Starting phenix.real_space_refine on Thu Mar 5 08:59:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lss_23507/03_2026/7lss_23507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lss_23507/03_2026/7lss_23507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lss_23507/03_2026/7lss_23507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lss_23507/03_2026/7lss_23507.map" model { file = "/net/cci-nas-00/data/ceres_data/7lss_23507/03_2026/7lss_23507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lss_23507/03_2026/7lss_23507.cif" } resolution = 3.72 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= 0.001 sd= 0.011 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 91 5.16 5 C 13153 2.51 5 N 3434 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20582 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5677 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 11 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ASN:plan1': 9, 'ASP:plan': 15, 'GLU:plan': 11, 'ARG:plan': 6, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 170 Chain: "B" Number of atoms: 7101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7101 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'ASN:plan1': 18, 'ASP:plan': 34, 'GLN:plan1': 10, 'HIS:plan': 2, 'GLU:plan': 21, 'PHE:plan': 3, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5496 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 38, 'TRANS': 746} Chain breaks: 11 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 26, 'GLN:plan1': 10, 'GLU:plan': 26, 'ASN:plan1': 15, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 321 Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.89, per 1000 atoms: 0.24 Number of scatterers: 20582 At special positions: 0 Unit cell: (124.844, 131.192, 206.31, 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 91 16.00 O 3904 8.00 N 3434 7.00 C 13153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 282 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C1098 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 41 sheets defined 26.5% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.895A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.488A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.555A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.025A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.274A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.648A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.542A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.468A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 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 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.553A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 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 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.640A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.310A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.115A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 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 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.650A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.617A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 27C Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.325A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.009A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.705A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.400A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.288A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.175A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.773A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.909A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.909A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.112A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.798A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.354A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.916A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.750A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 172 removed outlier: 5.305A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.293A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.744A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.532A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.811A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 655 through 660 removed outlier: 4.961A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.096A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.096A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.225A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.758A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.066A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.650A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.688A 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: 6.963A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.499A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.019A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.940A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.230A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.223A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.223A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.610A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.728A pdb=" N VAL H 35A" --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2652 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: 4.78 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6469 1.34 - 1.46: 5191 1.46 - 1.58: 9255 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 21030 Sorted by residual: bond pdb=" SD MET H 82C" pdb=" CE MET H 82C" ideal model delta sigma weight residual 1.791 1.709 0.082 2.50e-02 1.60e+03 1.08e+01 bond pdb=" CB GLN B 901 " pdb=" CG GLN B 901 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.81e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.12e+00 bond pdb=" CG1 ILE B 434 " pdb=" CD1 ILE B 434 " ideal model delta sigma weight residual 1.513 1.398 0.115 3.90e-02 6.57e+02 8.75e+00 bond pdb=" CB PRO A 897 " pdb=" CG PRO A 897 " ideal model delta sigma weight residual 1.492 1.361 0.131 5.00e-02 4.00e+02 6.89e+00 ... (remaining 