Starting phenix.real_space_refine on Tue Aug 26 18:57:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cg5_16631/08_2025/8cg5_16631_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cg5_16631/08_2025/8cg5_16631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cg5_16631/08_2025/8cg5_16631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cg5_16631/08_2025/8cg5_16631.map" model { file = "/net/cci-nas-00/data/ceres_data/8cg5_16631/08_2025/8cg5_16631_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cg5_16631/08_2025/8cg5_16631_trim.cif" } resolution = 2.7 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= -0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 86 5.16 5 C 12550 2.51 5 N 3545 2.21 5 O 3834 1.98 5 H 19691 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s 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: 39707 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 19248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 19248 Classifications: {'peptide': 1282} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1204} Chain: "B" Number of atoms: 19249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 19249 Classifications: {'peptide': 1282} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1204} Chain: "C" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1185 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'42X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.95, per 1000 atoms: 0.15 Number of scatterers: 39707 At special positions: 0 Unit cell: (196.8, 109.06, 122.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 1 15.00 O 3834 8.00 N 3545 7.00 C 12550 6.00 H 19691 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4924 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 18 sheets defined 49.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 32 through 51 Proline residue: A 43 - end of helix Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.640A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 77 removed outlier: 4.211A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 102 Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.439A pdb=" N THR A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 163 Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.996A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.039A pdb=" N LYS A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.541A pdb=" N GLN A 495 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASN A 497 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 515 through 518 Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 530 through 541 removed outlier: 3.579A pdb=" N GLY A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.539A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.793A pdb=" N THR A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 660 through 676 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 692 through 708 Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'A' and resid 737 through 753 Processing helix chain 'A' and resid 772 through 775 Processing helix chain 'A' and resid 838 through 856 Processing helix chain 'A' and resid 862 through 873 removed outlier: 3.628A pdb=" N GLN A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 906 removed outlier: 3.847A pdb=" N GLY A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 941 removed outlier: 3.527A pdb=" N TYR A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 958 Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 977 through 999 Processing helix chain 'A' and resid 1011 through 1020 removed outlier: 4.556A pdb=" N ALA A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1089 through 1101 Processing helix chain 'A' and resid 1117 through 1122 removed outlier: 3.751A pdb=" N VAL A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1123 through 1132 Processing helix chain 'A' and resid 1154 through 1158 removed outlier: 3.621A pdb=" N ASP A1157 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1169 removed outlier: 3.924A pdb=" N PHE A1163 " --> pdb=" O GLN A1159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A1164 " --> pdb=" O PRO A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1184 Processing helix chain 'A' and resid 1200 through 1210 removed outlier: 3.642A pdb=" N PHE A1204 " --> pdb=" O VAL A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1240 Processing helix chain 'A' and resid 1244 through 1250 removed outlier: 3.569A pdb=" N HIS A1249 " --> pdb=" O TRP A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1256 Processing helix chain 'A' and resid 1278 through 1282 Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 32 through 51 Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.205A pdb=" N ARG B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 102 Processing helix chain 'B' and resid 120 through 130 removed outlier: 4.393A pdb=" N THR B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 163 Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.505A pdb=" N LEU B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.085A pdb=" N SER B 365 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.669A pdb=" N GLN B 495 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 496 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 497 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 514 through 519 removed outlier: 3.831A pdb=" N ASN B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL B 519 " --> pdb=" O ALA B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.067A pdb=" N VAL B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 