Starting phenix.real_space_refine on Mon Aug 25 10:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gou_34181/08_2025/8gou_34181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gou_34181/08_2025/8gou_34181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gou_34181/08_2025/8gou_34181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gou_34181/08_2025/8gou_34181.map" model { file = "/net/cci-nas-00/data/ceres_data/8gou_34181/08_2025/8gou_34181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gou_34181/08_2025/8gou_34181.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 17316 2.51 5 N 4467 2.21 5 O 5202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27108 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7754 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 6, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7705 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 10, 'GLN:plan1': 10, 'ASN:plan1': 7, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 798 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.89, per 1000 atoms: 0.22 Number of scatterers: 27108 At special positions: 0 Unit cell: (142.68, 200.9, 180.4, 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 5202 8.00 N 4467 7.00 C 17316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 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 I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6554 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.654A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.516A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.497A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.507A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.783A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.667A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.902A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.621A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.996A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.090A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.786A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.559A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.822A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.020A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.026A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.543A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.595A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.574A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.699A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.565A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.502A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.092A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.880A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.684A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.423A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.183A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.751A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.433A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.754A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.937A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.047A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.047A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.099A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.402A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.601A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.232A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.983A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.266A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.585A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.838A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.684A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.993A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.993A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.542A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.457A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.501A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.601A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.564A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.198A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE2, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.421A pdb=" N LYS C 424 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.214A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.915A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.915A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.445A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.408A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 5.148A pdb=" N GLY I 16 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.155A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.281A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AF5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.517A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.210A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.555A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 1139 hydrogen bonds defined for protein. 