 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 887 THR 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 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 436 TRP 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 949 GLN 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 242 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 6 optimal weight: 0.0170 chunk 323 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 368 optimal weight: 30.0000 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111290 restraints weight = 49886.773| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.30 r_work: 0.3045 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29180 Z= 0.217 Angle : 0.695 11.292 39885 Z= 0.361 Chirality : 0.047 0.262 4670 Planarity : 0.005 0.055 5097 Dihedral : 4.936 48.435 3991 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 2.92 % Allowed : 13.37 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 3693 helix: 1.68 (0.21), residues: 660 sheet: -0.29 (0.15), residues: 1010 loop : -1.73 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.022 0.002 TYR B1067 PHE 0.032 0.002 PHE A 970 TRP 0.018 0.002 TRP J 35 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (29135) covalent geometry : angle 0.68277 / 0.36 (39795) SS BOND : bond 0.00792 / 0.49 ( 45) SS BOND : angle 2.83843 / 1.88 ( 90) hydrogen bonds : bond 0.05810 / 3.97 ( 1176) hydrogen bonds : angle 5.75372 / 3.97 ( 3255) *********************** 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 279 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 194 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8857 (m-80) cc_final: 0.8539 (m-80) REVERT: A 269 TYR cc_start: 0.7421 (m-80) cc_final: 0.7032 (m-80) REVERT: A 530 SER cc_start: 0.7128 (p) cc_final: 0.6820 (t) REVERT: A 574 ASP cc_start: 0.8540 (t70) cc_final: 0.8155 (t0) REVERT: A 754 LEU cc_start: 0.9449 (mm) cc_final: 0.8885 (pp) REVERT: A 964 LYS cc_start: 0.8622 (tppp) cc_final: 0.8109 (tmtt) REVERT: A 970 PHE cc_start: 0.8612 (m-80) cc_final: 0.8356 (m-10) REVERT: B 140 PHE cc_start: 0.6353 (p90) cc_final: 0.4610 (p90) REVERT: B 432 CYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6649 (m) REVERT: B 762 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: B 957 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 129 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8065 (tttm) REVERT: C 140 PHE cc_start: 0.5980 (p90) cc_final: 0.4858 (p90) REVERT: C 170 TYR cc_start: 0.7989 (t80) cc_final: 0.7604 (t80) REVERT: C 969 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9107 (mmmm) REVERT: C 994 ASP cc_start: 0.7784 (m-30) cc_final: 0.7543 (m-30) REVERT: J 46 LEU cc_start: 0.6282 (tp) cc_final: 0.5541 (tp) REVERT: J 102 GLN cc_start: 0.6860 (tp40) cc_final: 0.6386 (mp10) REVERT: K 34 MET cc_start: 0.6516 (mmm) cc_final: 0.6132 (mmm) REVERT: M 34 MET cc_start: 0.4475 (mmt) cc_final: 0.3849 (tpp) REVERT: M 82 MET cc_start: 0.1117 (ptp) cc_final: -0.0327 (ttt) outliers start: 85 outliers final: 48 residues processed: 263 average time/residue: 0.1671 time to fit residues: 74.2285 Evaluate side-chains 233 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 308 VAL Chi-restraints excluded: chain A residue 391 CYS 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 588 THR Chi-restraints excluded: chain A residue 590 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 961 THR 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 432 CYS Chi-restraints excluded: chain B residue 560 LEU 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 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 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 436 TRP 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 705 VAL Chi-restraints excluded: chain C residue 740 MET 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 C residue 1141 LEU 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 54 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 296 optimal weight: 0.8980 chunk 354 optimal weight: 30.0000 chunk 274 optimal weight: 0.8980 chunk 357 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 360 optimal weight: 30.0000 chunk 61 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 957 GLN ** 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 = 0.4370 r_free = 0.4370 target = 0.182138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109294 restraints weight = 50083.520| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.70 r_work: 0.3067 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29180 Z= 0.158 Angle : 0.640 15.494 39885 Z= 0.331 Chirality : 0.046 0.350 4670 Planarity : 0.005 0.056 5097 Dihedral : 4.781 46.217 3991 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 3.44 % Allowed : 14.51 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 3693 helix: 1.95 (0.21), residues: 654 