removed outlier: 3.517A pdb=" N ARG B 569 " --> pdb=" O ASN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 removed outlier: 3.970A pdb=" N THR B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 660 through 676 Processing helix chain 'B' and resid 692 through 708 Processing helix chain 'B' and resid 727 through 732 Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 771 through 776 removed outlier: 3.739A pdb=" N ARG B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 856 Processing helix chain 'B' and resid 862 through 873 removed outlier: 3.584A pdb=" N GLN B 866 " --> pdb=" O ALA B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 906 removed outlier: 3.679A pdb=" N GLY B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 941 Processing helix chain 'B' and resid 941 through 958 Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 977 through 999 Processing helix chain 'B' and resid 1011 through 1021 removed outlier: 4.622A pdb=" N ALA B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1043 Processing helix chain 'B' and resid 1056 through 1064 removed outlier: 3.674A pdb=" N ILE B1060 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1101 removed outlier: 3.727A pdb=" N ALA B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1123 through 1134 Processing helix chain 'B' and resid 1154 through 1158 removed outlier: 3.518A pdb=" N ASP B1157 " --> pdb=" O SER B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1169 removed outlier: 4.118A pdb=" N PHE B1163 " --> pdb=" O GLN B1159 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B1164 " --> pdb=" O PRO B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1184 Processing helix chain 'B' and resid 1200 through 1210 removed outlier: 3.573A pdb=" N PHE B1204 " --> pdb=" O VAL B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1224 through 1240 Processing helix chain 'B' and resid 1244 through 1249 Processing helix chain 'B' and resid 1252 through 1256 Processing helix chain 'B' and resid 1278 through 1283 removed outlier: 3.634A pdb=" N LEU B1281 " --> pdb=" O ASP B1278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B1283 " --> pdb=" O SER B1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.612A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 removed outlier: 8.309A pdb=" N ILE A 281 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 115 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N CYS A 114 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG A 8 " --> pdb=" O CYS A 114 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR A 116 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET A 7 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 335 " --> pdb=" O MET A 7 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 9 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 337 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA A 11 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.307A pdb=" N SER A 219 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA A 212 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLN A 217 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 177 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 546 through 549 removed outlier: 9.062A pdb=" N TYR A 547 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 501 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 549 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A 503 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 620 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A 391 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 622 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 389 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 624 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 640 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 811 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE A 645 " --> pdb=" O CYS A 809 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS A 809 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR A 647 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A 807 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 796 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG A 795 " --> pdb=" O ILE A 682 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 684 " --> pdb=" O ARG A 795 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 725 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 722 " --> pdb=" O HIS A 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 414 through 415 removed outlier: 4.307A pdb=" N ARG A 616 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AA7, first strand: chain 'A' and resid 830 through 836 Processing sheet with id=AA8, first strand: chain 'A' and resid 1150 through 1152 removed outlier: 3.675A pdb=" N LYS A1150 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE A1144 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A1006 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE A 919 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL A1007 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 921 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL A 920 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A1195 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA A 922 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A1192 " --> pdb=" O PHE A1216 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1073 through 1076 removed outlier: 5.305A pdb=" N PHE A1074 " --> pdb=" O GLY A1086 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY A1086 " --> pdb=" O PHE A1074 