3018 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: 6.20 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8650 1.34 - 1.48: 7601 1.48 - 1.62: 11339 1.62 - 1.76: 8 1.76 - 1.90: 147 Bond restraints: 27745 Sorted by residual: bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.86e+00 bond pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.23e-02 6.61e+03 8.87e+00 bond pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.69e+00 bond pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 1.808 1.900 -0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" N PHE A 377 " pdb=" CA PHE A 377 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.19e+00 ... (remaining 27740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 36798 2.52 - 5.05: 959 5.05 - 7.57: 91 7.57 - 10.09: 26 10.09 - 12.62: 3 Bond angle restraints: 37877 Sorted by residual: angle pdb=" CA CYS B 538 " pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " ideal model delta sigma weight residual 114.40 127.02 -12.62 2.30e+00 1.89e-01 3.01e+01 angle pdb=" N TYR K 51 " pdb=" CA TYR K 51 " pdb=" C TYR K 51 " ideal model delta sigma weight residual 109.52 101.09 8.43 1.55e+00 4.16e-01 2.96e+01 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 106.21 111.57 -5.36 1.07e+00 8.73e-01 2.51e+01 angle pdb=" N TYR J 51 " pdb=" CA TYR J 51 " pdb=" C TYR J 51 " ideal model delta sigma weight residual 109.52 101.84 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 ... (remaining 37872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 15256 17.32 - 34.63: 1189 34.63 - 51.95: 285 51.95 - 69.27: 67 69.27 - 86.58: 24 Dihedral angle restraints: 16821 sinusoidal: 6604 harmonic: 10217 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.60 -83.40 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.42 -81.58 1 1.00e+01 1.00e-02 8.19e+01 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 -86.00 -4.48 -81.52 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 16818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4296 0.128 - 0.255: 115 0.255 - 0.383: 2 0.383 - 0.511: 0 0.511 - 0.638: 1 Chirality restraints: 4414 Sorted by residual: chirality pdb=" CB THR B 167 " pdb=" CA THR B 167 " pdb=" OG1 THR B 167 " pdb=" CG2 THR B 167 " both_signs ideal model delta sigma weight residual False 2.55 1.91 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CB ILE C 434 " pdb=" CA ILE C 434 " pdb=" CG1 ILE C 434 " pdb=" CG2 ILE C 434 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA CYS A 649 " pdb=" N CYS A 649 " pdb=" C CYS A 649 " pdb=" CB CYS A 649 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4411 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO C 373 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.063 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO B 373 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 330 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.047 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 642 2.66 - 3.22: 26611 3.22 - 3.78: 41095 3.78 - 4.34: 54564 4.34 - 4.90: 90672 Nonbonded interactions: 213584 Sorted by model distance: nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.098 3.040 nonbonded pdb=" ND2 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.104 3.120 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.106 3.040 nonbonded pdb=" O ASN B 81 " pdb=" NE2 GLN B 239 " model vdw 2.125 3.120 nonbonded pdb=" O ASN C 978 " pdb=" OG SER C 982 " model vdw 2.125 3.040 ... (remaining 213579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 370 or (resid 371 through 372 and (name N or na \ me CA or name C or name O or name CB )) or resid 373 through 414 or (resid 415 a \ nd (name N or name CA or name C or name O or name CB )) or resid 416 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 and (name N or name CA or name C or name O or nam \ e CB )) or resid 422 through 426 or (resid 427 through 428 and (name N or name C \ A or name C or name O or name CB )) or resid 429 through 457 or (resid 458 and ( \ name N or name CA or name C or name O or name CB )) or resid 459 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 \ through 473 or (resid 474 through 475 and (name N or name CA or name C or name \ O or name CB )) or resid 476 through 477 or (resid 478 and (name N or name CA or \ name C or name O or name CB )) or resid 479 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 515 or (res \ id 516 and (name N or name CA or name C or name O or name CB )) or resid 517 thr \ ough 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) \ or resid 524 through 1312)) selection = (chain 'B' and resid 27 through 1312) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.990 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: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.540 Find NCS groups from input model: 0.550 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.008 0.139 27787 Z= 0.372 Angle : 0.985 12.618 37961 Z= 0.534 Chirality : 0.056 0.638 4414 Planarity : 0.005 0.101 4856 Dihedral : 13.468 86.582 10141 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.67 % Favored : 94.84 % Rotamer: Outliers : 1.54 % Allowed : 8.21 % Favored : 90.25 % 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 aren not related in a simple way. whole: -1.86 (0.13), residues: 3472 helix: 0.26 (0.20), residues: 641 sheet: -0.86 (0.15), residues: 938 loop : -2.02 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1000 TYR 0.039 0.003 TYR C 453 PHE 0.032 0.003 PHE A1089 TRP 0.050 0.004 TRP H 110 HIS 0.007 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00839 (27745) covalent geometry : angle 0.97245 (37877) SS BOND : bond 0.00759 ( 42) SS BOND : angle 3.42810 ( 84) hydrogen bonds : bond 0.21791 ( 1093) hydrogen bonds : angle 8.27244 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7564 (m-80) cc_final: 0.7329 (m-10) REVERT: A 169 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8591 (mm-30) REVERT: A 200 TYR cc_start: 0.9161 (m-80) cc_final: 0.8928 (m-80) REVERT: A 229 LEU cc_start: 0.9042 (mt) cc_final: 0.8833 (mt) REVERT: A 378 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8817 (mttt) REVERT: A 392 PHE cc_start: 0.8407 (m-80) cc_final: 0.8063 (m-10) REVERT: A 481 ASN cc_start: 0.9214 (m-40) cc_final: 0.8734 (p0) REVERT: A 516 