Starting phenix.real_space_refine on Fri Mar 6 06:09:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyc_27074/03_2026/8cyc_27074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyc_27074/03_2026/8cyc_27074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cyc_27074/03_2026/8cyc_27074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyc_27074/03_2026/8cyc_27074.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyc_27074/03_2026/8cyc_27074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyc_27074/03_2026/8cyc_27074.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 123 5.16 5 C 18247 2.51 5 N 4831 2.21 5 O 5496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s 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: 28697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8560 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1041} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8594 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1046} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8564 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1041} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "F" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 7.01, per 1000 atoms: 0.24 Number of scatterers: 28697 At special positions: 0 Unit cell: (159.43, 165.85, 194.74, 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 123 16.00 O 5496 8.00 N 4831 7.00 C 18247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6842 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 57 sheets defined 23.3% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.870A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.083A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 629 through 638 removed outlier: 5.767A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.536A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.126A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 920 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.840A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.766A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.706A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.571A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.120A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.570A pdb=" N ASP B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.875A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.791A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.609A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.567A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.680A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.708A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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 1032 removed outlier: 4.722A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.678A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.065A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.944A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.654A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.507A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 634 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.622A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.665A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.542A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.817A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.174A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.061A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 32 removed outlier: 3.524A pdb=" N SER D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.619A pdb=" N TYR D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 110' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 104 through 109 removed outlier: 3.645A pdb=" N TYR E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 104 through 114 removed outlier: 4.034A pdb=" N TYR F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN F 110 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU F 111 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP F 112 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU F 113 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR F 114 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.047A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.047A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.601A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.906A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 143 removed outlier: 