21025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 27320 2.32 - 4.65: 1275 4.65 - 6.97: 164 6.97 - 9.29: 12 9.29 - 11.62: 3 Bond angle restraints: 28774 Sorted by residual: angle pdb=" N GLY B 446 " pdb=" CA GLY B 446 " pdb=" C GLY B 446 " ideal model delta sigma weight residual 112.04 100.79 11.25 2.02e+00 2.45e-01 3.10e+01 angle pdb=" C TYR L 49 " pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " ideal model delta sigma weight residual 110.42 120.56 -10.14 1.99e+00 2.53e-01 2.60e+01 angle pdb=" N ASN H 82B" pdb=" CA ASN H 82B" pdb=" C ASN H 82B" ideal model delta sigma weight residual 111.02 116.83 -5.81 1.25e+00 6.40e-01 2.16e+01 angle pdb=" CA MET H 82C" pdb=" CB MET H 82C" pdb=" CG MET H 82C" ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 121.91 -8.01 1.80e+00 3.09e-01 1.98e+01 ... (remaining 28769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 12028 17.83 - 35.67: 672 35.67 - 53.50: 126 53.50 - 71.34: 24 71.34 - 89.17: 22 Dihedral angle restraints: 12872 sinusoidal: 4797 harmonic: 8075 Sorted by residual: dihedral pdb=" CA CYS A 131 " pdb=" C CYS A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO B 57 " pdb=" C PRO B 57 " pdb=" N PHE B 58 " pdb=" CA PHE B 58 " ideal model delta harmonic sigma weight residual -180.00 -150.21 -29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE C1115 " pdb=" C ILE C1115 " pdb=" N THR C1116 " pdb=" CA THR C1116 " ideal model delta harmonic sigma weight residual 180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 12869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 3477 0.178 - 0.356: 19 0.356 - 0.534: 4 0.534 - 0.712: 1 0.712 - 0.889: 1 Chirality restraints: 3502 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.94e+00 ... (remaining 3499 not shown) Planarity restraints: 3724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.013 2.00e-02 2.50e+03 3.10e-02 1.93e+01 pdb=" CG TYR L 49 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " 0.045 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.045 2.00e-02 2.50e+03 3.67e-02 1.68e+01 pdb=" C7 NAG B1310 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.038 2.00e-02 2.50e+03 3.53e-02 1.55e+01 pdb=" CG ASN B 709 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.036 2.00e-02 2.50e+03 ... (remaining 3721 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 121 2.57 - 3.16: 18392 3.16 - 3.74: 31368 3.74 - 4.32: 42592 4.32 - 4.90: 71351 Nonbonded interactions: 163824 Sorted by model distance: nonbonded pdb=" OE1 GLN B 580 " pdb=" C8 NAG B1310 " model vdw 1.993 3.460 nonbonded pdb=" O3 NAG D 1 " pdb=" O6 NAG D 2 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR L 92 " pdb=" O SER L 95 " model vdw 2.198 3.040 nonbonded pdb=" O3 NAG D 1 " pdb=" O5 NAG D 2 " model vdw 2.220 3.040 nonbonded pdb=" NE ARG H 66 " pdb=" OD1 ASN H 82B" model vdw 2.245 3.120 ... (remaining 163819 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 51 or (resid 52 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 67 or resid 81 through \ 97 or (resid 98 through 100 and (name N or name CA or name C or name O or name C \ B )) or resid 101 through 131 or (resid 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 or (resid 134 through 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 195 or (resid 196 thro \ ugh 198 and (name N or name CA or name C or name O or name CB )) or resid 199 th \ rough 238 or (resid 239 through 262 and (name N or name CA or name C or name O o \ r name CB )) or resid 265 through 283 or (resid 284 and (name N or name CA or na \ me C or name O or name CB )) or resid 285 through 292 or (resid 293 through 294 \ and (name N or name CA or name C or name O or name CB )) or resid 295 through 30 \ 3 or (resid 304 through 305 and (name N or name CA or name C or name O or name C \ B )) or resid 306 through 309 or (resid 310 and (name N or name CA or name C or \ name O or name CB )) or resid 311 through 318 or (resid 319 through 321 and (nam \ e N or name CA or name C or name O or name CB )) or resid 322 through 323 or (re \ sid 324 through 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 328 or (resid 532 through 534 and (name N or name CA or name C \ or name O or name CB )) or resid 535 or (resid 536 through 537 and (name N or n \ ame CA or name C or name O or name CB )) or resid 538 through 539 or (resid 540 \ and (name N or name CA or name C or name O or name CB )) or resid 541 through 54 \ 5 or (resid 546 and (name N or name CA or name C or name O or name CB )) or resi \ d 547 through 550 or (resid 551 and (name N or name CA or name C or name O or na \ me CB )) or resid 552 through 553 or (resid 554 and (name N or name CA or name C \ or name O or name CB )) or resid 555 or (resid 556 through 558 and (name N or n \ ame CA or name C or name O or name CB )) or resid 559 or (resid 560 and (name N \ or name CA or name C or name O or name CB )) or resid 561 through 570 or (resid \ 571 through 572 and (name N or name CA or name C or name O or name CB )) or resi \ d 573 through 581 or (resid 582 through 583 and (name N or name CA or name C or \ name O or name CB )) or resid 584 or (resid 585 through 586 and (name N or name \ CA or name C or name O or name CB )) or resid 587 or (resid 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 or resid 641 through 653 or (resid 654 and (name N or name CA or name C or \ name O or name CB )) or resid 655 through 676 or (resid 690 and (name N or name \ CA or name C or name O or name CB )) or resid 691 through 697 or (resid 698 and \ (name N or name CA or name C or name O or name CB )) or resid 699 through 703 o \ r (resid 704 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 05 through 724 or (resid 725 and (name N or name CA or name C or name O or name \ CB )) or resid 726 through 736 or (resid 737 and (name N or name CA or name C or \ name O or name CB )) or resid 738 or (resid 739 through 740 and (name N or name \ CA or name C or name O or name CB )) or resid 741 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 or (resid 747 \ through 748 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 49 through 750 or (resid 751 and (name N or name CA or name C or name O or name \ CB )) or resid 752 through 754 or (resid 755 and (name N or name CA or name C or \ name O or name CB )) or resid 756 through 757 or (resid 758 and (name