GLU cc_start: 0.8254 (tt0) cc_final: 0.7889 (tm-30) REVERT: A 773 GLU cc_start: 0.7870 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 777 ASN cc_start: 0.8499 (m-40) cc_final: 0.7714 (m110) REVERT: A 780 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 983 ARG cc_start: 0.9010 (ptm-80) cc_final: 0.8769 (ttp80) REVERT: B 223 LEU cc_start: 0.9001 (mp) cc_final: 0.8642 (mt) REVERT: B 353 TRP cc_start: 0.7214 (p-90) cc_final: 0.6193 (p-90) REVERT: B 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.7767 (m-80) REVERT: B 823 PHE cc_start: 0.8651 (m-80) cc_final: 0.8281 (m-80) REVERT: B 964 LYS cc_start: 0.9375 (tptp) cc_final: 0.9027 (tppt) REVERT: B 1002 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 1005 GLN cc_start: 0.9345 (tp-100) cc_final: 0.8799 (tp-100) REVERT: C 360 ASN cc_start: 0.8967 (t0) cc_final: 0.8750 (p0) REVERT: C 779 GLN cc_start: 0.9237 (mm-40) cc_final: 0.9029 (tp40) REVERT: C 960 ASN cc_start: 0.9509 (t0) cc_final: 0.9106 (t0) REVERT: I 67 ARG cc_start: 0.7553 (ptt180) cc_final: 0.7146 (ptt180) REVERT: J 50 ILE cc_start: 0.9398 (mm) cc_final: 0.9119 (mm) outliers start: 43 outliers final: 18 residues processed: 255 average time/residue: 0.1850 time to fit residues: 71.6484 Evaluate side-chains 142 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 540 ASN A 657 ASN A 955 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN B 188 ASN B 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1134 ASN C 69 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 354 ASN C 417 ASN C 505 HIS C 709 ASN C 762 GLN C 926 GLN C1088 HIS K 81 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.088434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.053931 restraints weight = 119790.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055720 restraints weight = 54237.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056798 restraints weight = 33448.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057550 restraints weight = 24849.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058043 restraints weight = 20677.510| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27787 Z= 0.197 Angle : 0.678 9.405 37961 Z= 0.357 Chirality : 0.045 0.161 4414 Planarity : 0.005 0.055 4856 Dihedral : 6.863 59.890 4575 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 1.39 % Allowed : 11.25 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -1.10 (0.13), residues: 3472 helix: 1.30 (0.21), residues: 653 sheet: -0.41 (0.16), residues: 923 loop : -1.68 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.020 0.002 TYR B1067 PHE 0.022 0.002 PHE A 515 TRP 0.020 0.002 TRP B 353 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00448 (27745) covalent geometry : angle 0.67173 (37877) SS BOND : bond 0.00516 ( 42) SS BOND : angle 2.05585 ( 84) hydrogen bonds : bond 0.05531 ( 1093) hydrogen bonds : angle 6.49389 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9262 (m-80) cc_final: 0.8978 (m-80) REVERT: A 298 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8686 (tm-30) REVERT: A 378 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8636 (mmtm) REVERT: A 516 GLU cc_start: 0.8006 (tt0) cc_final: 0.7745 (tm-30) REVERT: A 725 GLU cc_start: 0.8487 (tt0) cc_final: 0.8118 (tt0) REVERT: A 773 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 1002 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8627 (tm-30) REVERT: A 1029 MET cc_start: 0.9399 (tpp) cc_final: 0.8632 (tpp) REVERT: B 336 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7356 (m) REVERT: B 353 TRP cc_start: 0.6144 (p-90) cc_final: 0.5258 (p-90) REVERT: B 365 TYR cc_start: 0.8096 (m-80) cc_final: 0.7718 (m-80) REVERT: B 515 PHE cc_start: 0.8892 (p90) cc_final: 0.8556 (p90) REVERT: B 964 LYS cc_start: 0.9450 (tptp) cc_final: 0.9039 (tppt) REVERT: B 1005 GLN cc_start: 0.9444 (tp-100) cc_final: 0.8857 (tp-100) REVERT: B 1029 MET cc_start: 0.9480 (tpp) cc_final: 0.9260 (tpp) REVERT: B 1138 TYR cc_start: 0.8603 (m-80) cc_final: 0.8398 (m-10) REVERT: C 282 ASN cc_start: 0.9374 (OUTLIER) cc_final: 0.9099 (m-40) REVERT: C 754 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9309 (mt) REVERT: C 779 GLN cc_start: 0.9344 (mm-40) cc_final: 0.9075 (tp40) REVERT: C 960 ASN cc_start: 0.9546 (t0) cc_final: 0.9234 (m110) REVERT: C 1029 MET cc_start: 0.9527 (tpp) cc_final: 0.9323 (tpp) REVERT: I 100 VAL cc_start: 0.8022 (p) cc_final: 0.7808 (p) outliers start: 39 outliers final: 21 residues processed: 193 average time/residue: 0.1607 time to fit residues: 50.4283 Evaluate side-chains 147 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 166 optimal weight: 0.9990 chunk 263 optimal weight: 0.0070 chunk 9 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 137 optimal weight: 40.0000 chunk 234 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 544 ASN B 30 ASN B 417 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052457 restraints weight = 121813.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054158 restraints weight = 57139.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055271 restraints weight = 36096.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055886 restraints weight = 27136.