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 289 through 290 removed outlier: 8.232A pdb=" N ILE B 281 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE B 115 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG B 8 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N THR B 116 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 10 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET B 7 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER B 335 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 9 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 337 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 11 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.614A pdb=" N SER B 219 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 546 through 549 removed outlier: 9.076A pdb=" N TYR B 547 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 501 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE B 549 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR B 503 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 620 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B 391 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 622 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 389 " --> pdb=" O THR B 622 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 624 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 640 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 642 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU B 813 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 644 " --> pdb=" O VAL B 811 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B 795 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 684 " --> pdb=" O ARG B 795 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 722 " --> pdb=" O HIS B 778 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AB5, first strand: chain 'B' and resid 754 through 755 Processing sheet with id=AB6, first strand: chain 'B' and resid 830 through 836 Processing sheet with id=AB7, first strand: chain 'B' and resid 1003 through 1008 removed outlier: 7.470A pdb=" N PHE B 919 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B1006 " --> pdb=" O PHE B 919 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 921 " --> pdb=" O VAL B1006 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY B1008 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 923 " --> pdb=" O GLY B1008 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 918 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B1193 " --> pdb=" O SER B 918 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 920 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B1195 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 922 " --> pdb=" O ILE B1195 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N PHE B1216 " --> pdb=" O VAL B1190 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B1192 " --> pdb=" O PHE B1216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1073 through 1076 removed outlier: 6.874A pdb=" N VAL B1084 " --> pdb=" O SER B1075 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B1107 " --> pdb=" O ALA B1052 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1143 through 1145 removed outlier: 3.509A pdb=" N LYS B1150 " --> pdb=" O SER B1145 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.03 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19653 1.03 - 1.23: 81 1.23 - 1.42: 8417 1.42 - 1.62: 11858 1.62 - 1.81: 134 Bond restraints: 40143 Sorted by residual: bond pdb=" C22 42X C2000 " pdb=" N24 42X C2000 " ideal model delta sigma weight residual 1.335 1.450 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C32 42X C2000 " pdb=" N34 42X C2000 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C44 42X C2000 " pdb=" N42 42X C2000 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" CG PRO B 334 " pdb=" CD PRO B 334 " ideal model delta sigma weight residual 1.503 1.408 0.095 3.40e-02 8.65e+02 7.86e+00 bond pdb=" C22 42X C2000 " pdb=" O23 42X C2000 " ideal model delta sigma weight residual 1.238 1.184 0.054 2.00e-02 2.50e+03 7.24e+00 ... (remaining 40138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 72051 2.09 - 4.18: 458 4.18 - 6.26: 34 6.26 - 8.35: 14 8.35 - 10.44: 4 Bond angle restraints: 72561 Sorted by residual: angle pdb=" CA PRO B 334 " pdb=" N PRO B 334 " pdb=" CD PRO B 334 " ideal model delta sigma weight residual 112.00 101.56 10.44 1.40e+00 5.10e-01 5.56e+01 angle pdb=" CA PRO B 961 " pdb=" N PRO B 961 " pdb=" CD PRO B 961 " ideal model delta sigma weight residual 112.00 102.46 9.54 1.40e+00 5.10e-01 4.65e+01 angle pdb=" N PRO B 334 " pdb=" CD PRO B 334 " pdb=" CG PRO B 334 " ideal model delta sigma weight residual 103.20 95.00 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N PRO B 961 " pdb=" CD PRO B 961 " pdb=" CG PRO B 961 " ideal model delta sigma weight residual 103.20 95.59 7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" CA PRO A 269 " pdb=" N PRO A 269 " pdb=" CD PRO A 269 " ideal model delta sigma weight residual 112.00 106.31 5.69 1.40e+00 5.10e-01 1.65e+01 ... (remaining 72556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 17453 23.94 - 47.87: 1239 47.87 - 71.81: 308 71.81 - 95.74: 39 95.74 - 119.68: 2 Dihedral angle restraints: 19041 sinusoidal: 10417 harmonic: 8624 Sorted by residual: dihedral pdb=" CA VAL B 118 " pdb=" C VAL B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLU B 735 " pdb=" C GLU B 735 " pdb=" N SER B 736 " pdb=" CA SER B 736 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA A 552 " pdb=" C ALA A 552 " pdb=" N CYS A 553 " pdb=" CA