6.334A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.508A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.740A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.223A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.137A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.658A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.508A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.960A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.260A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.893A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.893A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.947A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.125A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.789A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.938A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.831A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.023A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.759A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.514A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.711A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.343A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.584A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.607A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.949A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.701A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 4.003A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.363A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 807 through 808 removed outlier: 4.469A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.000A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.089A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.069A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.069A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 98 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP D 116 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS E 22 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.902A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.172A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.112A pdb=" N VAL F 98 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP F 116 " --> pdb=" O VAL F 98 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 2997 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: 6.47 Time building geometry restraints manager: 2.98 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: 9348 1.34 - 1.46: 7064 1.46 - 1.58: 12807 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 29375 Sorted by residual: bond pdb=" N VAL B 826 " pdb=" CA VAL B 826 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" CA SER C 50 " pdb=" CB SER C 50 " ideal model delta sigma weight residual 1.527 1.492 0.034 1.27e-02 6.20e+03 7.34e+00 bond pdb=" N LEU B 822 " pdb=" CA LEU B 822 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.24e-02 6.50e+03 6.56e+00 bond pdb=" N ASP B 830 " pdb=" CA ASP B 830 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.62e+00 bond pdb=" N THR B 827 " pdb=" CA THR B 827 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.32e-02 5.74e+03 5.19e+00 ... (remaining 29370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 39091 1.51 - 3.03: 737 3.03 - 4.54: 113 4.54 - 6.05: 33 6.05 - 7.56: 10 Bond angle restraints: 39984 Sorted by residual: angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.50 6.73 1.36e+00 5.41e-01 2.45e+01 angle pdb=" N VAL C 83 " pdb=" CA VAL C 83 " pdb=" C VAL C 83 " ideal model delta sigma weight residual 111.77 107.75 4.02 1.04e+00 9.25e-01 1.49e+01 angle pdb=" N ILE C 410 " pdb=" CA ILE C 410 " pdb=" C ILE C 410 " ideal model delta sigma weight residual 112.29 108.80 3.49 9.40e-01 1.13e+00 1.38e+01 angle pdb=" CA THR B 827 " pdb=" C THR B 827 " pdb=" O THR B 827 " ideal model delta sigma weight residual 121.87 117.90 3.97 1.10e+00 8.26e-01 1.30e+01 angle pdb=" N PHE B 823 " pdb=" CA PHE B 823 " pdb=" C PHE B 823 " ideal model delta sigma weight residual 111.33 107.00 4.33 1.21e+00 6.83e-01 1.28e+01 ... (remaining 39979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15809 17.94 - 35.88: 1336 35.88 - 53.82: 228 53.82 - 71.76: 57 71.76 - 89.70: 26 Dihedral angle restraints: 17456 sinusoidal: 6778 harmonic: 10678 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 4.26 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.11 -75.89 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.81 -69.19 1 1.00e+01 1.00e-02 6.19e+01 ... (remaining 17453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3377 0.043 - 0.087: 746 0.087 - 0.130: 336 0.130 - 0.173: 13 0.173 - 0.217: 6 Chirality restraints: 4478 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN B 824 " pdb=" N ASN B 824 " pdb=" C ASN B 824 " pdb=" CB ASN B 824 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 4475 not shown) Planarity restraints: 5210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 104 " -0.019 2.00e-02 2.50e+03 1.83e-02 8.34e+00 pdb=" CG TRP A 104 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 104 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 104 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 104 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 104 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 421 " -0.017 2.00e-02 2.50e+03 1.91e-02 7.31e+00 pdb=" CG TYR C 421 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR C 421 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 421 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR C 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 421 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 421 