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056102 restraints weight = 22897.773| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 27787 Z= 0.256 Angle : 0.679 7.719 37961 Z= 0.354 Chirality : 0.045 0.184 4414 Planarity : 0.005 0.085 4856 Dihedral : 6.303 57.085 4562 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 2.71 % Allowed : 12.64 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.95 (0.14), residues: 3472 helix: 1.15 (0.20), residues: 663 sheet: -0.41 (0.16), residues: 942 loop : -1.42 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 983 TYR 0.022 0.002 TYR B1067 PHE 0.033 0.002 PHE A 375 TRP 0.017 0.002 TRP H 110 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00583 (27745) covalent geometry : angle 0.67323 (37877) SS BOND : bond 0.00553 ( 42) SS BOND : angle 1.92916 ( 84) hydrogen bonds : bond 0.05346 ( 1093) hydrogen bonds : angle 6.24320 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 126 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9238 (m-80) cc_final: 0.9015 (m-80) REVERT: A 298 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 378 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8724 (mmtm) REVERT: A 392 PHE cc_start: 0.8583 (m-80) cc_final: 0.8375 (m-80) REVERT: A 725 GLU cc_start: 0.8430 (tt0) cc_final: 0.8074 (tt0) REVERT: A 773 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 777 ASN cc_start: 0.8139 (m110) cc_final: 0.7889 (m-40) REVERT: A 1002 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 1029 MET cc_start: 0.9453 (tpp) cc_final: 0.8678 (tpp) REVERT: B 336 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7415 (m) REVERT: B 365 TYR cc_start: 0.7918 (m-80) cc_final: 0.7609 (m-80) REVERT: B 515 PHE cc_start: 0.8902 (p90) cc_final: 0.8677 (p90) REVERT: B 712 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9234 (mm) REVERT: B 791 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8787 (p) REVERT: B 960 ASN cc_start: 0.9584 (t0) cc_final: 0.9182 (t0) REVERT: B 964 LYS cc_start: 0.9488 (tptp) cc_final: 0.9119 (tppt) REVERT: B 1005 GLN cc_start: 0.9448 (tp-100) cc_final: 0.8893 (tp-100) REVERT: B 1029 MET cc_start: 0.9504 (tpp) cc_final: 0.9301 (tpp) REVERT: B 1138 TYR cc_start: 0.8591 (m-80) cc_final: 0.8368 (m-10) REVERT: C 712 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8916 (mm) REVERT: C 754 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9248 (mt) REVERT: C 779 GLN cc_start: 0.9358 (mm-40) cc_final: 0.9143 (tp-100) REVERT: C 960 ASN cc_start: 0.9537 (t0) cc_final: 0.9123 (t0) REVERT: C 1010 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8973 (mm-40) REVERT: I 67 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7484 (ptt-90) REVERT: J 8 ARG cc_start: 0.8292 (mmp-170) cc_final: 0.8008 (mmp-170) outliers start: 76 outliers final: 42 residues processed: 197 average time/residue: 0.1538 time to fit residues: 49.6154 Evaluate side-chains 160 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 87 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.087545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.052764 restraints weight = 120660.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054472 restraints weight = 56087.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055586 restraints weight = 35278.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056341 restraints weight = 26353.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056696 restraints weight = 22050.050| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 27787 Z= 0.184 Angle : 0.599 6.799 37961 Z= 0.315 Chirality : 0.043 0.159 4414 Planarity : 0.005 0.078 4856 Dihedral : 5.930 56.273 4560 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 3.11 % Allowed : 13.36 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.73 (0.14), residues: 3472 helix: 1.35 (0.20), residues: 663 sheet: -0.31 (0.16), residues: 929 loop : -1.27 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 112 TYR 0.018 0.001 TYR B1067 PHE 0.038 0.001 PHE A 371 TRP 0.016 0.001 TRP B 353 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00419 (27745) covalent geometry : angle 0.59471 (37877) SS BOND : bond 0.00489 ( 42) SS BOND : angle 1.64284 ( 84) hydrogen bonds : bond 0.04760 ( 1093) hydrogen bonds : angle 5.91828 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 129 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.9270 (m-80) cc_final: 0.8977 (m-80) REVERT: A 298 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8890 (tm-30) REVERT: A 378 LYS cc_start: 0.9224 (mmtm) cc_final: 0.8739 (mmtm) REVERT: A 392 PHE cc_start: 0.8504 (m-80) cc_final: 0.8239 (m-10) REVERT: A 725 GLU cc_start: 0.8450 (tt0) cc_final: 0.8166 (tt0) REVERT: A 773 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 1029 MET cc_start: 0.9374 (tpp) cc_final: 0.8500 (tpp) REVERT: B 242 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 336 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7294 (m) REVERT: B 353 TRP cc_start: 0.6146 (p-90) cc_final: 0.5029 (p-90) REVERT: B 365 TYR cc_start: 0.7811 (m-80) cc_final: 0.7509 (m-80) REVERT: B 515 PHE cc_start: 0.8932 (p90) cc_final: 0.8700 (p90) REVERT: B 712 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9209 (mm) REVERT: B 823 PHE cc_start: 0.8904 (m-80) cc_final: 0.8697 (m-80) REVERT: B 855 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: B 904 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: B 960 ASN cc_start: 0.9565 (t0) cc_final: 0.9188 (t0) REVERT: B 964 LYS cc_start: 0.9483 (tptp) cc_final: 0.9110 (tppt) REVERT: B 1005 GLN cc_start: 0.9459 (tp-100) cc_final: 0.8819 (tp-100) REVERT: C 712 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8904 (mm) REVERT: C 754 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9236 (mt) REVERT: C 779 GLN cc_start: 0.9347 (mm-40) cc_final: 0.9093 (tp-100) REVERT: C 960 ASN cc_start: 0.9529 (t0) cc_final: 0.9219 (m110) REVERT: I 67 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7469 (ptt-90) outliers start: 87 outliers final: 49 residues processed: 209 average time/residue: 0.1436 time to fit residues: 49.4096 Evaluate side-chains 170 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 53 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 166 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 965 GLN B 239 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.087786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054048 restraints weight = 120033.