CYS A 553 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 19038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2329 0.038 - 0.076: 604 0.076 - 0.114: 202 0.114 - 0.152: 46 0.152 - 0.190: 1 Chirality restraints: 3182 Sorted by residual: chirality pdb=" C18 42X C2000 " pdb=" C09 42X C2000 " pdb=" C22 42X C2000 " pdb=" O20 42X C2000 " both_signs ideal model delta sigma weight residual False 2.30 2.49 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CB VAL A1120 " pdb=" CA VAL A1120 " pdb=" CG1 VAL A1120 " pdb=" CG2 VAL A1120 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 755 " pdb=" N ILE A 755 " pdb=" C ILE A 755 " pdb=" CB ILE A 755 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 3179 not shown) Planarity restraints: 6140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 960 " -0.072 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO B 961 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 961 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 961 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 333 " 0.059 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO B 334 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 325 " 0.228 9.50e-02 1.11e+02 7.64e-02 7.12e+00 pdb=" NE ARG A 325 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 325 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 325 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 325 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 325 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 325 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 325 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 325 " 0.001 2.00e-02 2.50e+03 ... (remaining 6137 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1595 2.16 - 2.77: 75214 2.77 - 3.38: 111699 3.38 - 3.99: 146848 3.99 - 4.60: 231326 Nonbonded interactions: 566682 Sorted by model distance: nonbonded pdb=" OE1 GLU B 21 " pdb=" H GLU B 21 " model vdw 1.545 2.450 nonbonded pdb=" OE1 GLN A1137 " pdb="HH21 ARG B 167 " model vdw 1.554 2.450 nonbonded pdb=" HG SER A 184 " pdb=" OD2 ASP A 187 " model vdw 1.556 2.450 nonbonded pdb=" O ILE A 831 " pdb=" HG SER A 868 " model vdw 1.563 2.450 nonbonded pdb=" OE1 GLN B 186 " pdb=" H GLN B 186 " model vdw 1.568 2.450 ... (remaining 566677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 552 or (resid 553 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 554 through 1286)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 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: 0.180 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.760 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.004 0.115 20454 Z= 0.176 Angle : 0.581 10.440 27862 Z= 0.295 Chirality : 0.040 0.190 3182 Planarity : 0.006 0.104 3658 Dihedral : 17.870 119.677 7423 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.06 % Allowed : 29.85 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.78 (0.17), residues: 2634 helix: 1.63 (0.16), residues: 1132 sheet: 0.51 (0.32), residues: 288 loop : -0.54 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 325 TYR 0.013 0.001 TYR A1018 PHE 0.017 0.001 PHE A 973 TRP 0.011 0.001 TRP B1226 HIS 0.010 0.001 HIS B1165 Details of bonding type rmsd covalent geometry : bond 0.00390 (20452) covalent geometry : angle 0.58115 (27862) hydrogen bonds : bond 0.17334 ( 940) hydrogen bonds : angle 5.94845 ( 2670) Misc. bond : bond 0.06882 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 908 ARG cc_start: 0.8131 (mmp80) cc_final: 0.7914 (mmm160) outliers start: 44 outliers final: 43 residues processed: 176 average time/residue: 1.0047 time to fit residues: 207.0430 Evaluate side-chains 167 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1076 CYS Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 508 ASN A 897 GLN A 953 GLN A1140 GLN A1178 GLN A1214 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 348 GLN B 632 GLN B 680 ASN B1083 ASN B1178 GLN B1231 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.092007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.062171 restraints weight = 111034.819| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.72 r_work: 0.2718 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20454 Z= 0.242 Angle : 0.584 5.872 27862 Z= 0.306 Chirality : 0.043 0.148 3182 Planarity : 0.005 0.057 3658 Dihedral : 8.205 119.145 2911 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.08 % Allowed : 26.18 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.71 (0.17), residues: 2634 helix: 1.50 (0.16), residues: 1150 sheet: 0.69 (0.32), residues: 292 loop : -0.59 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 325 TYR 0.017 0.002 TYR B1018 PHE 0.011 0.001 PHE B 973 TRP 0.014 0.001 TRP A1226 HIS 0.006 0.001 HIS B1249 Details of bonding type rmsd covalent geometry : bond 0.00562 (20452) covalent geometry : angle 0.58395 (27862) hydrogen bonds : bond 0.05650 ( 940) hydrogen bonds : angle 4.87755 ( 2670) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 122 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 20 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7234 (tptp) outliers start: 87 outliers final: 48 residues processed: 197 average time/residue: 0.9885 time to fit residues: 229.2145 Evaluate side-chains 169 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 177 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 203 optimal weight: 0.0000 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 GLN A1093 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B1083 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.062962 