N or name \ CA or name C or name O or name CB )) or resid 759 through 760 or (resid 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 764 o \ r (resid 765 through 766 and (name N or name CA or name C or name O or name CB ) \ ) or resid 767 through 772 or (resid 773 and (name N or name CA or name C or nam \ e O or name CB )) or resid 774 through 775 or (resid 776 and (name N or name CA \ or name C or name O or name CB )) or resid 777 through 778 or (resid 779 through \ 780 and (name N or name CA or name C or name O or name CB )) or resid 781 throu \ gh 794 or (resid 795 and (name N or name CA or name C or name O or name CB )) or \ resid 796 through 809 or (resid 810 through 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 815 or (resid 816 and (name N or \ name CA or name C or name O or name CB )) or resid 817 through 819 or (resid 820 \ and (name N or name CA or name C or name O or name CB )) or resid 821 through 8 \ 26 or (resid 827 through 855 and (name N or name CA or name C or name O or name \ CB )) or resid 856 through 857 or (resid 858 and (name N or name CA or name C or \ name O or name CB )) or resid 859 or (resid 860 and (name N or name CA or name \ C or name O or name CB )) or resid 861 through 866 or (resid 867 through 868 and \ (name N or name CA or name C or name O or name CB )) or resid 869 through 874 o \ r (resid 875 through 876 and (name N or name CA or name C or name O or name CB ) \ ) or resid 877 through 920 or (resid 921 and (name N or name CA or name C or nam \ e O or name CB )) or resid 922 through 932 or (resid 933 through 934 and (name N \ or name CA or name C or name O or name CB )) or resid 935 through 936 or (resid \ 937 through 944 and (name N or name CA or name C or name O or name CB )) or res \ id 945 through 949 or (resid 950 and (name N or name CA or name C or name O or n \ ame CB )) or resid 951 through 973 or (resid 974 through 977 and (name N or name \ CA or name C or name O or name CB )) or resid 978 or (resid 979 and (name N or \ name CA or name C or name O or name CB )) or resid 980 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 9 \ 87 or (resid 988 through 991 and (name N or name CA or name C or name O or name \ CB )) or resid 992 or (resid 993 through 994 and (name N or name CA or name C or \ name O or name CB )) or resid 995 through 1018 or (resid 1019 through 1020 and \ (name N or name CA or name C or name O or name CB )) or resid 1021 through 1030 \ or (resid 1031 and (name N or name CA or name C or name O or name CB )) or resid \ 1032 through 1039 or (resid 1040 through 1041 and (name N or name CA or name C \ or name O or name CB )) or resid 1042 through 1050 or (resid 1051 and (name N or \ name CA or name C or name O or name CB )) or resid 1052 through 1054 or (resid \ 1055 through 1056 and (name N or name CA or name C or name O or name CB )) or re \ sid 1057 through 1059 or (resid 1060 through 1061 and (name N or name CA or name \ C or name O or name CB )) or resid 1062 through 1065 or (resid 1066 and (name N \ or name CA or name C or name O or name CB )) or resid 1067 or (resid 1068 and ( \ name N or name CA or name C or name O or name CB )) or resid 1069 through 1072 o \ r (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid \ 1074 through 1083 or (resid 1084 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1085 or (resid 1086 through 1087 and (name N or name CA or na \ me C or name O or name CB )) or resid 1088 through 1091 or (resid 1092 and (name \ N or name CA or name C or name O or name CB )) or resid 1093 through 1096 or (r \ esid 1097 and (name N or name CA or name C or name O or name CB )) or resid 1098 \ through 1099 or (resid 1100 and (name N or name CA or name C or name O or name \ CB )) or resid 1101 through 1110 or (resid 1111 and (name N or name CA or name C \ or name O or name CB )) or resid 1112 through 1115 or (resid 1116 through 1118 \ and (name N or name CA or name C or name O or name CB )) or resid 1119 through 1 \ 121 or (resid 1122 through 1123 and (name N or name CA or name C or name O or na \ me CB )) or resid 1124 or (resid 1125 and (name N or name CA or name C or name O \ or name CB )) or resid 1126 or (resid 1127 through 1128 and (name N or name CA \ or name C or name O or name CB )) or resid 1129 or (resid 1130 and (name N or na \ me CA or name C or name O or name CB )) or resid 1131 through 1132 or (resid 113 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 1134 or (res \ id 1135 through 1136 and (name N or name CA or name C or name O or name CB )) or \ resid 1137 through 1138 or (resid 1139 and (name N or name CA or name C or name \ O or name CB )) or resid 1140 through 1143 or (resid 1144 and (name N or name C \ A or name C or name O or name CB )) or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 41 or (r \ esid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 thr \ ough 44 or (resid 45 through 47 and (name N or name CA or name C or name O or na \ me CB )) or resid 48 through 50 or (resid 51 through 54 and (name N or name CA o \ r name C or name O or name CB )) or resid 55 through 61 or (resid 62 and (name N \ or name CA or name C or name O or name CB )) or resid 63 through 83 or (resid 8 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 85 through 9 \ 9 or (resid 100 and (name N or name CA or name C or name O or name CB )) or resi \ d 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 116 or (resid 117 through 130 and (name N or name CA or name C \ or name O or name CB )) or resid 131 through 140 or (resid 141 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 173 or (resid 187 \ through 188 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 9 or (resid 190 through 191 and (name N or name CA or name C or name O or name C \ B )) or resid 192 through 194 or (resid 195 through 198 and (name N or name CA o \ r name C or name O or name CB )) or resid 199 through 210 or (resid 215 and (nam \ e N or name CA or name C or name O or name CB )) or resid 216 through 220 or (re \ sid 221 through 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 through 227 or (resid 228 through 229 and (name N or name CA or name C \ or name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 236 through 239 or (resid 240 through 264 \ and (name N or name CA or name C or name O or name CB )) or