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 421 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO A 337 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.036 5.00e-02 4.00e+02 ... (remaining 5207 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1369 2.73 - 3.27: 28063 3.27 - 3.81: 47436 3.81 - 4.36: 54668 4.36 - 4.90: 95587 Nonbonded interactions: 227123 Sorted by model distance: nonbonded pdb=" OE2 GLU B 773 " pdb=" NE2 GLN B 774 " model vdw 2.186 3.120 nonbonded pdb=" OG SER C 721 " pdb=" OG1 THR C1066 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR C 380 " pdb=" O SER F 30 " model vdw 2.212 3.040 nonbonded pdb=" NZ LYS B 733 " pdb=" O PRO B 862 " model vdw 2.220 3.120 nonbonded pdb=" OE1 GLN A 134 " pdb=" OG SER A 161 " model vdw 2.238 3.040 ... (remaining 227118 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' selection = (chain 'B' and (resid 13 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 827 or resid 854 through 1147)) \ selection = (chain 'C' and (resid 13 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.620 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 29418 Z= 0.118 Angle : 0.529 7.565 40070 Z= 0.294 Chirality : 0.043 0.217 4478 Planarity : 0.004 0.066 5210 Dihedral : 13.709 89.703 10485 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.42 % Favored : 94.28 % Rotamer: Outliers : 0.16 % Allowed : 0.31 % Favored : 99.53 % 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: -0.06 (0.14), residues: 3653 helix: 1.65 (0.20), residues: 724 sheet: 0.61 (0.18), residues: 816 loop : -0.95 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 357 TYR 0.047 0.001 TYR C 421 PHE 0.017 0.001 PHE C1121 TRP 0.048 0.001 TRP A 104 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00208 (29375) covalent geometry : angle 0.52954 (39984) SS BOND : bond 0.00130 ( 43) SS BOND : angle 0.46057 ( 86) hydrogen bonds : bond 0.13821 ( 1077) hydrogen bonds : angle 6.44267 ( 2997) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 331 time to evaluate : 1.038 Fit side-chains REVERT: B 146 HIS cc_start: 0.7101 (m90) cc_final: 0.6545 (m90) REVERT: B 153 MET cc_start: 0.6648 (mpp) cc_final: 0.6300 (mpt) REVERT: C 113 LYS cc_start: 0.9052 (tptp) cc_final: 0.8814 (tptp) REVERT: C 198 ASP cc_start: 0.7640 (t0) cc_final: 0.7393 (t0) REVERT: C 1138 TYR cc_start: 0.6768 (t80) cc_final: 0.6471 (t80) REVERT: D 83 MET cc_start: -0.0579 (mmt) cc_final: -0.1271 (mpt) outliers start: 5 outliers final: 4 residues processed: 334 average time/residue: 0.4824 time to fit residues: 198.0192 Evaluate side-chains 212 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0030 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 913 GLN B 954 GLN C 146 HIS C 580 GLN C 856 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.181812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.131318 restraints weight = 62049.429| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.60 r_work: 0.3791 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29418 Z= 0.115 Angle : 0.542 10.746 40070 Z= 0.277 Chirality : 0.044 0.184 4478 Planarity : 0.004 0.050 5210 Dihedral : 4.164 129.368 3983 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.42 % Favored : 94.36 % Rotamer: Outliers : 1.32 % Allowed : 8.44 % Favored : 90.24 % 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: -0.07 (0.14), residues: 3653 helix: 1.58 (0.20), residues: 730 sheet: 0.55 (0.17), residues: 846 loop : -0.93 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 765 TYR 0.018 0.001 TYR B1067 PHE 0.032 0.001 PHE A 201 TRP 0.036 0.001 TRP A 104 HIS 0.004 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00250 (29375) covalent geometry : angle 0.54207 (39984) SS BOND : bond 0.00515 ( 43) SS BOND : angle 0.56680 ( 86) hydrogen bonds : bond 0.03324 ( 1077) hydrogen bonds : angle 5.20948 ( 2997) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7891 (m-10) cc_final: 0.7504 (m-10) REVERT: A 80 ASP cc_start: 0.7015 (m-30) cc_final: 0.6303 (m-30) REVERT: A 81 ASN cc_start: 0.7922 (m-40) cc_final: 0.7657 (p0) REVERT: A 177 MET cc_start: 0.2856 (mpt) cc_final: 0.2471 (pmm) REVERT: A 675 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7735 (pp30) REVERT: A 1081 ILE cc_start: 0.5292 (OUTLIER) cc_final: 0.4784 (mp) REVERT: B 146 HIS cc_start: 0.7323 (m90) cc_final: 0.6529 (m90) REVERT: B 153 MET cc_start: 0.7582 (mpp) cc_final: 0.6493 (mpt) REVERT: B 269 TYR cc_start: 0.7544 (m-80) cc_final: 0.7324 (m-80) REVERT: B 731 MET cc_start: 0.5013 (ppp) cc_final: 0.4697 (ppp) REVERT: B 869 MET cc_start: 0.6242 (ptt) cc_final: 0.5834 (ptm) REVERT: C 113 LYS cc_start: 0.9174 (tptp) cc_final: 0.8931 (tptp) REVERT: C 129 LYS cc_start: 0.7353 (tptt) cc_final: 0.7065 (tptt) REVERT: C 198 ASP cc_start: 0.8141 (t0) cc_final: 0.7767 (t0) REVERT: C 202 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7560 (mmtm) REVERT: C 238 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7788 (p90) REVERT: C 314 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: C 354 ASN cc_start: 0.6998 (t0) cc_final: 0.6524 (p0) REVERT: C 614 ASP cc_start: 0.7070 (t70) cc_final: 