sheet: -0.11 (0.15), residues: 1009 loop : -1.60 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.022 0.001 TYR A1138 PHE 0.022 0.001 PHE A 970 TRP 0.018 0.001 TRP J 35 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (29135) covalent geometry : angle 0.62682 / 0.33 (39795) SS BOND : bond 0.00596 / 0.37 ( 45) SS BOND : angle 2.74849 / 1.76 ( 90) hydrogen bonds : bond 0.05105 / 3.47 ( 1176) hydrogen bonds : angle 5.51730 / 3.82 ( 3255) *********************** 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 286 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 186 time to evaluate : 0.947 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: 0.8832 (m-80) cc_final: 0.8549 (m-80) REVERT: A 269 TYR cc_start: 0.7384 (m-80) cc_final: 0.7006 (m-80) REVERT: A 530 SER cc_start: 0.7043 (p) cc_final: 0.6716 (t) REVERT: A 574 ASP cc_start: 0.8541 (t70) cc_final: 0.8199 (t0) REVERT: A 754 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8919 (pp) REVERT: A 964 LYS cc_start: 0.8551 (tppp) cc_final: 0.8032 (tmtt) REVERT: B 88 ASP cc_start: 0.8318 (m-30) cc_final: 0.8094 (m-30) REVERT: B 200 TYR cc_start: 0.8822 (m-80) cc_final: 0.8570 (m-80) REVERT: B 432 CYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6668 (m) REVERT: B 957 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 129 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7921 (tmtt) REVERT: C 140 PHE cc_start: 0.6014 (p90) cc_final: 0.4881 (p90) REVERT: C 170 TYR cc_start: 0.8059 (t80) cc_final: 0.7653 (t80) REVERT: C 365 TYR cc_start: 0.7732 (m-80) cc_final: 0.7526 (m-80) REVERT: C 480 CYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3934 (p) REVERT: C 969 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9092 (mmmm) REVERT: C 979 ASP cc_start: 0.8793 (t0) cc_final: 0.8554 (t0) REVERT: C 994 ASP cc_start: 0.7728 (m-30) cc_final: 0.7479 (m-30) REVERT: H 104 THR cc_start: -0.1720 (OUTLIER) cc_final: -0.1999 (t) REVERT: K 34 MET cc_start: 0.6482 (mmm) cc_final: 0.6103 (mmm) REVERT: M 34 MET cc_start: 0.4518 (mmt) cc_final: 0.3935 (tpp) REVERT: M 82 MET cc_start: 0.1111 (ptp) cc_final: -0.0304 (ttt) outliers start: 100 outliers final: 64 residues processed: 269 average time/residue: 0.1498 time to fit residues: 68.7813 Evaluate side-chains 244 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 175 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 231 ILE 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 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 590 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 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 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 649 CYS Chi-restraints excluded: chain B residue 776 LYS 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 B residue 1096 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS 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 743 CYS 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 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 I residue 27 ILE Chi-restraints excluded: chain I residue 37 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 35 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 368 optimal weight: 50.0000 chunk 207 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 275 optimal weight: 0.0170 chunk 228 optimal weight: 2.9990 chunk 292 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 326 optimal weight: 40.0000 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 957 GLN H 90 GLN ** J 6 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 = 0.4377 r_free = 0.4377 target = 0.184163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113630 restraints weight = 49694.052| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.88 r_work: 0.3073 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29180 Z= 0.146 Angle : 0.621 17.017 39885 Z= 0.322 Chirality : 0.045 0.384 4670 Planarity : 0.004 0.055 5097 Dihedral : 4.664 44.284 3991 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.71 % Allowed : 14.95 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3693 helix: 2.14 (0.21), residues: 649 sheet: 0.04 (0.15), residues: 984 loop : -1.56 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.021 0.001 TYR J 49 PHE 0.020 0.001 PHE A 970 TRP 0.014 0.001 TRP J 35 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (29135) covalent geometry : angle 0.60695 / 0.32 (39795) SS BOND : bond 0.00579 / 0.36 ( 45) SS BOND : angle 2.87724 / 1.81 ( 90) hydrogen bonds : bond 0.04822 / 3.28 ( 1176) hydrogen bonds : angle 5.33784 / 3.71 ( 3255) *********************** 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 294 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 186 time to evaluate : 1.096 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: 0.8810 (m-80) cc_final: 0.8550 (m-80) REVERT: A 269 TYR cc_start: 0.7319 (m-80) cc_final: 0.6973 (m-80) REVERT: A 530 SER cc_start: 0.7016 (p) cc_final: 0.6733 (t) REVERT: A 574 ASP cc_start: 0.8548 (t70) cc_final: 0.8215 (t0) REVERT: A 754 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8945 (pp) REVERT: A 1017 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8642 (tt0) REVERT: B 88 ASP cc_start: 0.8296 (m-30) cc_final: 0.8016 (m-30) REVERT: B 200 TYR cc_start: 0.8735 (m-80) cc_final: 0.8490 (m-80) REVERT: B 432 CYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6664 (m) REVERT: B 957 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 106 PHE cc_start: 0.7658 (m-80) cc_final: 0.7367 (m-80) REVERT: C 129 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7966 (tmtt) REVERT: C 140 PHE cc_start: 0.5897 (p90) cc_final: 0.4742 (p90) REVERT: C 480 CYS cc_start: 0.4227 (OUTLIER) cc_final: 0.3950 (p) REVERT: C 546 LEU cc_start: 0.8107 (tt) cc_final: 0.7646 (pp) REVERT: C 969 LYS cc_start: 0.9398 (mtpp) cc_final: 0.9072 (mmmm) REVERT: C 994 ASP cc_start: 0.7693 (m-30) cc_final: 0.7444 (m-30) REVERT: H 104 THR cc_start: -0.1853 (OUTLIER) cc_final: -0.2148 (t) REVERT: K 34 MET cc_start: 0.6401 (mmm) cc_final: 0.6109 (mmm) REVERT: M 34 MET cc_start: 0.4541 (mmt) cc_final: 0.3964 (tpp) REVERT: M 82 MET cc_start: 0.1048 (ptp) cc_final: -0.0325 (ttt) outliers start: 108 outliers final: 72 residues processed: 277 average time/residue: 0.1557 time to fit residues: 73.2717 Evaluate side-chains 247 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 302 THR Chi-restraints excluded: chain A residue 308 VAL 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 588 THR Chi-restraints excluded: chain A residue 590 CYS 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 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 1118 ASP Chi-restraints excluded: chain B residue 287 ASP 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 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS 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 436 TRP Chi-restraints excluded: chain C residue 480 CYS 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 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 878 LEU Chi-restraints excluded: chain C residue 886 TRP 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 84 SER Chi-restraints excluded: chain K residue 52 PHE 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 346 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 205 optimal weight: 0.0670 chunk 224 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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** ** 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 = 0.4360 r_free = 0.4360 target = 0.188102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116343 restraints weight = 50007.474| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 4.69 r_work: 0.3025 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29180 Z= 0.206 Angle : 0.655 11.236 39885 Z= 0.339 Chirality : 0.046 0.214 4670 Planarity : 0.005 0.057 5097 Dihedral : 4.811 42.460 3991 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 4.13 % Allowed : 15.40 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3693 helix: 2.03 (0.21), residues: 649 sheet: 0.04 (0.15), residues: 994 loop : -1.61 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.022 0.001 TYR B1067 PHE 0.025 0.002 PHE B 168 TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (29135) covalent geometry : angle 0.64357 / 0.33 (39795) SS BOND : bond 0.00695 / 0.48 ( 45) SS BOND : angle 2.62204 / 1.68 ( 90) hydrogen bonds : bond 0.05517 / 3.78 ( 1176) hydrogen bonds : angle 5.43726 / 3.77 ( 3255) *********************** 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 302 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 182 time to evaluate : 0.886 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: 0.8849 (m-80) cc_final: 0.8619 (m-80) REVERT: A 269 TYR cc_start: 0.7420 (m-80) cc_final: 0.6913 (m-80) REVERT: A 544 ASN cc_start: 0.8981 (m-40) cc_final: 0.8333 (t0) REVERT: A 553 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8772 (p) REVERT: A 574 ASP cc_start: 0.8533 (t70) cc_final: 0.8216 (t0) REVERT: A 754 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8992 (pp) REVERT: B 432 CYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6747 (m) REVERT: B 957 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 129 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7919 (tmtt) REVERT: C 140 PHE cc_start: 0.5911 (p90) cc_final: 0.4669 (p90) REVERT: C 170 TYR cc_start: 0.8163 (t80) cc_final: 0.7665 (t80) REVERT: C 480 CYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3899 (p) REVERT: C 546 LEU cc_start: 0.8249 (tt) cc_final: 0.7797 (pp) REVERT: H 4 MET cc_start: 0.2876 (OUTLIER) cc_final: -0.0376 (pmm) REVERT: H 104 THR cc_start: -0.2025 (OUTLIER) cc_final: -0.2321 (t) REVERT: J 4 MET