restraints weight = 110702.779| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.72 r_work: 0.2724 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20454 Z= 0.153 Angle : 0.531 5.234 27862 Z= 0.275 Chirality : 0.041 0.144 3182 Planarity : 0.004 0.049 3658 Dihedral : 7.827 117.273 2901 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.00 % Allowed : 26.23 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.80 (0.17), residues: 2634 helix: 1.63 (0.16), residues: 1152 sheet: 0.75 (0.32), residues: 292 loop : -0.60 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 908 TYR 0.014 0.001 TYR B1018 PHE 0.084 0.001 PHE C 64 TRP 0.011 0.001 TRP A1226 HIS 0.005 0.001 HIS A1166 Details of bonding type rmsd covalent geometry : bond 0.00354 (20452) covalent geometry : angle 0.53101 (27862) hydrogen bonds : bond 0.04701 ( 940) hydrogen bonds : angle 4.58721 ( 2670) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: A 1002 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7094 (pp30) REVERT: B 1004 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (pttt) REVERT: B 1082 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.7219 (mpp80) outliers start: 64 outliers final: 45 residues processed: 183 average time/residue: 1.0188 time to fit residues: 217.7717 Evaluate side-chains 170 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1004 LYS Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.062568 restraints weight = 110929.195| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.71 r_work: 0.2725 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20454 Z= 0.178 Angle : 0.525 5.176 27862 Z= 0.271 Chirality : 0.041 0.146 3182 Planarity : 0.004 0.046 3658 Dihedral : 7.694 113.143 2899 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.52 % Allowed : 25.06 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.84 (0.17), residues: 2634 helix: 1.70 (0.16), residues: 1152 sheet: 0.71 (0.32), residues: 292 loop : -0.62 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 80 TYR 0.015 0.001 TYR B1018 PHE 0.010 0.001 PHE B 973 TRP 0.011 0.001 TRP A1226 HIS 0.003 0.001 HIS B1249 Details of bonding type rmsd covalent geometry : bond 0.00416 (20452) covalent geometry : angle 0.52549 (27862) hydrogen bonds : bond 0.04398 ( 940) hydrogen bonds : angle 4.45634 ( 2670) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 120 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 512 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: A 814 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: A 1002 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7129 (pp30) REVERT: B 375 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 1004 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8571 (pttt) REVERT: B 1082 ARG cc_start: 0.7688 (mpt-90) cc_final: 0.7183 (mpp80) REVERT: C 20 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7202 (tptp) outliers start: 75 outliers final: 50 residues processed: 188 average time/residue: 1.1157 time to fit residues: 242.4538 Evaluate side-chains 170 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1004 LYS Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.062614 restraints weight = 111165.509| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.72 r_work: 0.2727 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20454 Z= 0.164 Angle : 0.518 5.485 27862 Z= 0.267 Chirality : 0.041 0.145 3182 Planarity : 0.004 0.047 3658 Dihedral : 7.588 109.357 2896 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.28 % Allowed : 25.25 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.89 (0.17), residues: 2634 helix: 1.77 (0.16), residues: 1152 sheet: 0.70 (0.32), residues: 292 loop : -0.60 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 80 TYR 0.014 0.001 TYR B1018 PHE 0.008 0.001 PHE C 83 TRP 0.011 0.001 TRP A1226 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00384 (20452) covalent geometry : angle 0.51766 (27862) hydrogen bonds : bond 0.04220 ( 940) hydrogen bonds : angle 4.36602 ( 2670) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 116 time to evaluate : 0.854 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 479 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: A 508 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6057 (p0) REVERT: A 512 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: A 1002 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7116 (pp30) REVERT: B 363 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7327 (pt) REVERT: B 375 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: B 1004 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (pttt) REVERT: B 1082 ARG cc_start: 0.7687 (mpt-90) cc_final: 0.7206 (mpp80) REVERT: C 20 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7214 (tptp) outliers start: 70 outliers final: 47 residues processed: 180 average time/residue: 1.0747 time to fit residues: 223.7904 Evaluate side-chains 167 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1004 LYS Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B1083 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.062799 restraints weight = 111192.743| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.71 r_work: 0.2731 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20454 Z= 0.154 Angle : 0.507 5.465 27862 Z= 0.261 Chirality : 0.040 0.146 3182 Planarity : 0.004 0.047 3658 Dihedral : 7.432 106.389 2892 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.33 % Allowed : 25.06 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.95 (0.17), residues: 2634 helix: 1.80 (0.16), residues: 1156 sheet: 0.73 (0.32), residues: 288 loop : -0.55 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 80 TYR 0.014 0.001 TYR B1018 PHE 0.012 0.001 PHE B 973 TRP 0.011 0.001 TRP A1226 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00359 (20452) covalent geometry : angle 0.50730 (27862) hydrogen bonds : bond 0.04048 ( 940) hydrogen bonds : angle 4.29757 ( 2670) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 118 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: A 450 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (mm-30) REVERT: A 479 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: A 512 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: A 1002 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7125 (pp30) REVERT: B 363 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7352 (pt) REVERT: B 375 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: B 908 ARG cc_start: 0.8092 (mmp80) cc_final: 0.7883 (mmm160) REVERT: B 1004 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8564 (pttt) REVERT: B 1082 ARG cc_start: 0.7638 (mpt-90) cc_final: 0.7165 (mpp80) REVERT: C 20 LYS cc_start: 0.7623 (ttpp) cc_final: 0.7187 (tptp) outliers start: 71 outliers final: 50 residues processed: 183 average time/residue: 1.0750 time to fit residues: 227.4271 Evaluate side-chains 168 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 112 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1004 LYS Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 5 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 257 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.062704 restraints weight = 111022.411| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.72 r_work: 0.2731 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20454 Z= 0.155 Angle : 0.509 5.591 27862 Z= 0.261 Chirality : 0.040 0.145 3182 Planarity : 0.004 0.047 3658 Dihedral : 7.374 105.099 2888 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.52 % Allowed : 24.96 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.98 (0.17), residues: 2634 helix: 1.82 (0.16), residues: 1156 sheet: 0.73 (0.32), residues: 288 loop : -0.54 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 80 TYR 0.014 0.001 TYR B1018 PHE 0.009 0.001 PHE C 83 TRP 0.009 0.001 TRP A 421 HIS 0.006 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00363 (20452) covalent geometry : angle 0.50867 (27862) hydrogen bonds : bond 0.04009 ( 940) hydrogen bonds : angle 4.26488 ( 2670) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 1.000 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 450 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8583 (mm-30) REVERT: A 479 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 512 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: A 1002 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7003 (pp30) REVERT: B 363 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7329 (pt) REVERT: B 375 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: B 908 ARG cc_start: 0.8094 (mmp80) cc_final: 0.7879 (mmm160) REVERT: B 1004 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8561 (pttt) REVERT: B 1082 ARG cc_start: 0.7649 (mpt-90) cc_final: 0.7184 (mpp80) REVERT: C 20 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7209 (tptp) outliers start: 75 outliers final: 52 residues processed: 187 average time/residue: 1.1643 time to fit residues: 249.8155 Evaluate side-chains 172 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1004 LYS Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 83 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.062693 restraints weight = 110943.436| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.71 r_work: 0.2730 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20454 Z= 0.157 Angle : 0.508 5.256 27862 Z= 0.261 Chirality : 0.040 0.144 3182 Planarity : 0.004 0.046 3658 Dihedral : 7.345 103.861 2887 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 24.96 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.00 (0.17), residues: 2634 helix: 1.84 (0.16), residues: 1156 sheet: 0.75 (0.32), residues: 288 loop : -0.53 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 80 TYR 0.014 0.001 TYR B1018 PHE 0.013 0.001 PHE B 973 TRP 0.009 0.001 TRP A1226 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00368 (20452) covalent geometry : angle 0.50847 (27862) hydrogen bonds : bond 0.03988 ( 940) hydrogen bonds : angle 4.24191 ( 2670) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 116 time to evaluate : 0.860 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 450 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8606 (mm-30) REVERT: A 479 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: A 512 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: A 1002 GLN cc_start: 0.7981 (mm-40) cc_final: 0.6991 (pp30) REVERT: A 1077 ARG cc_start: 0.6960 (mtt-85) cc_final: 0.6547 (mtt90) REVERT: B 183 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 363 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7314 (pt) REVERT: B 375 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: B 908 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7871 (mmm160) REVERT: B 1004 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8575 (pttt) REVERT: B 1082 ARG cc_start: 0.7642 (mpt-90) cc_final: 0.7192 (mpp80) REVERT: C 20 LYS cc_start: 0.7625 (ttpp) cc_final: 0.7206 (tptp) outliers start: 69 outliers final: 51 residues processed: 177 average time/residue: 1.2008 time to fit residues: 242.1334 Evaluate side-chains 171 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 113 