0.6804 (t0) REVERT: C 661 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: C 823 PHE cc_start: 0.7005 (t80) cc_final: 0.6541 (t80) REVERT: C 1138 TYR cc_start: 0.7287 (t80) cc_final: 0.6765 (t80) REVERT: D 83 MET cc_start: -0.0041 (mmt) cc_final: -0.1253 (mpt) outliers start: 42 outliers final: 11 residues processed: 266 average time/residue: 0.4785 time to fit residues: 157.0523 Evaluate side-chains 224 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 661 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 306 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 255 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 347 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 86 optimal weight: 0.3980 chunk 194 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN B 954 GLN C 856 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.176689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.124611 restraints weight = 61311.109| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.86 r_work: 0.3658 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29418 Z= 0.172 Angle : 0.575 8.959 40070 Z= 0.299 Chirality : 0.045 0.178 4478 Planarity : 0.004 0.049 5210 Dihedral : 3.867 26.636 3978 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.47 % Favored : 94.31 % Rotamer: Outliers : 1.89 % Allowed : 10.65 % Favored : 87.46 % 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: -0.20 (0.14), residues: 3653 helix: 1.40 (0.19), residues: 706 sheet: 0.42 (0.17), residues: 859 loop : -0.93 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.020 0.001 TYR A1067 PHE 0.024 0.002 PHE B 898 TRP 0.029 0.002 TRP E 36 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00395 (29375) covalent geometry : angle 0.57466 (39984) SS BOND : bond 0.00313 ( 43) SS BOND : angle 0.70274 ( 86) hydrogen bonds : bond 0.03922 ( 1077) hydrogen bonds : angle 5.18209 ( 2997) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8120 (m-40) cc_final: 0.7814 (p0) REVERT: A 542 ASN cc_start: 0.9138 (t0) cc_final: 0.8933 (t0) REVERT: A 675 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7944 (pp30) REVERT: A 1081 ILE cc_start: 0.5263 (OUTLIER) cc_final: 0.4657 (mp) REVERT: B 146 HIS cc_start: 0.7408 (m90) cc_final: 0.6650 (m90) REVERT: B 153 MET cc_start: 0.7621 (mpp) cc_final: 0.6605 (mpt) REVERT: B 242 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7639 (tm) REVERT: B 731 MET cc_start: 0.5690 (ppp) cc_final: 0.5392 (ppp) REVERT: B 906 PHE cc_start: 0.7338 (m-80) cc_final: 0.6589 (t80) REVERT: C 113 LYS cc_start: 0.9204 (tptp) cc_final: 0.8981 (tptp) REVERT: C 129 LYS cc_start: 0.7457 (tptt) cc_final: 0.7075 (tptt) REVERT: C 153 MET cc_start: 0.8641 (tpp) cc_final: 0.8331 (tmm) REVERT: C 238 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8010 (p90) REVERT: C 354 ASN cc_start: 0.7075 (t0) cc_final: 0.6630 (p0) REVERT: C 614 ASP cc_start: 0.7452 (t70) cc_final: 0.7195 (t0) REVERT: C 661 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: C 785 VAL cc_start: 0.7589 (p) cc_final: 0.7337 (m) REVERT: C 823 PHE cc_start: 0.6902 (t80) cc_final: 0.6457 (t80) REVERT: C 957 GLN cc_start: 0.8134 (tp40) cc_final: 0.7701 (tp40) REVERT: C 1038 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6143 (tmtt) REVERT: C 1138 TYR cc_start: 0.7433 (t80) cc_final: 0.6794 (t80) REVERT: D 83 MET cc_start: 0.0069 (mmt) cc_final: -0.1337 (mpt) outliers start: 60 outliers final: 23 residues processed: 254 average time/residue: 0.4384 time to fit residues: 140.1546 Evaluate side-chains 216 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 138 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 341 optimal weight: 3.9990 chunk 315 optimal weight: 0.5980 chunk 323 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 356 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN B 954 GLN C 146 HIS C 856 ASN F 1 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.174944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.123008 restraints weight = 59985.589| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.41 r_work: 0.3675 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29418 Z= 0.179 Angle : 0.576 9.137 40070 Z= 0.296 Chirality : 0.045 0.274 4478 Planarity : 0.004 0.054 5210 Dihedral : 3.968 21.730 3977 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % Rotamer: Outliers : 2.17 % Allowed : 12.94 % Favored : 84.88 % 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: -0.36 (0.14), residues: 3653 helix: 1.12 (0.19), residues: 719 sheet: 0.30 (0.17), residues: 854 loop : -0.97 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.016 0.001 TYR C 279 PHE 0.030 0.002 PHE A 106 TRP 0.026 0.002 TRP A 104 HIS 0.010 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00414 (29375) covalent geometry : angle 0.57615 (39984) SS BOND : bond 0.00304 ( 43) SS BOND : angle 0.67954 ( 86) hydrogen bonds : bond 0.03913 ( 1077) hydrogen bonds : angle 5.23287 ( 2997) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 0.910 Fit side-chains REVERT: A 79 PHE cc_start: 0.8119 (m-10) cc_final: 0.7774 (m-10) REVERT: A 177 MET cc_start: 0.2963 (mpt) cc_final: 