cc_start: 0.5997 (mtt) cc_final: 0.5761 (mtp) REVERT: K 34 MET cc_start: 0.6353 (mmm) cc_final: 0.6109 (mmm) REVERT: M 34 MET cc_start: 0.4710 (mmt) cc_final: 0.4146 (tpp) REVERT: M 82 MET cc_start: 0.0992 (ptp) cc_final: -0.0368 (ttt) outliers start: 120 outliers final: 82 residues processed: 276 average time/residue: 0.1436 time to fit residues: 68.5461 Evaluate side-chains 262 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 173 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 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 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 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ASP 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 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 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 129 LYS 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 510 VAL 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 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL 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 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 4 MET 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 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 52 PHE 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 362 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 176 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 304 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 321 optimal weight: 20.0000 chunk 118 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN A1098 ASN B 239 GLN B 751 ASN C 207 HIS C 422 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.183634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112056 restraints weight = 49054.741| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.73 r_work: 0.3074 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29180 Z= 0.114 Angle : 0.591 22.470 39885 Z= 0.306 Chirality : 0.044 0.376 4670 Planarity : 0.004 0.056 5097 Dihedral : 4.471 40.894 3991 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 3.03 % Allowed : 17.05 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3693 helix: 2.36 (0.21), residues: 651 sheet: 0.21 (0.16), residues: 981 loop : -1.49 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE B 92 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (29135) covalent geometry : angle 0.58057 / 0.30 (39795) SS BOND : bond 0.00647 / 0.37 ( 45) SS BOND : angle 2.39275 / 1.48 ( 90) hydrogen bonds : bond 0.04192 / 2.82 ( 1176) hydrogen bonds : angle 5.08575 / 3.54 ( 3255) *********************** 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 269 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 181 time to evaluate : 1.105 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 239 GLN cc_start: 0.8364 (mt0) cc_final: 0.8077 (mm110) REVERT: A 269 TYR cc_start: 0.7248 (m-80) cc_final: 0.6862 (m-80) REVERT: A 544 ASN cc_start: 0.9008 (m-40) cc_final: 0.8380 (t0) REVERT: A 553 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8685 (p) REVERT: A 574 ASP cc_start: 0.8446 (t70) cc_final: 0.8128 (t0) REVERT: A 582 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7387 (mt) REVERT: A 754 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8980 (pp) REVERT: A 1017 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8585 (tt0) REVERT: B 169 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: B 200 TYR cc_start: 0.8690 (m-80) cc_final: 0.8432 (m-80) REVERT: B 432 CYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6866 (m) REVERT: B 957 GLN cc_start: 0.8269 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 129 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7882 (tmtt) REVERT: C 140 PHE cc_start: 0.5779 (p90) cc_final: 0.4557 (p90) REVERT: C 440 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8364 (mmmt) REVERT: C 480 CYS cc_start: 0.4007 (OUTLIER) cc_final: 0.3725 (p) REVERT: C 546 LEU cc_start: 0.8142 (tt) cc_final: 0.7673 (pp) REVERT: H 4 MET cc_start: 0.2745 (OUTLIER) cc_final: -0.1515 (pmm) REVERT: H 104 THR cc_start: -0.2024 (OUTLIER) cc_final: -0.2315 (t) REVERT: J 4 MET cc_start: 0.5953 (mtt) cc_final: 0.5749 (mtp) REVERT: K 18 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.4963 (mp) REVERT: K 34 MET cc_start: 0.6535 (mmm) cc_final: 0.6324 (mmm) REVERT: M 34 MET cc_start: 0.4734 (mmt) cc_final: 0.4247 (tpp) REVERT: M 82 MET cc_start: 0.1052 (ptp) cc_final: -0.0271 (ttt) outliers start: 88 outliers final: 60 residues processed: 251 average time/residue: 0.1473 time to fit residues: 63.7153 Evaluate side-chains 242 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL 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 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 855 PHE 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 1098 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 312 