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1004 LYS Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 166 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 GLN B 680 ASN B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.062630 restraints weight = 110915.808| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.72 r_work: 0.2730 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20454 Z= 0.159 Angle : 0.511 5.343 27862 Z= 0.262 Chirality : 0.041 0.144 3182 Planarity : 0.004 0.047 3658 Dihedral : 7.340 102.644 2887 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.14 % Allowed : 24.92 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.03 (0.17), residues: 2634 helix: 1.85 (0.16), residues: 1156 sheet: 0.76 (0.32), residues: 288 loop : -0.50 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 80 TYR 0.014 0.001 TYR B1018 PHE 0.008 0.001 PHE C 83 TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00373 (20452) covalent geometry : angle 0.51100 (27862) hydrogen bonds : bond 0.03982 ( 940) hydrogen bonds : angle 4.22155 ( 2670) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 116 time to evaluate : 1.015 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 450 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8603 (mm-30) REVERT: A 479 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: A 512 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: A 1002 GLN cc_start: 0.7978 (mm-40) cc_final: 0.6990 (pp30) REVERT: A 1077 ARG cc_start: 0.6964 (mtt-85) cc_final: 0.6547 (mtt90) REVERT: B 183 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 363 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7323 (pt) REVERT: B 375 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: B 908 ARG cc_start: 0.8111 (mmp80) cc_final: 0.7896 (mmm160) REVERT: B 1082 ARG cc_start: 0.7633 (mpt-90) cc_final: 0.7041 (mpp80) REVERT: C 20 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7212 (tptp) outliers start: 67 outliers final: 49 residues processed: 178 average time/residue: 1.1517 time to fit residues: 236.3367 Evaluate side-chains 168 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 176 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 250 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.063058 restraints weight = 110523.140| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.70 r_work: 0.2738 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20454 Z= 0.136 Angle : 0.504 5.738 27862 Z= 0.258 Chirality : 0.040 0.145 3182 Planarity : 0.004 0.047 3658 Dihedral : 7.310 101.778 2886 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.67 % Allowed : 25.39 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.09 (0.17), residues: 2634 helix: 1.90 (0.16), residues: 1156 sheet: 0.83 (0.32), residues: 286 loop : -0.47 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 80 TYR 0.013 0.001 TYR B1018 PHE 0.013 0.001 PHE B 973 TRP 0.009 0.001 TRP B1226 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00319 (20452) covalent geometry : angle 0.50424 (27862) hydrogen bonds : bond 0.03825 ( 940) hydrogen bonds : angle 4.16759 ( 2670) Misc. bond : bond 0.00053 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 1.098 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 450 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8591 (mm-30) REVERT: A 512 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: A 1002 GLN cc_start: 0.7989 (mm-40) cc_final: 0.6998 (pp30) REVERT: A 1077 ARG cc_start: 0.6953 (mtt-85) cc_final: 0.6521 (mtt90) REVERT: A 1171 VAL cc_start: 0.8506 (t) cc_final: 0.8278 (m) REVERT: A 1175 ASP cc_start: 0.9375 (t0) cc_final: 0.9091 (t0) REVERT: B 183 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 363 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7283 (pt) REVERT: B 375 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: B 908 ARG cc_start: 0.8097 (mmp80) cc_final: 0.7884 (mmm160) REVERT: B 1082 ARG cc_start: 0.7603 (mpt-90) cc_final: 0.7161 (mpp80) REVERT: B 1183 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: C 20 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7205 (tptp) outliers start: 57 outliers final: 44 residues processed: 169 average time/residue: 1.1325 time to fit residues: 219.1421 Evaluate side-chains 164 residues out of total 2131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1054 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1127 LEU Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 130 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B 981 GLN B1083 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063561 restraints weight = 110960.004| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.72 r_work: 0.2750 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20454 Z= 0.112 Angle : 0.497 6.929 27862 Z= 0.253 Chirality : 0.040 0.145 3182 Planarity : 0.004 0.047 3658 Dihedral : 7.226 100.650 2884 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.44 % Allowed : 25.67 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.18 (0.17), residues: 2634 helix: 1.98 (0.16), residues: 1156 sheet: 0.82 (0.32), residues: 288 loop : -0.42 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 80 TYR 0.011 0.001 TYR B1018 PHE 0.008 0.001 PHE C 83 TRP 0.010 0.001 TRP B1226 HIS 0.007 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00262 (20452) covalent geometry : angle 0.49710 (27862) hydrogen bonds : bond 0.03598 ( 940) hydrogen bonds : angle 4.09676 ( 2670) Misc. bond : bond 0.00021 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11242.89 seconds wall clock time: 190 minutes 29.66 seconds (11429.66 seconds total)