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056147 restraints weight = 59605.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056457 restraints weight = 31156.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056742 restraints weight = 24381.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056905 restraints weight = 25597.820| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27787 Z= 0.166 Angle : 0.590 9.029 37961 Z= 0.309 Chirality : 0.043 0.190 4414 Planarity : 0.004 0.055 4856 Dihedral : 5.665 55.264 4559 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 3.61 % Allowed : 14.25 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.62 (0.14), residues: 3472 helix: 1.53 (0.21), residues: 656 sheet: -0.24 (0.16), residues: 923 loop : -1.22 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.024 0.001 TYR I 80 PHE 0.025 0.001 PHE A 371 TRP 0.021 0.001 TRP B 353 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00378 (27745) covalent geometry : angle 0.58561 (37877) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.69179 ( 84) hydrogen bonds : bond 0.04555 ( 1093) hydrogen bonds : angle 5.73949 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 128 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 200 TYR cc_start: 0.9282 (m-80) cc_final: 0.9032 (m-80) REVERT: A 298 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8987 (tp30) REVERT: A 378 LYS cc_start: 0.9239 (mmtm) cc_final: 0.8750 (mmtm) REVERT: A 392 PHE cc_start: 0.8533 (m-80) cc_final: 0.8216 (m-10) REVERT: A 523 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8661 (t) REVERT: A 725 GLU cc_start: 0.8500 (tt0) cc_final: 0.8141 (tt0) REVERT: A 762 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.9093 (mp10) REVERT: A 773 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 239 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7470 (tp40) REVERT: B 333 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7835 (m) REVERT: B 336 CYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7511 (m) REVERT: B 353 TRP cc_start: 0.6117 (p-90) cc_final: 0.5419 (p-90) REVERT: B 365 TYR cc_start: 0.7741 (m-80) cc_final: 0.7408 (m-80) REVERT: B 712 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9193 (mm) REVERT: B 791 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 823 PHE cc_start: 0.8903 (m-80) cc_final: 0.8684 (m-80) REVERT: B 855 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: B 904 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: B 960 ASN cc_start: 0.9553 (t0) cc_final: 0.9181 (t0) REVERT: B 964 LYS cc_start: 0.9476 (tptp) cc_final: 0.9075 (tppt) REVERT: B 1005 GLN cc_start: 0.9423 (tp-100) cc_final: 0.8817 (tp-100) REVERT: C 282 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.8935 (m-40) REVERT: C 712 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 754 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9214 (mt) REVERT: C 960 ASN cc_start: 0.9523 (t0) cc_final: 0.9215 (m110) REVERT: I 67 ARG cc_start: 0.7811 (ptt180) cc_final: 0.7507 (ptt-90) outliers start: 101 outliers final: 59 residues processed: 223 average time/residue: 0.1520 time to fit residues: 56.7471 Evaluate side-chains 187 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 115 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 239 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 338 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 308 optimal weight: 50.0000 chunk 199 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 288 optimal weight: 0.9980 chunk 321 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.089075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054633 restraints weight = 116637.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056322 restraints weight = 55257.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057453 restraints weight = 35156.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058044 restraints weight = 26370.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058044 restraints weight = 22298.590| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27787 Z= 0.146 Angle : 0.572 8.485 37961 Z= 0.299 Chirality : 0.043 0.165 4414 Planarity : 0.004 0.059 4856 Dihedral : 5.510 55.699 4559 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.04 % Allowed : 15.82 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.48 (0.14), residues: 3472 helix: 1.66 (0.21), residues: 656 sheet: -0.17 (0.16), residues: 916 loop : -1.12 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.022 0.001 TYR I 80 PHE 0.025 0.001 PHE B 238 TRP 0.017 0.001 TRP B 353 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00334 (27745) covalent geometry : angle 0.56826 (37877) SS BOND : bond 0.00457 ( 42) SS BOND : angle 1.53603 ( 84) hydrogen bonds : bond 0.04423 ( 1093) hydrogen bonds : angle 5.60468 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 127 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8148 (t) REVERT: A 200 TYR cc_start: 0.9240 (m-80) cc_final: 0.8975 (m-80) REVERT: A 298 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8989 (tp30) REVERT: A 378 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8769 (mmtm) REVERT: A 392 PHE cc_start: 0.8599 (m-80) cc_final: 0.8248 (m-10) REVERT: A 523 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 725 GLU cc_start: 0.8536 (tt0) cc_final: 0.8270 (tt0) REVERT: A 762 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.9108 (mp10) REVERT: A 1002 GLN cc_start: 0.9236 (tp40) cc_final: 0.8894 (tp-100) REVERT: A 1029 MET cc_start: 0.9341 (tpp) cc_final: 0.8446 (tpp) REVERT: B 242 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8743 (mt) REVERT: B 333 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7833 (m) REVERT: B 336 CYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6964 (m) REVERT: B 365 TYR cc_start: 0.7682 (m-80) cc_final: 0.7400 (m-80) REVERT: B 712 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9148 (mm) REVERT: B 791 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8829 (p) REVERT: B 823 PHE cc_start: 0.8926 (m-80) cc_final: 0.8698 (m-80) REVERT: B 855 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: B 904 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: B 960 ASN cc_start: 0.9538 (t0) cc_final: 0.9170 (t0) REVERT: B 964 LYS cc_start: 0.9472 (tptp) cc_final: 0.9041 (tppt) REVERT: B 1005 GLN cc_start: 0.9407 (tp-100) cc_final: 0.8773 (tp-100) REVERT: C 282 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.8916 (m-40) REVERT: C 712 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8914 (mm) REVERT: C 754 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9212 (mt) REVERT: C 960 ASN cc_start: 0.9521 (t0) cc_final: 0.9218 (m110) REVERT: H 34 MET cc_start: 0.4161 (mmt) cc_final: 0.3729 (tmm) outliers start: 85 outliers final: 57 residues processed: 206 average time/residue: 0.1577 time to fit residues: 53.3755 Evaluate side-chains 188 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 118 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 242 optimal weight: 20.0000 chunk 241 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.090512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056073 restraints weight = 114321.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057794 restraints weight = 54199.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058919 restraints weight = 34499.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059503 restraints weight = 26057.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060045 restraints weight = 22188.939| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27787 Z= 0.111 Angle : 0.549 12.302 37961 Z= 0.286 Chirality : 0.043 0.168 4414 Planarity : 0.004 0.060 4856 Dihedral : 5.208 54.982 4559 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.79 % Allowed : 16.21 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.31 (0.14), residues: 3472 helix: 1.64 (0.21), residues: 669 sheet: -0.01 (0.17), residues: 903 loop : -0.99 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 983 TYR 0.020 0.001 TYR I 80 PHE 0.026 0.001 PHE I 107 TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00246 (27745) covalent geometry : angle 0.54598 (37877) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.31212 ( 84) hydrogen bonds : bond 0.04015 ( 1093) hydrogen bonds : angle 5.34988 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 132 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8056 (t) REVERT: A 200 TYR cc_start: 0.9227 (m-80) cc_final: 0.8956 (m-80) REVERT: A 378 LYS cc_start: 0.9300 (mmtm) cc_final: 0.8807 (mmtm) REVERT: A 392 PHE cc_start: 0.8603 (m-80) cc_final: 0.8244 (m-10) REVERT: A 523 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8557 (t) REVERT: A 725 GLU cc_start: 0.8511 (tt0) cc_final: 0.8256 (tt0) REVERT: A 762 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: A 1002 GLN cc_start: 0.9197 (tp40) cc_final: 0.8812 (tp-100) REVERT: A 1029 MET cc_start: 0.9307 (tpp) cc_final: 0.8385 (tpp) REVERT: B 242 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8720 (mt) REVERT: B 333 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7852 (m) REVERT: B 336 CYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6597 (m) REVERT: B 365 TYR cc_start: 0.7609 (m-80) cc_final: 0.7368 (m-10) REVERT: B 712 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9133 (mm) REVERT: B 823 PHE cc_start: 0.8864 (m-80) cc_final: 0.8632 (m-80) REVERT: B 904 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: B 960 ASN cc_start: 0.9516 (t0) cc_final: 0.9157 (t0) REVERT: B 964 LYS cc_start: 0.9430 (tptp) cc_final: 0.8984 (tppt) REVERT: C 282 ASN cc_start: 0.9381 (OUTLIER) cc_final: 0.8931 (m-40) REVERT: C 712 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 754 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9220 (mt) REVERT: C 777 ASN cc_start: 0.8950 (m-40) cc_final: 0.8676 (m110) REVERT: C 779 GLN cc_start: 0.9335 (mm-40) cc_final: 0.9055 (tp-100) REVERT: C 904 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (m-10) REVERT: C 960 ASN cc_start: 0.9498 (t0) cc_final: 0.9196 (m110) REVERT: I 67 ARG cc_start: 0.7972 (ptt180) cc_final: 0.7597 (ptt-90) REVERT: I 107 PHE cc_start: 0.8540 (t80) cc_final: 0.8183 (t80) REVERT: H 34 MET cc_start: 0.4109 (mmt) cc_final: 0.3705 (tmm) outliers start: 78 outliers final: 55 residues processed: 202 average time/residue: 0.1496 time to fit residues: 50.7534 Evaluate side-chains 185 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 118 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 62 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 310 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 506 GLN B 437 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.091338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056725 restraints weight = 111950.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058373 restraints weight = 53995.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059485 restraints weight = 34986.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060194 restraints weight = 26555.