resid 265 through 27 \ 2 or (resid 273 and (name N or name CA or name C or name O or name CB )) or resi \ d 274 through 289 or (resid 290 and (name N or name CA or name C or name O or na \ me CB )) or resid 291 through 293 or (resid 294 and (name N or name CA or name C \ or name O or name CB )) or resid 295 through 297 or (resid 298 through 299 and \ (name N or name CA or name C or name O or name CB )) or resid 300 through 301 or \ (resid 302 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 3 through 304 or (resid 305 and (name N or name CA or name C or name O or name C \ B )) or resid 306 through 313 or (resid 314 through 315 and (name N or name CA o \ r name C or name O or name CB )) or resid 316 through 319 or (resid 320 through \ 321 and (name N or name CA or name C or name O or name CB )) or resid 322 throug \ h 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 617 or (resid 618 through 619 and (name N or name CA or name C \ or name O or name CB )) or resid 620 through 818 or (resid 819 through 820 and \ (name N or name CA or name C or name O or name CB )) or resid 821 through 1309)) \ } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } 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=0.52 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.140 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.011 0.131 21105 Z= 0.493 Angle : 1.155 17.259 28966 Z= 0.629 Chirality : 0.064 0.889 3502 Planarity : 0.007 0.063 3688 Dihedral : 12.452 89.169 7555 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.63 (0.15), residues: 2711 helix: 0.35 (0.19), residues: 610 sheet: -0.06 (0.19), residues: 665 loop : -0.89 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.010 ARG B1039 TYR 0.047 0.006 TYR L 49 PHE 0.042 0.004 PHE B 464 TRP 0.032 0.006 TRP C 886 HIS 0.017 0.004 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.01100 (21030) covalent geometry : angle 1.11018 (28774) SS BOND : bond 0.00531 ( 33) SS BOND : angle 1.99215 ( 66) hydrogen bonds : bond 0.16587 ( 962) hydrogen bonds : angle 8.36383 ( 2652) link_BETA1-4 : bond 0.00551 ( 6) link_BETA1-4 : angle 3.03148 ( 18) link_NAG-ASN : bond 0.00824 ( 36) link_NAG-ASN : angle 5.06876 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.719 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: 0.7745 (m-80) cc_final: 0.7122 (m-10) REVERT: A 981 LEU cc_start: 0.9630 (tp) cc_final: 0.9308 (pp) REVERT: B 562 PHE cc_start: 0.7156 (t80) cc_final: 0.6452 (t80) REVERT: B 869 MET cc_start: 0.8887 (mtm) cc_final: 0.8649 (ptp) REVERT: B 900 MET cc_start: 0.8473 (mtt) cc_final: 0.8203 (mtt) REVERT: B 902 MET cc_start: 0.8622 (tpp) cc_final: 0.8019 (tpp) REVERT: B 1050 MET cc_start: 0.8463 (ptp) cc_final: 0.7681 (ptp) REVERT: C 190 ARG cc_start: 0.5429 (mtt180) cc_final: 0.5033 (ptp90) REVERT: C 223 LEU cc_start: 0.8856 (mt) cc_final: 0.8316 (mp) REVERT: C 298 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 697 MET cc_start: 0.8177 (ptm) cc_final: 0.7958 (ptm) REVERT: C 699 LEU cc_start: 0.9048 (mt) cc_final: 0.8793 (mt) REVERT: C 796 ASP cc_start: 0.8330 (t0) cc_final: 0.7898 (t0) REVERT: C 819 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8621 (mt-10) REVERT: C 1002 GLN cc_start: 0.9378 (tt0) cc_final: 0.8701 (tp40) REVERT: C 1017 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8886 (tm-30) REVERT: L 26 THR cc_start: 0.7998 (m) cc_final: 0.7771 (p) REVERT: L 78 LEU cc_start: 0.8149 (mt) cc_final: 0.7916 (tp) REVERT: H 56 ASP cc_start: 0.7937 (t0) cc_final: 0.7397 (t0) REVERT: H 71 LYS cc_start: 0.7880 (pttp) cc_final: 0.7517 (ptmt) REVERT: H 72 ASP cc_start: 0.8721 (t0) cc_final: 0.7824 (p0) REVERT: H 82 MET cc_start: 0.7290 (pmm) cc_final: 0.6715 (ptt) REVERT: H 90 TYR cc_start: 0.6316 (m-80) cc_final: 0.5951 (m-10) REVERT: H 97 ILE cc_start: 0.8966 (mm) cc_final: 0.8654 (mm) REVERT: H 98 GLU cc_start: 0.8374 (pt0) cc_final: 0.8117 (tm-30) REVERT: H 105 GLN cc_start: 0.7676 (tp40) cc_final: 0.7398 (pm20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1612 time to fit residues: 32.8272 Evaluate side-chains 82 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 613 GLN B 437 ASN B1135 ASN H 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046378 restraints weight = 87279.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048003 restraints weight = 42029.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.049083 restraints weight = 26633.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049788 restraints weight = 19746.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050239 restraints weight = 16179.114| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21105 Z= 0.139 Angle : 0.666 11.580 28966 Z= 0.342 Chirality : 0.047 0.445 3502 Planarity : 0.004 0.043 3688 Dihedral : 7.560 58.548 3806 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.53 % Allowed : 3.93 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.35 (0.16), residues: 2711 helix: 1.88 (0.20), residues: 631 sheet: 0.23 (0.19), residues: 650 loop : -0.48 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 99 TYR 0.030 0.002 TYR L 49 PHE 0.031 0.001 PHE A 201 TRP 0.019 0.002 TRP B 64 HIS 0.005 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00295 (21030) covalent geometry : angle 0.62412 (28774) SS BOND : bond 0.00184 ( 33) SS BOND : angle 0.99750 ( 66) hydrogen bonds : bond 0.04473 ( 962) hydrogen bonds : angle 6.19347 ( 2652) link_BETA1-4 : bond 0.00649 ( 6) link_BETA1-4 : angle 2.17796 ( 18) link_NAG-ASN : bond 0.00570 ( 36) link_NAG-ASN : angle 3.69283 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9171 (mp) cc_final: 0.8917 (mt) REVERT: A 981 LEU cc_start: 0.9634 (tp) cc_final: 0.9341 (pp) REVERT: B 86 PHE cc_start: 0.8053 (t80) cc_final: 0.7700 (t80) REVERT: B 900 MET cc_start: 0.8693 (mtt) cc_final: 0.8425 (mtt) REVERT: C 190 ARG cc_start: 0.5668 (mtt180) cc_final: 0.5219 (mtt90) REVERT: C 223 LEU cc_start: 0.8886 (mt) cc_final: 0.8357 (mp) REVERT: C 298 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7867 (mt-10) REVERT: C 733 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8969 (mtmt) REVERT: C 796 ASP cc_start: 0.8075 (t0) cc_final: 0.7783 (t0) REVERT: C 819 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8324 (mt-10) REVERT: C 1002 GLN cc_start: 0.9262 (tt0) cc_final: 0.8681 (tp40) REVERT: L 17 GLN cc_start: 0.7334 (pt0) cc_final: 0.6660 (pp30) REVERT: L 26 THR cc_start: 0.8193 (m) cc_final: 0.7741 (p) REVERT: L 27 VAL cc_start: 0.7930 (p) cc_final: 0.7486 (p) REVERT: L 32 TYR cc_start: 0.5867 (m-80) cc_final: 0.5345 (m-80) REVERT: L 78 LEU cc_start: 0.7807 (mt) cc_final: 0.7163 (tp) REVERT: H 56 ASP cc_start: 0.8078 (t0) cc_final: 0.7777 (t0) REVERT: H 72 ASP cc_start: 0.9084 (t0) cc_final: 0.8645 (t70) REVERT: H 97 ILE cc_start: 0.8825 (mm) cc_final: 0.8471 (mm) REVERT: H 105 GLN cc_start: 0.8185 (tp40) cc_final: 0.7544 (pm20) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 0.1431 time to fit residues: 26.5144 Evaluate side-chains 86 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 257 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.045598 restraints weight = 87919.