ILE 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 472 ILE Chi-restraints excluded: chain B residue 524 VAL 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 878 LEU 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 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS 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 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 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain H residue 4 MET 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 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 18 LEU 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 353 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 30.0000 chunk 276 optimal weight: 0.9990 chunk 319 optimal weight: 50.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4327 r_free = 0.4327 target = 0.179216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107448 restraints weight = 50036.633| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.92 r_work: 0.2998 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29180 Z= 0.228 Angle : 0.665 17.848 39885 Z= 0.345 Chirality : 0.047 0.320 4670 Planarity : 0.004 0.058 5097 Dihedral : 4.724 40.546 3991 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 3.54 % Allowed : 17.19 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3693 helix: 2.09 (0.21), residues: 650 sheet: 0.17 (0.16), residues: 992 loop : -1.58 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.022 0.001 TYR B1067 PHE 0.020 0.002 PHE C 643 TRP 0.010 0.001 TRP A 64 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (29135) covalent geometry : angle 0.65380 / 0.34 (39795) SS BOND : bond 0.00580 / 0.38 ( 45) SS BOND : angle 2.69542 / 1.70 ( 90) hydrogen bonds : bond 0.05569 / 3.82 ( 1176) hydrogen bonds : angle 5.34260 / 3.72 ( 3255) *********************** 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 278 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 175 time to evaluate : 0.735 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: A 269 TYR cc_start: 0.7392 (m-80) cc_final: 0.6774 (m-80) REVERT: A 544 ASN cc_start: 0.9045 (m-40) cc_final: 0.8589 (t0) REVERT: A 553 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8704 (p) REVERT: A 574 ASP cc_start: 0.8467 (t70) cc_final: 0.8142 (t0) REVERT: A 582 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 754 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9026 (pp) REVERT: B 200 TYR cc_start: 0.8779 (m-80) cc_final: 0.8510 (m-80) REVERT: B 432 CYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6804 (m) REVERT: B 957 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8028 (tm-30) REVERT: C 129 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7855 (tmtt) REVERT: C 140 PHE cc_start: 0.5908 (p90) cc_final: 0.4596 (p90) REVERT: C 380 TYR cc_start: 0.4867 (OUTLIER) cc_final: 0.2787 (m-80) REVERT: C 480 CYS cc_start: 0.4102 (OUTLIER) cc_final: 0.3851 (p) REVERT: C 546 LEU cc_start: 0.8294 (tt) cc_final: 0.7802 (pp) REVERT: H 4 MET cc_start: 0.2802 (OUTLIER) cc_final: -0.1598 (pmm) REVERT: H 104 THR cc_start: -0.2032 (OUTLIER) cc_final: -0.2328 (t) REVERT: J 46 LEU cc_start: 0.6417 (tp) cc_final: 0.6179 (tp) REVERT: K 34 MET cc_start: 0.6588 (mmm) cc_final: 0.6361 (mmm) REVERT: K 52 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4256 (t80) REVERT: K 94 TYR cc_start: 0.5118 (m-80) cc_final: 0.4851 (m-10) REVERT: L 4 MET cc_start: 0.1095 (mmm) cc_final: 0.0602 (mmm) REVERT: M 34 MET cc_start: 0.4713 (mmt) cc_final: 0.4192 (tpp) REVERT: M 82 MET cc_start: 0.1063 (ptp) cc_final: -0.0297 (ttt) outliers start: 103 outliers final: 84 residues processed: 258 average time/residue: 0.1484 time to fit residues: 66.4772 Evaluate side-chains 263 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 169 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS 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 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 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL 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 327 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 524 VAL 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 776 LYS 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 1060 VAL 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 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 436 TRP 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 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 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 4 MET 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 I residue 84 SER Chi-restraints excluded: chain J residue 47 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 265 optimal weight: 0.9980 chunk 351 optimal weight: 40.0000 chunk 82 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 338 optimal weight: 0.0770 