0.2605 (pmm) REVERT: A 542 ASN cc_start: 0.9055 (t0) cc_final: 0.8854 (t0) REVERT: A 1081 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.4861 (mp) REVERT: B 94 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7628 (t) REVERT: B 146 HIS cc_start: 0.7395 (m90) cc_final: 0.6655 (m90) REVERT: B 153 MET cc_start: 0.7595 (mpp) cc_final: 0.6595 (mpt) REVERT: B 731 MET cc_start: 0.6170 (ppp) cc_final: 0.5836 (ppp) REVERT: B 740 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8512 (ttt) REVERT: B 773 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: C 113 LYS cc_start: 0.9117 (tptp) cc_final: 0.8899 (tptp) REVERT: C 153 MET cc_start: 0.8597 (tpp) cc_final: 0.8394 (tmm) REVERT: C 198 ASP cc_start: 0.8288 (t0) cc_final: 0.8074 (t0) REVERT: C 238 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8016 (p90) REVERT: C 354 ASN cc_start: 0.7139 (t0) cc_final: 0.6679 (p0) REVERT: C 614 ASP cc_start: 0.7501 (t70) cc_final: 0.7213 (t0) REVERT: C 661 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: C 957 GLN cc_start: 0.8072 (tp40) cc_final: 0.7622 (tp40) REVERT: C 1017 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: C 1038 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6117 (tmtt) REVERT: C 1138 TYR cc_start: 0.7493 (t80) cc_final: 0.6886 (t80) REVERT: D 83 MET cc_start: 0.0064 (mmt) cc_final: -0.1284 (mpt) outliers start: 69 outliers final: 31 residues processed: 244 average time/residue: 0.4742 time to fit residues: 143.9564 Evaluate side-chains 216 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 chunk 255 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 GLN C 764 ASN C 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.174775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.121175 restraints weight = 60904.208| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.65 r_work: 0.3638 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29418 Z= 0.140 Angle : 0.554 9.939 40070 Z= 0.283 Chirality : 0.044 0.170 4478 Planarity : 0.004 0.052 5210 Dihedral : 3.925 22.468 3977 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.53 % Favored : 94.25 % Rotamer: Outliers : 2.05 % Allowed : 14.14 % Favored : 83.81 % 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: -0.36 (0.14), residues: 3653 helix: 1.22 (0.19), residues: 721 sheet: 0.25 (0.17), residues: 861 loop : -1.00 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.017 0.001 TYR A1067 PHE 0.031 0.001 PHE B 888 TRP 0.022 0.001 TRP E 36 HIS 0.021 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00319 (29375) covalent geometry : angle 0.55403 (39984) SS BOND : bond 0.00237 ( 43) SS BOND : angle 0.61074 ( 86) hydrogen bonds : bond 0.03721 ( 1077) hydrogen bonds : angle 5.15462 ( 2997) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 1.016 Fit side-chains REVERT: A 542 ASN cc_start: 0.9079 (t0) cc_final: 0.8848 (t0) REVERT: A 1063 LEU cc_start: 0.6921 (mt) cc_final: 0.6694 (mp) REVERT: A 1081 ILE cc_start: 0.5343 (OUTLIER) cc_final: 0.4819 (mp) REVERT: B 94 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7666 (t) REVERT: B 146 HIS cc_start: 0.7409 (m90) cc_final: 0.6960 (m90) REVERT: B 153 MET cc_start: 0.7646 (mpp) cc_final: 0.7317 (mpt) REVERT: B 731 MET cc_start: 0.6054 (ppp) cc_final: 0.5671 (ppp) REVERT: B 740 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8510 (ttt) REVERT: B 773 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: B 886 TRP cc_start: 0.6799 (p90) cc_final: 0.6541 (p90) REVERT: C 113 LYS cc_start: 0.9148 (tptp) cc_final: 0.8925 (tptp) REVERT: C 153 MET cc_start: 0.8599 (tpp) cc_final: 0.8155 (pp-130) REVERT: C 198 ASP cc_start: 0.8553 (t0) cc_final: 0.8302 (t0) REVERT: C 238 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7888 (p90) REVERT: C 354 ASN cc_start: 0.7098 (t0) cc_final: 0.6644 (p0) REVERT: C 571 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8269 (t0) REVERT: C 614 ASP cc_start: 0.7620 (t70) cc_final: 0.7339 (t0) REVERT: C 661 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: C 957 GLN cc_start: 0.8235 (tp40) cc_final: 0.7746 (tp40) REVERT: C 1017 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7589 (mm-30) REVERT: C 1038 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5942 (tmtt) REVERT: C 1138 TYR cc_start: 0.7423 (t80) cc_final: 0.6761 (t80) REVERT: D 83 MET cc_start: 0.0147 (mmt) cc_final: -0.1231 (mpt) outliers start: 65 outliers final: 33 residues processed: 244 average time/residue: 0.4189 time to fit residues: 128.8358 Evaluate side-chains 222 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1063 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 247 optimal weight: 0.7980 chunk 301 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 157 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 913 GLN C 87 ASN C 580 GLN C 856 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.172398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.121166 restraints weight = 60638.445| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.47 r_work: 0.3634 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29418 Z= 0.205 Angle : 0.618 10.206 