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.047183 restraints weight = 42311.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048210 restraints weight = 26848.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048904 restraints weight = 20088.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049353 restraints weight = 16499.920| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21105 Z= 0.175 Angle : 0.616 9.666 28966 Z= 0.315 Chirality : 0.046 0.409 3502 Planarity : 0.004 0.049 3688 Dihedral : 6.828 59.135 3806 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.22 % Allowed : 5.47 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.38 (0.16), residues: 2711 helix: 2.01 (0.21), residues: 633 sheet: -0.04 (0.19), residues: 684 loop : -0.37 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.019 0.002 TYR L 49 PHE 0.034 0.001 PHE A 201 TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00392 (21030) covalent geometry : angle 0.58224 (28774) SS BOND : bond 0.00210 ( 33) SS BOND : angle 0.89596 ( 66) hydrogen bonds : bond 0.04061 ( 962) hydrogen bonds : angle 5.78310 ( 2652) link_BETA1-4 : bond 0.00238 ( 6) link_BETA1-4 : angle 1.79351 ( 18) link_NAG-ASN : bond 0.00455 ( 36) link_NAG-ASN : angle 3.24835 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9150 (mp) cc_final: 0.8879 (mt) REVERT: A 981 LEU cc_start: 0.9637 (tp) cc_final: 0.9329 (pp) REVERT: B 86 PHE cc_start: 0.8178 (t80) cc_final: 0.7971 (t80) REVERT: B 562 PHE cc_start: 0.7105 (t80) cc_final: 0.6864 (t80) REVERT: B 900 MET cc_start: 0.8756 (mtt) cc_final: 0.8422 (mtt) REVERT: C 190 ARG cc_start: 0.5677 (mtt180) cc_final: 0.5205 (mtt90) REVERT: C 223 LEU cc_start: 0.8889 (mt) cc_final: 0.8496 (mp) REVERT: C 298 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7901 (mt-10) REVERT: C 796 ASP cc_start: 0.8228 (t0) cc_final: 0.7952 (t0) REVERT: C 819 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 1002 GLN cc_start: 0.9272 (tt0) cc_final: 0.8700 (tp40) REVERT: L 17 GLN cc_start: 0.7352 (pt0) cc_final: 0.6729 (pp30) REVERT: L 26 THR cc_start: 0.8120 (m) cc_final: 0.7673 (p) REVERT: L 27 VAL cc_start: 0.8017 (p) cc_final: 0.7765 (p) REVERT: L 78 LEU cc_start: 0.7844 (mt) cc_final: 0.7259 (tp) REVERT: H 55 ASP cc_start: 0.8623 (m-30) cc_final: 0.8221 (t0) REVERT: H 66 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7095 (ttt180) REVERT: H 72 ASP cc_start: 0.8935 (t0) cc_final: 0.8482 (t70) REVERT: H 75 LYS cc_start: 0.9542 (ptpt) cc_final: 0.9114 (ptpp) REVERT: H 77 GLN cc_start: 0.8963 (mt0) cc_final: 0.8672 (pp30) REVERT: H 97 ILE cc_start: 0.8776 (mm) cc_final: 0.8478 (mm) REVERT: H 105 GLN cc_start: 0.8312 (tp40) cc_final: 0.7580 (pm20) outliers start: 23 outliers final: 11 residues processed: 107 average time/residue: 0.1436 time to fit residues: 24.5193 Evaluate side-chains 90 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain H residue 69 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 69 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 265 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 157 optimal weight: 0.4980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047521 restraints weight = 85061.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049030 restraints weight = 43095.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.050016 restraints weight = 28394.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050649 restraints weight = 21684.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051069 restraints weight = 18261.021| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21105 Z= 0.202 Angle : 0.614 8.501 28966 Z= 0.313 Chirality : 0.046 0.399 3502 Planarity : 0.004 0.048 3688 Dihedral : 6.456 53.269 3806 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.27 % Allowed : 6.53 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.37 (0.16), residues: 2711 helix: 2.04 (0.21), residues: 628 sheet: -0.05 (0.19), residues: 661 loop : -0.37 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.019 0.002 TYR L 49 PHE 0.032 0.002 PHE A 201 TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00453 (21030) covalent geometry : angle 0.58534 (28774) SS BOND : bond 0.00207 ( 33) SS BOND : angle 0.85810 ( 66) hydrogen bonds : bond 0.03903 ( 962) hydrogen bonds : angle 5.59445 ( 2652) link_BETA1-4 : bond 0.00318 ( 6) link_BETA1-4 : angle 1.73724 ( 18) link_NAG-ASN : bond 0.00445 ( 36) link_NAG-ASN : angle 2.99527 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9194 (mp) cc_final: 0.8921 (mt) REVERT: A 904 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 981 LEU cc_start: 0.9634 (tp) cc_final: 0.9331 (pp) REVERT: B 562 PHE cc_start: 0.7157 (t80) cc_final: 0.6843 (t80) REVERT: B 900 MET cc_start: 0.8800 (mtt) cc_final: 0.8476 (mtt) REVERT: C 223 LEU cc_start: 0.8913 (mt) cc_final: 0.8553 (mp) REVERT: C 298 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 796 ASP cc_start: 0.8361 (t0) cc_final: 0.8116 (t0) REVERT: C 819 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8317 (mt-10) REVERT: C 1002 GLN cc_start: 0.9238 (tt0) cc_final: 0.8851 (tp40) REVERT: C 1050 MET cc_start: 0.8420 (ptp) cc_final: 0.7718 (ptp) REVERT: L 17 GLN cc_start: 0.7359 (pt0) cc_final: 0.6754 (pp30) REVERT: L 26 THR cc_start: 0.8182 (m) cc_final: 0.7759 (p) REVERT: L 27 VAL cc_start: 0.7957 (p) cc_final: 0.7671 (p) REVERT: L 78 LEU cc_start: 0.7917 (mt) cc_final: 0.7298 (tp) REVERT: H 55 ASP cc_start: 0.8829 (m-30) cc_final: 0.8162 (t0) REVERT: H 58 ARG cc_start: 0.6343 (mmt-90) cc_final: 0.5991 (mmt-90) REVERT: H 72 ASP cc_start: 0.8786 (t0) cc_final: 0.8296 (t0) REVERT: H 75 LYS cc_start: 0.9543 (ptpt) cc_final: 0.9341 (ptpt) REVERT: H 82 MET cc_start: 0.8321 (mmm) cc_final: 0.7538 (mmm) REVERT: H 105 GLN cc_start: 0.8298 (tp40) cc_final: 0.7595 (pm20) outliers start: 24 outliers final: 15 residues processed: 108 average time/residue: 0.1351 time to fit residues: 23.9812 Evaluate side-chains 94 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 69 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 231 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 180 optimal weight: 0.3980 chunk 233 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048701 restraints weight = 82713.