chunk 329 optimal weight: 50.0000 chunk 120 optimal weight: 30.0000 chunk 182 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 336 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1098 ASN ** B 81 ASN ** 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 = 0.4385 r_free = 0.4385 target = 0.183741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111097 restraints weight = 49965.570| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.50 r_work: 0.3072 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29180 Z= 0.120 Angle : 0.597 17.578 39885 Z= 0.310 Chirality : 0.044 0.367 4670 Planarity : 0.004 0.056 5097 Dihedral : 4.486 39.564 3991 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 3.20 % Allowed : 17.81 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3693 helix: 2.33 (0.21), residues: 652 sheet: 0.23 (0.16), residues: 1008 loop : -1.49 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.027 0.001 TYR C 170 PHE 0.014 0.001 PHE C 643 TRP 0.016 0.001 TRP L 94 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (29135) covalent geometry : angle 0.58603 / 0.31 (39795) SS BOND : bond 0.00488 / 0.30 ( 45) SS BOND : angle 2.48544 / 1.51 ( 90) hydrogen bonds : bond 0.04414 / 2.98 ( 1176) hydrogen bonds : angle 5.07784 / 3.54 ( 3255) *********************** 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 262 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 169 time to evaluate : 0.831 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: A 239 GLN cc_start: 0.7979 (mt0) cc_final: 0.7420 (mm-40) REVERT: A 269 TYR cc_start: 0.7140 (m-80) cc_final: 0.6704 (m-80) REVERT: A 544 ASN cc_start: 0.8975 (m-40) cc_final: 0.8413 (t0) REVERT: A 553 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8763 (p) REVERT: A 574 ASP cc_start: 0.8327 (t70) cc_final: 0.8028 (t0) REVERT: A 582 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7453 (mt) REVERT: A 754 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9078 (pp) REVERT: B 200 TYR cc_start: 0.8731 (m-80) cc_final: 0.8478 (m-80) REVERT: B 432 CYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6966 (m) REVERT: B 957 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 1141 LEU cc_start: 0.8858 (tp) cc_final: 0.8603 (tt) REVERT: C 129 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7896 (tmtt) REVERT: C 140 PHE cc_start: 0.5679 (p90) cc_final: 0.4414 (p90) REVERT: C 380 TYR cc_start: 0.4649 (OUTLIER) cc_final: 0.2940 (m-80) REVERT: C 440 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8326 (mmmt) REVERT: C 480 CYS cc_start: 0.3964 (OUTLIER) cc_final: 0.3702 (p) REVERT: C 546 LEU cc_start: 0.8190 (tt) cc_final: 0.7783 (pp) REVERT: C 751 ASN cc_start: 0.9095 (m110) cc_final: 0.8738 (p0) REVERT: H 4 MET cc_start: 0.3150 (OUTLIER) cc_final: -0.1229 (pmm) REVERT: H 104 THR cc_start: -0.1825 (OUTLIER) cc_final: -0.2127 (t) REVERT: J 46 LEU cc_start: 0.6228 (tp) cc_final: 0.5980 (tp) REVERT: K 52 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4269 (t80) REVERT: K 94 TYR cc_start: 0.5167 (m-80) cc_final: 0.4962 (m-10) REVERT: L 4 MET cc_start: 0.1154 (mmm) cc_final: 0.0647 (mmm) REVERT: M 34 MET cc_start: 0.4845 (mmt) cc_final: 0.4281 (tpp) REVERT: M 82 MET cc_start: 0.1134 (ptp) cc_final: -0.0126 (ttt) outliers start: 93 outliers final: 79 residues processed: 243 average time/residue: 0.1411 time to fit residues: 59.1159 Evaluate side-chains 257 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 168 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU 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 649 CYS 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 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR 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 327 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 524 VAL Chi-restraints excluded: chain B residue 551 VAL 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 878 LEU 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 129 LYS 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 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 436 TRP 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 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 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 4 MET 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 I residue 84 SER Chi-restraints excluded: chain J residue 47 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 27 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 323 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN ** C 207 HIS ** 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 = 0.4321 r_free = 0.4321 target = 0.179478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107243 restraints weight = 49434.130| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.77 r_work: 0.2971 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29180 