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060535 restraints weight = 22345.947| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27787 Z= 0.113 Angle : 0.552 14.248 37961 Z= 0.285 Chirality : 0.043 0.395 4414 Planarity : 0.004 0.059 4856 Dihedral : 5.032 55.813 4558 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.79 % Allowed : 16.61 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.23 (0.14), residues: 3472 helix: 1.66 (0.21), residues: 671 sheet: 0.11 (0.17), residues: 895 loop : -0.96 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 983 TYR 0.024 0.001 TYR I 80 PHE 0.025 0.001 PHE I 107 TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00256 (27745) covalent geometry : angle 0.54888 (37877) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.33258 ( 84) hydrogen bonds : bond 0.03927 ( 1093) hydrogen bonds : angle 5.26327 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 129 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8004 (t) REVERT: A 200 TYR cc_start: 0.9235 (m-80) cc_final: 0.8955 (m-80) REVERT: A 229 LEU cc_start: 0.9080 (mt) cc_final: 0.8859 (mt) REVERT: A 378 LYS cc_start: 0.9300 (mmtm) cc_final: 0.8829 (mmtm) REVERT: A 392 PHE cc_start: 0.8643 (m-80) cc_final: 0.8321 (m-10) REVERT: A 523 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 725 GLU cc_start: 0.8479 (tt0) cc_final: 0.8233 (tt0) REVERT: A 1002 GLN cc_start: 0.9203 (tp40) cc_final: 0.8821 (tp-100) REVERT: A 1029 MET cc_start: 0.9358 (tpp) cc_final: 0.8544 (tpp) REVERT: B 242 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8701 (mt) REVERT: B 298 GLU cc_start: 0.9361 (tt0) cc_final: 0.8980 (mt-10) REVERT: B 336 CYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6534 (m) REVERT: B 353 TRP cc_start: 0.6736 (p-90) cc_final: 0.6222 (p-90) REVERT: B 365 TYR cc_start: 0.7570 (m-80) cc_final: 0.7272 (m-80) REVERT: B 712 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9106 (mm) REVERT: B 791 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8837 (p) REVERT: B 823 PHE cc_start: 0.8817 (m-80) cc_final: 0.8563 (m-80) REVERT: B 904 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7797 (m-10) REVERT: B 960 ASN cc_start: 0.9491 (t0) cc_final: 0.9128 (t0) REVERT: B 964 LYS cc_start: 0.9419 (tptp) cc_final: 0.8994 (tppt) REVERT: C 282 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.8895 (m-40) REVERT: C 712 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8881 (mm) REVERT: C 777 ASN cc_start: 0.8864 (m-40) cc_final: 0.8633 (m110) REVERT: C 779 GLN cc_start: 0.9342 (mm-40) cc_final: 0.9051 (tp-100) REVERT: C 904 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8268 (m-10) REVERT: C 960 ASN cc_start: 0.9497 (t0) cc_final: 0.9209 (m110) REVERT: I 107 PHE cc_start: 0.8544 (t80) cc_final: 0.8092 (t80) REVERT: H 34 MET cc_start: 0.3954 (mmt) cc_final: 0.3569 (tmm) outliers start: 78 outliers final: 57 residues processed: 199 average time/residue: 0.1454 time to fit residues: 48.6242 Evaluate side-chains 193 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 125 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 263 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.087053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.052701 restraints weight = 120579.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054332 restraints weight = 56334.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.055461 restraints weight = 35689.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056057 restraints weight = 26727.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056057 restraints weight = 22349.702| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27787 Z= 0.192 Angle : 0.607 13.897 37961 Z= 0.313 Chirality : 0.044 0.374 4414 Planarity : 0.004 0.060 4856 Dihedral : 5.239 55.952 4556 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.64 % Allowed : 17.07 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.32 (0.14), residues: 3472 helix: 1.48 (0.21), residues: 677 sheet: -0.05 (0.17), residues: 921 loop : -0.93 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 983 TYR 0.025 0.001 TYR I 80 PHE 0.019 0.001 PHE I 107 TRP 0.013 0.001 TRP B 353 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00438 (27745) covalent geometry : angle 0.60246 (37877) SS BOND : bond 0.00449 ( 42) SS BOND : angle 1.60291 ( 84) hydrogen bonds : bond 0.04396 ( 1093) hydrogen bonds : angle 5.54146 ( 3018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 121 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8088 (t) REVERT: A 200 TYR cc_start: 0.9299 (m-80) cc_final: 0.8986 (m-80) REVERT: A 378 LYS cc_start: 0.9336 (mmtm) cc_final: 0.8964 (mmtm) REVERT: A 392 PHE cc_start: 0.8639 (m-80) cc_final: 0.8262 (m-10) REVERT: A 523 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8574 (t) REVERT: A 725 GLU cc_start: 0.8558 (tt0) cc_final: 0.8267 (tt0) REVERT: A 762 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.9052 (pm20) REVERT: A 1002 GLN cc_start: 0.9225 (tp40) cc_final: 0.8832 (tp-100) REVERT: A 1029 MET cc_start: 0.9394 (tpp) cc_final: 0.8563 (tpp) REVERT: B 81 ASN cc_start: 0.6470 (OUTLIER) cc_final: 0.5801 (t0) REVERT: B 242 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8692 (mt) REVERT: B 298 GLU cc_start: 0.9344 (tt0) cc_final: 0.8932 (tp30) REVERT: B 336 CYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6876 (m) REVERT: B 353 TRP cc_start: 0.6296 (p-90) cc_final: 0.5813 (p-90) REVERT: B 365 TYR cc_start: 0.7605 (m-80) cc_final: 0.7281 (m-80) REVERT: B 712 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9149 (mm) REVERT: B 791 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 855 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.5938 (m-80) REVERT: B 904 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: B 960 ASN cc_start: 0.9562 (t0) cc_final: 0.9199 (t0) REVERT: B 964 LYS cc_start: 0.9479 (tptp) cc_final: 0.9075 (tppt) REVERT: C 282 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8830 (m-40) REVERT: C 298 GLU cc_start: 0.9283 (tp30) cc_final: 