40070 Z= 0.317 Chirality : 0.046 0.199 4478 Planarity : 0.004 0.055 5210 Dihedral : 4.237 24.533 3977 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.43 % Rotamer: Outliers : 2.68 % Allowed : 14.39 % Favored : 82.93 % 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: -0.62 (0.14), residues: 3653 helix: 0.87 (0.19), residues: 713 sheet: 0.11 (0.17), residues: 858 loop : -1.12 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.022 0.001 TYR C 873 PHE 0.032 0.002 PHE B 888 TRP 0.026 0.002 TRP E 36 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00472 (29375) covalent geometry : angle 0.61728 (39984) SS BOND : bond 0.00344 ( 43) SS BOND : angle 0.75577 ( 86) hydrogen bonds : bond 0.04275 ( 1077) hydrogen bonds : angle 5.40067 ( 2997) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 192 time to evaluate : 1.202 Fit side-chains REVERT: A 177 MET cc_start: 0.3032 (mpt) cc_final: 0.2577 (pmm) REVERT: B 94 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7615 (t) REVERT: B 146 HIS cc_start: 0.7342 (m90) cc_final: 0.6636 (m90) REVERT: B 153 MET cc_start: 0.7427 (mpp) cc_final: 0.6912 (mpt) REVERT: B 173 GLN cc_start: 0.8333 (pp30) cc_final: 0.7902 (pp30) REVERT: B 628 GLN cc_start: 0.7660 (mp10) cc_final: 0.7385 (pm20) REVERT: B 731 MET cc_start: 0.6255 (ppp) cc_final: 0.6040 (ppp) REVERT: C 113 LYS cc_start: 0.9091 (tptp) cc_final: 0.8859 (tptp) REVERT: C 129 LYS cc_start: 0.7577 (tptt) cc_final: 0.7370 (tptt) REVERT: C 153 MET cc_start: 0.8604 (tpp) cc_final: 0.8184 (pp-130) REVERT: C 354 ASN cc_start: 0.7307 (t0) cc_final: 0.6806 (p0) REVERT: C 614 ASP cc_start: 0.7713 (t70) cc_final: 0.7494 (t0) REVERT: C 661 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: C 957 GLN cc_start: 0.8172 (tp40) cc_final: 0.7681 (tp-100) REVERT: C 1038 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6080 (tmtt) REVERT: C 1138 TYR cc_start: 0.7355 (t80) cc_final: 0.6822 (t80) REVERT: D 53 TRP cc_start: 0.1000 (p90) cc_final: 0.0450 (p90) REVERT: D 83 MET cc_start: 0.0160 (mmt) cc_final: -0.1287 (mpt) outliers start: 85 outliers final: 47 residues processed: 260 average time/residue: 0.4454 time to fit residues: 144.7990 Evaluate side-chains 228 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain F residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 286 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 344 optimal weight: 0.3980 chunk 314 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 214 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 137 ASN B 474 GLN B 913 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.174681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123061 restraints weight = 60567.394| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.83 r_work: 0.3654 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29418 Z= 0.124 Angle : 0.574 10.885 40070 Z= 0.288 Chirality : 0.044 0.183 4478 Planarity : 0.004 0.070 5210 Dihedral : 4.008 23.364 3977 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer: Outliers : 2.02 % Allowed : 16.03 % Favored : 81.95 % 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 (0.14), residues: 3653 helix: 1.25 (0.20), residues: 706 sheet: 0.10 (0.17), residues: 865 loop : -1.07 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.017 0.001 TYR A1067 PHE 0.035 0.001 PHE B 888 TRP 0.031 0.001 TRP E 36 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00279 (29375) covalent geometry : angle 0.57408 (39984) SS BOND : bond 0.00218 ( 43) SS BOND : angle 0.61221 ( 86) hydrogen bonds : bond 0.03668 ( 1077) hydrogen bonds : angle 5.19449 ( 2997) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7308 (p0) cc_final: 0.6994 (p0) REVERT: A 230 PRO cc_start: 0.9014 (Cg_endo) cc_final: 0.8665 (Cg_exo) REVERT: A 542 ASN cc_start: 0.9080 (t0) cc_final: 0.8778 (t0) REVERT: B 94 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7569 (t) REVERT: B 146 HIS cc_start: 0.7296 (m90) cc_final: 0.6883 (m90) REVERT: B 153 MET cc_start: 0.7444 (mpp) cc_final: 0.7223 (mpt) REVERT: B 731 MET cc_start: 0.6258 (ppp) cc_final: 0.5946 (ppp) REVERT: C 113 LYS cc_start: 0.9103 (tptp) cc_final: 0.8875 (tptp) REVERT: C 153 MET cc_start: 0.8549 (tpp) cc_final: 0.8272 (pp-130) REVERT: C 244 LEU cc_start: 0.4506 (pt) cc_final: 0.4076 (pt) REVERT: C 354 ASN cc_start: 0.7297 (t0) cc_final: 0.6790 (p0) REVERT: C 614 ASP cc_start: 0.7722 (t70) cc_final: 0.7466 (t0) REVERT: C 661 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: C 901 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5626 (pt0) REVERT: C 957 GLN cc_start: 0.8120 (tp40) cc_final: 0.7629 (tp-100) REVERT: C 1038 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5965 (tmtt) REVERT: C 1060 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 1138 TYR cc_start: 0.7356 (t80) cc_final: 0.6786 (t80) REVERT: D 83 MET cc_start: 0.0461 (mmt) cc_final: -0.0875 (mpt) outliers start: 64 outliers final: 39 residues processed: 255 average time/residue: 0.4440 time to fit residues: 141.8074 Evaluate side-chains 231 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1063 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 