Z= 0.247 Angle : 0.688 15.412 39885 Z= 0.357 Chirality : 0.048 0.336 4670 Planarity : 0.005 0.059 5097 Dihedral : 4.813 41.396 3991 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 3.30 % Allowed : 17.94 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3693 helix: 2.01 (0.21), residues: 651 sheet: 0.11 (0.16), residues: 1000 loop : -1.61 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 983 TYR 0.023 0.002 TYR B1067 PHE 0.019 0.002 PHE C 643 TRP 0.028 0.002 TRP L 94 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (29135) covalent geometry : angle 0.67564 / 0.35 (39795) SS BOND : bond 0.00572 / 0.37 ( 45) SS BOND : angle 2.84408 / 1.77 ( 90) hydrogen bonds : bond 0.05901 / 4.05 ( 1176) hydrogen bonds : angle 5.38259 / 3.75 ( 3255) ********************** 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 271 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 175 time to evaluate : 0.866 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 239 GLN cc_start: 0.8265 (mt0) cc_final: 0.7680 (mm-40) REVERT: A 269 TYR cc_start: 0.7450 (m-80) cc_final: 0.6885 (m-80) REVERT: A 544 ASN cc_start: 0.9079 (m-40) cc_final: 0.8513 (t0) REVERT: A 553 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8703 (p) REVERT: A 574 ASP cc_start: 0.8490 (t70) cc_final: 0.8182 (t0) REVERT: A 582 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7629 (mt) REVERT: A 754 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9081 (pp) REVERT: B 200 TYR cc_start: 0.8828 (m-80) cc_final: 0.8561 (m-80) REVERT: B 432 CYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7039 (m) REVERT: B 957 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 1141 LEU cc_start: 0.8866 (tp) cc_final: 0.8614 (tt) REVERT: C 129 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7913 (ttpp) REVERT: C 140 PHE cc_start: 0.5629 (p90) cc_final: 0.4246 (p90) REVERT: C 170 TYR cc_start: 0.8188 (t80) cc_final: 0.7854 (t80) REVERT: C 380 TYR cc_start: 0.4947 (OUTLIER) cc_final: 0.3384 (m-80) REVERT: C 480 CYS cc_start: 0.3917 (OUTLIER) cc_final: 0.3661 (p) REVERT: C 546 LEU cc_start: 0.8340 (tt) cc_final: 0.7840 (pp) REVERT: H 4 MET cc_start: 0.3145 (OUTLIER) cc_final: -0.1283 (pmm) REVERT: H 104 THR cc_start: -0.1909 (OUTLIER) cc_final: -0.2193 (t) REVERT: K 52 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4051 (t80) REVERT: K 94 TYR cc_start: 0.5138 (m-80) cc_final: 0.4869 (m-10) REVERT: L 4 MET cc_start: 0.1316 (mmm) cc_final: 0.0806 (mmm) REVERT: M 34 MET cc_start: 0.4738 (mmt) cc_final: 0.4404 (tpp) outliers start: 96 outliers final: 83 residues processed: 253 average time/residue: 0.1539 time to fit residues: 67.1659 Evaluate side-chains 268 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 175 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 649 CYS 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 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL 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 327 VAL 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 524 VAL 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 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU 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 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 436 TRP 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 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 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 4 MET 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 I residue 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 27 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 154 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 317 optimal weight: 40.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1098 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.181179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109295 restraints weight = 49598.047| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.32 r_work: 0.3036 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29180 Z= 0.157 Angle : 0.624 14.414 39885 Z= 0.324 Chirality : 0.045 0.317 4670 Planarity : 0.004 0.075 5097 Dihedral : 4.637 41.171 3991 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 3.47 % Allowed : 18.01 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3693 helix: 2.23 (0.21), residues: 651 sheet: 0.14 (0.16), residues: 1012 loop : -1.55 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE C 643 TRP 0.025 0.001 TRP L 94 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (29135) covalent geometry : angle 0.61300 / 0.32 (39795) SS BOND : bond 0.00501 / 0.32 ( 45) SS BOND : angle 2.57629 / 1.59 ( 90) hydrogen bonds : bond 0.04950 / 3.36 ( 1176) hydrogen bonds : angle 5.19894 / 3.62 ( 3255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9717.20 seconds wall clock time: 166 minutes 7.89 seconds (9967.89 seconds total)