0.9047 (tp30) REVERT: C 712 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8931 (mm) REVERT: C 779 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9062 (tp-100) REVERT: C 904 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8279 (m-10) REVERT: C 960 ASN cc_start: 0.9540 (t0) cc_final: 0.9245 (m110) REVERT: I 107 PHE cc_start: 0.8551 (t80) cc_final: 0.8133 (t80) REVERT: H 34 MET cc_start: 0.4027 (mmt) cc_final: 0.3612 (tmm) outliers start: 74 outliers final: 54 residues processed: 192 average time/residue: 0.1439 time to fit residues: 46.1589 Evaluate side-chains 184 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 117 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 273 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 308 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.089819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055615 restraints weight = 115258.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057321 restraints weight = 54854.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058194 restraints weight = 35047.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059011 restraints weight = 27443.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059011 restraints weight = 22714.721| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27787 Z= 0.115 Angle : 0.567 15.224 37961 Z= 0.292 Chirality : 0.043 0.358 4414 Planarity : 0.004 0.060 4856 Dihedral : 5.134 55.560 4556 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.39 % Allowed : 17.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.21 (0.14), residues: 3472 helix: 1.58 (0.21), residues: 677 sheet: 0.02 (0.17), residues: 922 loop : -0.87 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 983 TYR 0.028 0.001 TYR I 80 PHE 0.023 0.001 PHE A 168 TRP 0.035 0.001 TRP C 104 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00258 (27745) covalent geometry : angle 0.56351 (37877) SS BOND : bond 0.00386 ( 42) SS BOND : angle 1.38487 ( 84) hydrogen bonds : bond 0.04073 ( 1093) hydrogen bonds : angle 5.34166 ( 3018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8006 (t) REVERT: A 200 TYR cc_start: 0.9253 (m-80) cc_final: 0.8960 (m-80) REVERT: A 378 LYS cc_start: 0.9328 (mmtm) cc_final: 0.8880 (mmtm) REVERT: A 392 PHE cc_start: 0.8610 (m-80) cc_final: 0.8285 (m-10) REVERT: A 523 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8588 (t) REVERT: A 725 GLU cc_start: 0.8552 (tt0) cc_final: 0.8284 (tt0) REVERT: A 762 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9024 (pm20) REVERT: A 1002 GLN cc_start: 0.9200 (tp40) cc_final: 0.8795 (tp-100) REVERT: A 1029 MET cc_start: 0.9339 (tpp) cc_final: 0.8480 (tpp) REVERT: B 242 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 298 GLU cc_start: 0.9354 (tt0) cc_final: 0.9010 (mt-10) REVERT: B 336 CYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6643 (m) REVERT: B 353 TRP cc_start: 0.6675 (p-90) cc_final: 0.6208 (p-90) REVERT: B 365 TYR cc_start: 0.7478 (m-80) cc_final: 0.7189 (m-80) REVERT: B 712 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9103 (mm) REVERT: B 823 PHE cc_start: 0.8853 (m-80) cc_final: 0.8587 (m-80) REVERT: B 855 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: B 904 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7840 (m-10) REVERT: B 960 ASN cc_start: 0.9505 (t0) cc_final: 0.9142 (t0) REVERT: B 964 LYS cc_start: 0.9431 (tptp) cc_final: 0.9027 (tppt) REVERT: C 282 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.8878 (m-40) REVERT: C 298 GLU cc_start: 0.9272 (tp30) cc_final: 0.9033 (tp30) REVERT: C 712 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8901 (mm) REVERT: C 777 ASN cc_start: 0.8963 (m-40) cc_final: 0.8662 (m110) REVERT: C 779 GLN cc_start: 0.9341 (mm-40) cc_final: 0.8959 (tp40) REVERT: C 904 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8247 (m-10) REVERT: C 960 ASN cc_start: 0.9511 (t0) cc_final: 0.9232 (m110) REVERT: I 107 PHE cc_start: 0.8567 (t80) cc_final: 0.8137 (t80) REVERT: H 34 MET cc_start: 0.3785 (mmt) cc_final: 0.3400 (tmm) outliers start: 67 outliers final: 54 residues processed: 189 average time/residue: 0.1406 time to fit residues: 45.0289 Evaluate side-chains 188 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 296 optimal weight: 0.0270 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 210 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.090681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056573 restraints weight = 113985.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058312 restraints weight = 54246.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059471 restraints weight = 34579.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060230 restraints weight = 26017.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060579 restraints weight = 21793.444| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27787 Z= 0.100 Angle : 0.552 14.995 37961 Z= 0.283 Chirality : 0.043 0.380 4414 Planarity : 0.004 0.058 4856 Dihedral : 4.821 55.034 4556 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.29 % Allowed : 17.61 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -0.13 (0.14), residues: 3472 helix: 1.54 (0.21), residues: 689 sheet: 0.18 (0.17), residues: 894 loop : -0.84 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.026 0.001 TYR I 80 PHE 0.022 0.001 PHE A 168 TRP 0.035 0.001 TRP C 104 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00220 (27745) covalent geometry : angle 0.54987 (37877) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.20461 ( 84) hydrogen bonds : bond 0.03677 ( 1093) hydrogen bonds : angle 5.10316 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5040.05 seconds wall clock time: 87 minutes 28.38 seconds (5248.38 seconds total)