185 optimal weight: 0.6980 chunk 139 optimal weight: 0.3980 chunk 157 optimal weight: 20.0000 chunk 248 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 247 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 GLN C 762 GLN C 856 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.175454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.123933 restraints weight = 61108.065| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.60 r_work: 0.3687 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29418 Z= 0.111 Angle : 0.575 10.782 40070 Z= 0.287 Chirality : 0.044 0.179 4478 Planarity : 0.004 0.061 5210 Dihedral : 3.913 24.247 3977 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.58 % Favored : 94.17 % Rotamer: Outliers : 1.95 % Allowed : 16.91 % Favored : 81.13 % 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: -0.39 (0.14), residues: 3653 helix: 1.39 (0.20), residues: 707 sheet: 0.15 (0.17), residues: 855 loop : -1.04 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.014 0.001 TYR C 612 PHE 0.030 0.001 PHE C 823 TRP 0.040 0.001 TRP E 36 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00247 (29375) covalent geometry : angle 0.57454 (39984) SS BOND : bond 0.00192 ( 43) SS BOND : angle 0.60451 ( 86) hydrogen bonds : bond 0.03507 ( 1077) hydrogen bonds : angle 5.08118 ( 2997) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7292 (p0) cc_final: 0.6935 (p0) REVERT: A 102 ARG cc_start: 0.6463 (mmp80) cc_final: 0.5807 (mpp-170) REVERT: A 177 MET cc_start: 0.3292 (mpt) cc_final: 0.2831 (pmm) REVERT: A 230 PRO cc_start: 0.8870 (Cg_endo) cc_final: 0.8592 (Cg_exo) REVERT: B 94 SER cc_start: 0.7845 (OUTLIER) cc_final: 0.7565 (t) REVERT: B 146 HIS cc_start: 0.7328 (m90) cc_final: 0.6902 (m90) REVERT: B 153 MET cc_start: 0.7404 (mpp) cc_final: 0.7164 (mpt) REVERT: B 173 GLN cc_start: 0.8280 (pp30) cc_final: 0.7942 (pp30) REVERT: B 269 TYR cc_start: 0.7592 (m-80) cc_final: 0.7391 (m-80) REVERT: B 731 MET cc_start: 0.6080 (ppp) cc_final: 0.5720 (ppp) REVERT: B 985 ASP cc_start: 0.7791 (p0) cc_final: 0.7531 (p0) REVERT: C 153 MET cc_start: 0.8552 (tpp) cc_final: 0.8304 (pp-130) REVERT: C 244 LEU cc_start: 0.4576 (pt) cc_final: 0.4262 (pt) REVERT: C 354 ASN cc_start: 0.7254 (t0) cc_final: 0.6762 (p0) REVERT: C 365 TYR cc_start: 0.6534 (p90) cc_final: 0.4949 (p90) REVERT: C 614 ASP cc_start: 0.7660 (t70) cc_final: 0.7406 (t0) REVERT: C 661 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: C 957 GLN cc_start: 0.8047 (tp40) cc_final: 0.7570 (tp40) REVERT: C 1038 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5925 (tmtt) REVERT: C 1060 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7984 (p) REVERT: C 1138 TYR cc_start: 0.7358 (t80) cc_final: 0.6800 (t80) REVERT: D 83 MET cc_start: 0.0818 (mmt) cc_final: -0.0522 (mpt) outliers start: 62 outliers final: 42 residues processed: 248 average time/residue: 0.4444 time to fit residues: 138.2987 Evaluate side-chains 227 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1063 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 336 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 GLN C 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.174244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.122446 restraints weight = 60808.849| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.79 r_work: 0.3643 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29418 Z= 0.148 Angle : 0.602 11.155 40070 Z= 0.301 Chirality : 0.045 0.193 4478 Planarity : 0.004 0.055 5210 Dihedral : 4.003 26.293 3977 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.02 % Favored : 93.73 % Rotamer: Outliers : 1.92 % Allowed : 17.13 % Favored : 80.94 % 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: -0.45 (0.14), residues: 3653 helix: 1.26 (0.20), residues: 715 sheet: 0.09 (0.17), residues: 863 loop : -1.05 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.027 0.001 TYR A1067 PHE 0.032 0.001 PHE C 823 TRP 0.044 0.002 TRP E 36 HIS 0.003 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00337 (29375) covalent geometry : angle 0.60192 (39984) SS BOND : bond 0.00235 ( 43) SS BOND : angle 0.61798 ( 86) hydrogen bonds : bond 0.03754 ( 1077) hydrogen bonds : angle 5.13101 ( 2997) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7390 (p0) cc_final: 0.7033 (p0) REVERT: A 102 ARG cc_start: 0.6488 (mmp80) cc_final: 0.6069 (mpp-170) REVERT: A 177 MET cc_start: 0.3364 (mpt) cc_final: 0.2904 (pmm) REVERT: A 230 PRO cc_start: 0.8912 (Cg_endo) cc_final: 0.8553 (Cg_exo) REVERT: A 636 TYR cc_start: 0.7134 (m-80) cc_final: 0.6651 (m-80) REVERT: B 94 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7588 (t) REVERT: B 146 HIS cc_start: 0.7413 (m90) cc_final: 0.6976 (m90) REVERT: B 153 MET cc_start: 0.7483 (mpp) cc_final: 0.7218 (mpt) REVERT: B 731 MET cc_start: 0.6187 (ppp) cc_final: 0.5878 (ppp) REVERT: B 821 LEU cc_start: 0.8407 (mp) cc_final: 0.8171 (mm) REVERT: C 102 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8091 (mpt180) REVERT: C 153 MET cc_start: 0.8579 (tpp) cc_final: 0.8280 (pp-130) REVERT: C 244 LEU cc_start: 0.4794 (pt) cc_final: 0.4450 (pt) REVERT: C 354 ASN cc_start: 0.7233 (t0) cc_final: 0.6747 (p0) REVERT: C 365 TYR cc_start: 0.6608 (p90) cc_final: 0.4975 (p90) REVERT: C 614 ASP cc_start: 0.7822 (t70) cc_final: 0.7591 (t0) REVERT: C 661 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: C 957 GLN cc_start: 0.8142 (tp40) cc_final: 0.7662 (tp40) REVERT: C 1038 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5993 (tmtt) REVERT: C 1060 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7969 (p) REVERT: C 1138 TYR cc_start: 0.7453 (t80) cc_final: 0.6872 (t80) REVERT: D 83 MET cc_start: 0.0872 (mmt) cc_final: -0.0479 (mpt) outliers start: 61 outliers final: 43 residues processed: 243 average time/residue: 0.4368 time to fit residues: 133.3066 Evaluate side-chains 233 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1063 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 143 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 GLN C 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.123182 restraints weight = 60818.917| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.86 r_work: 0.3641 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29418 Z= 0.130 Angle : 0.594 10.111 40070 Z= 0.298 Chirality : 0.044 0.197 4478 Planarity : 0.004 0.053 5210 Dihedral : 3.983 26.485 3977 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.02 % Favored : 93.73 % Rotamer: Outliers : 1.70 % Allowed : 17.48 % Favored : 80.82 % 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: -0.44 (0.14), residues: 3653 helix: 1.30 (0.20), residues: 709 sheet: 0.13 (0.18), residues: 851 loop : -1.06 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.017 0.001 TYR C 612 PHE 0.053 0.001 PHE C 515 TRP 0.046 0.002 TRP E 36 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00297 (29375) covalent geometry : angle 0.59448 (39984) SS BOND : bond 0.00215 ( 43) SS BOND : angle 0.60083 ( 86) hydrogen bonds : bond 0.03651 ( 1077) hydrogen bonds : angle 5.10595 ( 2997) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7383 (p0) cc_final: 0.7015 (p0) REVERT: A 102 ARG cc_start: 0.6509 (mmp80) cc_final: 0.5795 (mpp-170) REVERT: A 177 MET cc_start: 0.3225 (mpt) cc_final: 0.2747 (pmm) REVERT: A 230 PRO cc_start: 0.8866 (Cg_endo) cc_final: 0.8522 (Cg_exo) REVERT: A 636 TYR cc_start: 0.7139 (m-80) cc_final: 0.6664 (m-80) REVERT: A 1067 TYR cc_start: 0.7444 (t80) cc_final: 0.7215 (t80) REVERT: B 94 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7579 (t) REVERT: B 146 HIS cc_start: 0.7402 (m90) cc_final: 0.6927 (m90) REVERT: B 153 MET cc_start: 0.7487 (mpp) cc_final: 0.7184 (mpt) REVERT: B 173 GLN cc_start: 0.8312 (pp30) cc_final: 0.7971 (pp30) REVERT: B 731 MET cc_start: 0.6162 (ppp) cc_final: 0.5857 (ppp) REVERT: B 821 LEU cc_start: 0.8422 (mp) cc_final: 0.8199 (mm) REVERT: C 153 MET cc_start: 0.8574 (tpp) cc_final: 0.8277 (pp-130) REVERT: C 244 LEU cc_start: 0.4820 (pt) cc_final: 0.4517 (pt) REVERT: C 354 ASN cc_start: 0.7232 (t0) cc_final: 0.6746 (p0) REVERT: C 614 ASP cc_start: 0.7858 (t70) cc_final: 0.7623 (t0) REVERT: C 661 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: C 957 GLN cc_start: 0.8159 (tp40) cc_final: 0.7681 (tp40) REVERT: C 1038 LYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5982 (tmtt) REVERT: C 1060 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7976 (p) REVERT: C 1138 TYR cc_start: 0.7401 (t80) cc_final: 0.6817 (t80) REVERT: D 83 MET cc_start: 0.0785 (mmt) cc_final: -0.0551 (mpt) outliers start: 54 outliers final: 43 residues processed: 238 average time/residue: 0.4607 time to fit residues: 136.5019 Evaluate side-chains 233 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1063 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 146 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 217 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 297 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 GLN C 146 HIS C 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.175002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.123642 restraints weight = 61015.304| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.86 r_work: 0.3658 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29418 Z= 0.122 Angle : 0.596 11.277 40070 Z= 0.297 Chirality : 0.044 0.204 4478 Planarity : 0.004 0.052 5210 Dihedral : 3.945 26.095 3977 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.02 % Favored : 93.73 % Rotamer: Outliers : 1.89 % Allowed : 17.45 % Favored : 80.66 % 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: -0.39 (0.14), residues: 3653 helix: 1.39 (0.20), residues: 708 sheet: 0.17 (0.18), residues: 844 loop : -1.05 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.015 0.001 TYR C 612 PHE 0.031 0.001 PHE C 823 TRP 0.045 0.002 TRP E 36 HIS 0.004 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00276 (29375) covalent geometry : angle 0.59555 (39984) SS BOND : bond 0.00198 ( 43) SS BOND : angle 0.58979 ( 86) hydrogen bonds : bond 0.03574 ( 1077) hydrogen bonds : angle 5.06161 ( 2997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11163.87 seconds wall clock time: 190 minutes 16.25 seconds (11416.25 seconds total)