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.050178 restraints weight = 42313.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051159 restraints weight = 27975.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051795 restraints weight = 21342.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052219 restraints weight = 17871.945| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21105 Z= 0.144 Angle : 0.561 8.316 28966 Z= 0.287 Chirality : 0.045 0.363 3502 Planarity : 0.004 0.047 3688 Dihedral : 6.101 50.240 3806 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.33 % Allowed : 7.38 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.46 (0.17), residues: 2711 helix: 2.12 (0.21), residues: 629 sheet: -0.02 (0.19), residues: 662 loop : -0.32 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 66 TYR 0.017 0.001 TYR B 449 PHE 0.030 0.001 PHE A 201 TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00320 (21030) covalent geometry : angle 0.53338 (28774) SS BOND : bond 0.00152 ( 33) SS BOND : angle 0.75723 ( 66) hydrogen bonds : bond 0.03629 ( 962) hydrogen bonds : angle 5.37417 ( 2652) link_BETA1-4 : bond 0.00286 ( 6) link_BETA1-4 : angle 1.67297 ( 18) link_NAG-ASN : bond 0.00407 ( 36) link_NAG-ASN : angle 2.80979 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9147 (mp) cc_final: 0.8858 (mt) REVERT: A 904 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: A 981 LEU cc_start: 0.9628 (tp) cc_final: 0.9336 (pp) REVERT: B 900 MET cc_start: 0.8771 (mtt) cc_final: 0.8455 (mtt) REVERT: C 574 ASP cc_start: 0.8141 (t70) cc_final: 0.7935 (t0) REVERT: C 819 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8273 (mt-10) REVERT: C 1002 GLN cc_start: 0.9163 (tt0) cc_final: 0.8872 (tp40) REVERT: C 1050 MET cc_start: 0.8459 (ptp) cc_final: 0.7748 (ptp) REVERT: L 17 GLN cc_start: 0.7306 (pt0) cc_final: 0.6721 (pp30) REVERT: L 26 THR cc_start: 0.8112 (m) cc_final: 0.7677 (p) REVERT: L 27 VAL cc_start: 0.7970 (p) cc_final: 0.7704 (p) REVERT: L 78 LEU cc_start: 0.7944 (mt) cc_final: 0.7236 (tp) REVERT: H 55 ASP cc_start: 0.8776 (m-30) cc_final: 0.8131 (t0) REVERT: H 58 ARG cc_start: 0.6394 (mmt-90) cc_final: 0.6153 (mmt-90) REVERT: H 82 MET cc_start: 0.7503 (mmm) cc_final: 0.7071 (mmm) outliers start: 25 outliers final: 15 residues processed: 110 average time/residue: 0.1292 time to fit residues: 23.6762 Evaluate side-chains 96 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 214 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.048742 restraints weight = 82992.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.050210 restraints weight = 42750.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.051202 restraints weight = 28272.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.051831 restraints weight = 21609.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.052274 restraints weight = 18105.807| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21105 Z= 0.137 Angle : 0.553 8.224 28966 Z= 0.281 Chirality : 0.044 0.358 3502 Planarity : 0.004 0.045 3688 Dihedral : 5.844 50.372 3806 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.86 % Allowed : 7.43 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.57 (0.17), residues: 2711 helix: 2.24 (0.21), residues: 629 sheet: 0.10 (0.19), residues: 664 loop : -0.29 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 66 TYR 0.016 0.001 TYR L 49 PHE 0.030 0.001 PHE A 201 TRP 0.017 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00305 (21030) covalent geometry : angle 0.52706 (28774) SS BOND : bond 0.00251 ( 33) SS BOND : angle 0.73944 ( 66) hydrogen bonds : bond 0.03548 ( 962) hydrogen bonds : angle 5.23586 ( 2652) link_BETA1-4 : bond 0.00261 ( 6) link_BETA1-4 : angle 1.62131 ( 18) link_NAG-ASN : bond 0.00388 ( 36) link_NAG-ASN : angle 2.70664 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9134 (mp) cc_final: 0.8837 (mt) REVERT: A 904 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: A 981 LEU cc_start: 0.9615 (tp) cc_final: 0.9322 (pp) REVERT: B 86 PHE cc_start: 0.7861 (t80) cc_final: 0.7639 (t80) REVERT: B 900 MET cc_start: 0.8783 (mtt) cc_final: 0.8446 (mtt) REVERT: C 819 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8215 (mt-10) REVERT: C 1002 GLN cc_start: 0.9129 (tt0) cc_final: 0.8914 (tp40) REVERT: C 1050 MET cc_start: 0.8446 (ptp) cc_final: 0.7968 (ptp) REVERT: L 17 GLN cc_start: 0.7312 (pt0) cc_final: 0.6757 (pp30) REVERT: L 26 THR cc_start: 0.8082 (m) cc_final: 0.7653 (p) REVERT: L 27 VAL cc_start: 0.7980 (p) cc_final: 0.7699 (p) REVERT: L 78 LEU cc_start: 0.7888 (mt) cc_final: 0.7178 (tp) REVERT: H 55 ASP cc_start: 0.8768 (m-30) cc_final: 0.8081 (t0) REVERT: H 58 ARG cc_start: 0.6574 (mmt-90) cc_final: 0.6297 (mmt-90) REVERT: H 72 ASP cc_start: 0.8982 (t0) cc_final: 0.8676 (t70) REVERT: H 75 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8789 (pttm) REVERT: H 77 GLN cc_start: 0.9192 (mt0) cc_final: 0.8944 (mp10) REVERT: H 82 MET cc_start: 0.7731 (mmm) cc_final: 0.7135 (mmm) outliers start: 35 outliers final: 17 residues processed: 112 average time/residue: 0.1239 time to fit residues: 23.4958 Evaluate side-chains 100 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 75 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.049213 restraints weight = 81434.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.050446 restraints weight = 44492.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.051305 restraints weight = 30762.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051839 restraints weight = 24411.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052220 restraints weight = 21116.373| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21105 Z= 0.286 Angle : 0.650 7.947 28966 Z= 0.332 Chirality : 0.047 0.405 3502 Planarity : 0.004 0.048 3688 Dihedral : 6.126 49.264 3806 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.59 % Allowed : 8.81 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.33 (0.16), residues: 2711 helix: 2.05 (0.21), residues: 623 sheet: -0.06 (0.19), residues: 672 loop : -0.43 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.025 0.002 TYR C 269 PHE 0.031 0.002 PHE A 201 TRP 0.013 0.002 TRP B 64 HIS 0.006 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00643 (21030) covalent geometry : angle 0.62647 (28774) SS BOND : bond 0.00225 ( 33) SS BOND : angle 0.84579 ( 66) hydrogen bonds : bond 0.03947 ( 962) hydrogen bonds : angle 5.53098 ( 2652) link_BETA1-4 : bond 0.00343 ( 6) link_BETA1-4 : angle 1.66342 ( 18) link_NAG-ASN : bond 0.00470 ( 36) link_NAG-ASN : angle 2.83347 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9199 (mp) cc_final: 0.8925 (mt) REVERT: A 902 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8721 (tpp) REVERT: A 904 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: A 981 LEU cc_start: 0.9612 (tp) cc_final: 0.9333 (pp) REVERT: B 351 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7350 (t80) REVERT: B 900 MET cc_start: 0.8850 (mtt) cc_final: 0.8555 (mtt) REVERT: C 574 ASP cc_start: 0.8356 (t70) cc_final: 0.7896 (t0) REVERT: C 819 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8260 (mt-10) REVERT: C 1002 GLN cc_start: 0.9172 (tt0) cc_final: 0.8968 (tp40) REVERT: C 1050 MET cc_start: 0.8471 (ptp) cc_final: 0.7868 (ptp) REVERT: L 17 GLN cc_start: 0.7248 (pt0) cc_final: 0.6719 (pp30) REVERT: L 26 THR cc_start: 0.8066 (m) cc_final: 0.7678 (p) REVERT: L 78 LEU cc_start: 0.8031 (mt) cc_final: 0.7357 (tp) REVERT: H 55 ASP cc_start: 0.8794 (m-30) cc_final: 0.8110 (t0) REVERT: H 72 ASP cc_start: 0.8919 (t0) cc_final: 0.8670 (t70) REVERT: H 82 MET cc_start: 0.7746 (mmm) cc_final: 0.7197 (mmm) REVERT: H 105 GLN cc_start: 0.8367 (tp40) cc_final: 0.7658 (mp10) outliers start: 30 outliers final: 17 residues processed: 102 average time/residue: 0.1375 time to fit residues: 23.3834 Evaluate side-chains 92 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 1 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 8 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 257 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 254 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047862 restraints weight = 84296.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049337 restraints weight = 43360.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050320 restraints weight = 28674.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050967 restraints weight = 21878.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051374 restraints weight = 18298.930| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21105 Z= 0.135 Angle : 0.559 10.182 28966 Z= 0.285 Chirality : 0.044 0.359 3502 Planarity : 0.004 0.048 3688 Dihedral : 5.799 49.891 3806 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.49 % Allowed : 9.18 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.47 (0.17), residues: 2711 helix: 2.16 (0.21), residues: 636 sheet: 0.00 (0.19), residues: 665 loop : -0.35 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 58 TYR 0.014 0.001 TYR L 49 PHE 0.029 0.001 PHE A 201 TRP 0.017 0.001 TRP B 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (21030) covalent geometry : angle 0.53184 (28774) SS BOND : bond 0.00139 ( 33) SS BOND : angle 0.73989 ( 66) hydrogen bonds : bond 0.03588 ( 962) hydrogen bonds : angle 5.23784 ( 2652) link_BETA1-4 : bond 0.00304 ( 6) link_BETA1-4 : angle 1.61223 ( 18) link_NAG-ASN : bond 0.00481 ( 36) link_NAG-ASN : angle 2.77674 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9136 (mp) cc_final: 0.8853 (mt) REVERT: A 902 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8826 (mmt) REVERT: A 904 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: A 981 LEU cc_start: 0.9601 (tp) cc_final: 0.9315 (pp) REVERT: B 86 PHE cc_start: 0.7859 (t80) cc_final: 0.7501 (t80) REVERT: B 118 LEU cc_start: 0.8512 (tp) cc_final: 0.8083 (mp) REVERT: B 900 MET cc_start: 0.8792 (mtt) cc_final: 0.8429 (mtt) REVERT: C 574 ASP cc_start: 0.8404 (t70) cc_final: 0.7873 (t0) REVERT: C 819 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 1002 GLN cc_start: 0.9161 (tt0) cc_final: 0.8939 (tp40) REVERT: C 1050 MET cc_start: 0.8424 (ptp) cc_final: 0.7812 (ptp) REVERT: L 17 GLN cc_start: 0.7162 (pt0) cc_final: 0.6631 (pp30) REVERT: L 31 ASN cc_start: 0.8585 (t0) cc_final: 0.8281 (t0) REVERT: L 78 LEU cc_start: 0.8085 (mt) cc_final: 0.7401 (tp) REVERT: H 55 ASP cc_start: 0.8796 (m-30) cc_final: 0.8084 (t0) REVERT: H 58 ARG cc_start: 0.6569 (mmt-90) cc_final: 0.6286 (mmt-90) REVERT: H 72 ASP cc_start: 0.9069 (t0) cc_final: 0.8793 (t70) REVERT: H 82 MET cc_start: 0.7800 (mmm) cc_final: 0.7175 (mmm) REVERT: H 105 GLN cc_start: 0.8383 (tp40) cc_final: 0.7683 (mp10) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 0.1277 time to fit residues: 21.5213 Evaluate side-chains 99 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 1 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 31 optimal weight: 0.0670 chunk 241 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 245 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054728 restraints weight = 75625.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056020 restraints weight = 42010.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.056831 restraints weight = 29457.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057383 restraints weight = 23852.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.057653 restraints weight = 20818.448| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21105 Z= 0.096 Angle : 0.529 10.062 28966 Z= 0.269 Chirality : 0.044 0.321 3502 Planarity : 0.004 0.048 3688 Dihedral : 5.321 51.419 3806 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.06 % Allowed : 9.55 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.64 (0.17), residues: 2711 helix: 2.26 (0.21), residues: 636 sheet: 0.26 (0.20), residues: 646 loop : -0.31 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 58 TYR 0.015 0.001 TYR L 49 PHE 0.013 0.001 PHE A 201 TRP 0.021 0.001 TRP B 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00204 (21030) covalent geometry : angle 0.50400 (28774) SS BOND : bond 0.00432 ( 33) SS BOND : angle 0.71105 ( 66) hydrogen bonds : bond 0.03319 ( 962) hydrogen bonds : angle 4.96948 ( 2652) link_BETA1-4 : bond 0.00312 ( 6) link_BETA1-4 : angle 1.51544 ( 18) link_NAG-ASN : bond 0.00414 ( 36) link_NAG-ASN : angle 2.57160 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9094 (mp) cc_final: 0.8763 (mt) REVERT: A 900 MET cc_start: 0.8785 (mmt) cc_final: 0.7754 (mmt) REVERT: A 904 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: A 981 LEU cc_start: 0.9613 (tp) cc_final: 0.9299 (pp) REVERT: B 86 PHE cc_start: 0.7857 (t80) cc_final: 0.7488 (t80) REVERT: B 118 LEU cc_start: 0.8329 (tp) cc_final: 0.7946 (mp) REVERT: B 900 MET cc_start: 0.8718 (mtt) cc_final: 0.8476 (mtt) REVERT: C 574 ASP cc_start: 0.8223 (t70) cc_final: 0.7828 (t0) REVERT: C 819 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8290 (mt-10) REVERT: C 1002 GLN cc_start: 0.9222 (tt0) cc_final: 0.8907 (tp40) REVERT: C 1050 MET cc_start: 0.8499 (ptp) cc_final: 0.7800 (ptp) REVERT: L 17 GLN cc_start: 0.7238 (pt0) cc_final: 0.6550 (pp30) REVERT: L 31 ASN cc_start: 0.8580 (t0) cc_final: 0.8261 (t0) REVERT: L 78 LEU cc_start: 0.7925 (mt) cc_final: 0.7307 (mm) REVERT: H 55 ASP cc_start: 0.8772 (m-30) cc_final: 0.8037 (t0) REVERT: H 58 ARG cc_start: 0.6454 (mmt-90) cc_final: 0.6236 (mmt-90) REVERT: H 72 ASP cc_start: 0.9073 (t0) cc_final: 0.8810 (t70) REVERT: H 82 MET cc_start: 0.7829 (mmm) cc_final: 0.7132 (mmm) REVERT: H 105 GLN cc_start: 0.8557 (tp40) cc_final: 0.7852 (mp10) outliers start: 20 outliers final: 14 residues processed: 106 average time/residue: 0.1329 time to fit residues: 23.2646 Evaluate side-chains 92 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 183 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.049785 restraints weight = 77053.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.051054 restraints weight = 43405.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.051956 restraints weight = 30533.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.052568 restraints weight = 24395.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.052962 restraints weight = 21086.125| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21105 Z= 0.263 Angle : 0.639 9.992 28966 Z= 0.326 Chirality : 0.047 0.382 3502 Planarity : 0.004 0.046 3688 Dihedral : 5.696 48.970 3806 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.06 % Allowed : 10.14 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.16), residues: 2711 helix: 2.16 (0.21), residues: 625 sheet: -0.03 (0.19), residues: 698 loop : -0.45 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.024 0.002 TYR H 90 PHE 0.024 0.002 PHE A 92 TRP 0.012 0.002 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00589 (21030) covalent geometry : angle 0.61670 (28774) SS BOND : bond 0.00209 ( 33) SS BOND : angle 0.77744 ( 66) hydrogen bonds : bond 0.03788 ( 962) hydrogen bonds : angle 5.34957 ( 2652) link_BETA1-4 : bond 0.00291 ( 6) link_BETA1-4 : angle 1.60716 ( 18) link_NAG-ASN : bond 0.00431 ( 36) link_NAG-ASN : angle 2.73707 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9177 (mp) cc_final: 0.8899 (mt) REVERT: A 904 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: B 86 PHE cc_start: 0.7994 (t80) cc_final: 0.7543 (t80) REVERT: B 118 LEU cc_start: 0.8633 (tp) cc_final: 0.8123 (mp) REVERT: B 900 MET cc_start: 0.8828 (mtt) cc_final: 0.8594 (mtt) REVERT: B 1050 MET cc_start: 0.8763 (ptt) cc_final: 0.8559 (mtm) REVERT: C 574 ASP cc_start: 0.8359 (t70) cc_final: 0.7900 (t0) REVERT: C 697 MET cc_start: 0.8382 (mmm) cc_final: 0.8174 (mmm) REVERT: C 819 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 1002 GLN cc_start: 0.9278 (tt0) cc_final: 0.8987 (tp40) REVERT: C 1050 MET cc_start: 0.8587 (ptp) cc_final: 0.7831 (ptp) REVERT: L 17 GLN cc_start: 0.7054 (pt0) cc_final: 0.6525 (pp30) REVERT: L 31 ASN cc_start: 0.8499 (t0) cc_final: 0.8203 (t0) REVERT: L 50 ASP cc_start: 0.9119 (m-30) cc_final: 0.8749 (m-30) REVERT: L 78 LEU cc_start: 0.8259 (mt) cc_final: 0.7548 (tp) REVERT: H 55 ASP cc_start: 0.8755 (m-30) cc_final: 0.8067 (t0) REVERT: H 72 ASP cc_start: 0.8971 (t0) cc_final: 0.8712 (t0) REVERT: H 82 MET cc_start: 0.5288 (pmm) cc_final: 0.4857 (pmm) REVERT: H 82 MET cc_start: 0.7821 (mmm) cc_final: 0.7153 (mmm) REVERT: H 105 GLN cc_start: 0.8322 (tp40) cc_final: 0.7627 (mp10) outliers start: 20 outliers final: 15 residues processed: 89 average time/residue: 0.1217 time to fit residues: 18.6570 Evaluate side-chains 91 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 198 optimal weight: 5.9990 chunk 263 optimal weight: 0.0970 chunk 204 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 202 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.050884 restraints weight = 76856.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.052269 restraints weight = 41645.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.053219 restraints weight = 28796.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053872 restraints weight = 22752.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054225 restraints weight = 19393.937| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21105 Z= 0.107 Angle : 0.543 10.194 28966 Z= 0.276 Chirality : 0.044 0.325 3502 Planarity : 0.004 0.046 3688 Dihedral : 5.381 50.763 3806 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.90 % Allowed : 10.19 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.57 (0.16), residues: 2711 helix: 2.24 (0.21), residues: 634 sheet: 0.16 (0.19), residues: 669 loop : -0.34 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 58 TYR 0.014 0.001 TYR C1047 PHE 0.010 0.001 PHE B 238 TRP 0.019 0.001 TRP B 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00235 (21030) covalent geometry : angle 0.51928 (28774) SS BOND : bond 0.00116 ( 33) SS BOND : angle 0.70596 ( 66) hydrogen bonds : bond 0.03400 ( 962) hydrogen bonds : angle 5.00916 ( 2652) link_BETA1-4 : bond 0.00310 ( 6) link_BETA1-4 : angle 1.50082 ( 18) link_NAG-ASN : bond 0.00413 ( 36) link_NAG-ASN : angle 2.58172 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.94 seconds wall clock time: 57 minutes 6.08 seconds (3426.08 seconds total)