Starting phenix.real_space_refine on Thu Aug 6 05:30:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kof_62474/08_2026/9kof_62474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kof_62474/08_2026/9kof_62474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kof_62474/08_2026/9kof_62474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kof_62474/08_2026/9kof_62474.map" model { file = "/net/cci-nas-00/data/ceres_data/9kof_62474/08_2026/9kof_62474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kof_62474/08_2026/9kof_62474.cif" } resolution = 3.07 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= -0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 28 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 8382 2.51 5 N 2336 2.21 5 O 2419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13225 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3201 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 19, 'TRANS': 411} Chain breaks: 6 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 10, 'TYR:plan': 2, 'GLN:plan1': 6, 'PHE:plan': 2, 'ASP:plan': 5, 'HIS:plan': 3, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 185 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2877 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3153 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 369} Chain breaks: 5 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 861 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3027 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.22 Number of scatterers: 13225 At special positions: 0 Unit cell: (91.545, 109.854, 158.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 2419 8.00 N 2336 7.00 C 8382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 530 " distance=1.84 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 543 " distance=1.85 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 547 " distance=1.87 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 549 " distance=1.87 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 543 " distance=2.19 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 549 " distance=2.18 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 553 " distance=2.05 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 536 " distance=2.04 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 547 " distance=2.21 Simple disulfide: pdb=" SG CYS A 547 " - pdb=" SG CYS A 549 " distance=2.20 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 571 " distance=2.11 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 573 " distance=1.91 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 580 " distance=1.93 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 585 " distance=2.07 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 588 " distance=1.96 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 601 " distance=2.35 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 566 " distance=1.94 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 571 " distance=1.92 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 588 " distance=2.24 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 571 " distance=2.24 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 588 " distance=1.88 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 573 " distance=2.12 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 588 " distance=1.79 Simple disulfide: pdb=" SG CYS A 573 " - pdb=" SG CYS A 580 " distance=2.27 Simple disulfide: pdb=" SG CYS A 573 " - pdb=" SG CYS A 588 " distance=2.09 Simple disulfide: pdb=" SG CYS A 573 " - pdb=" SG CYS A 601 " distance=1.89 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 585 " distance=2.01 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 601 " distance=1.86 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 604 " distance=1.97 Simple disulfide: pdb=" SG CYS A 588 " - pdb=" SG CYS A 601 " distance=2.06 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 604 " distance=2.06 Simple disulfide: pdb=" SG CYS D 409 " - pdb=" SG CYS D 429 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 620.8 milliseconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 23 sheets defined 20.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 36 through 62 removed outlier: 4.223A pdb=" N LEU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.015A pdb=" N VAL A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.452A pdb=" N ILE A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 475 removed outlier: 3.782A pdb=" N VAL A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.670A pdb=" N ALA A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.870A pdb=" N ASP A 652 " --> pdb=" O GLN A 648 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.810A pdb=" N GLY D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 278 removed outlier: 3.948A pdb=" N ALA D 273 " --> pdb=" O ARG D 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 275 " --> pdb=" O MET D 271 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.698A pdb=" N ILE D 343 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 553 removed outlier: 3.869A pdb=" N THR G 550 " --> pdb=" O ARG G 546 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG G 551 " --> pdb=" O PHE G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 563 Processing helix chain 'G' and resid 574 through 580 removed outlier: 4.328A pdb=" N LYS G 578 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR G 579 " --> pdb=" O ILE G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 595 removed outlier: 3.812A pdb=" N LYS G 588 " --> pdb=" O ASP G 584 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU G 595 " --> pdb=" O LYS G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 686 removed outlier: 3.667A pdb=" N GLU G 686 " --> pdb=" O ASN G 683 " (cutoff:3.500A) Processing helix chain 'G' and resid 795 through 799 removed outlier: 3.759A pdb=" N SER G 798 " --> pdb=" O GLU G 795 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 799 " --> pdb=" O THR G 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 795 through 799' Processing helix chain 'G' and resid 907 through 919 removed outlier: 3.552A pdb=" N LEU G 912 " --> pdb=" O LEU G 908 " (cutoff:3.500A) Processing helix chain 'G' and resid 950 through 956 removed outlier: 3.917A pdb=" N HIS G 955 " --> pdb=" O GLN G 952 " (cutoff:3.500A) Processing helix chain 'G' and resid 1037 through 1050 removed outlier: 3.750A pdb=" N GLU G1042 " --> pdb=" O GLU G1038 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR G1044 " --> pdb=" O LEU G1040 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN G1047 " --> pdb=" O LYS G1043 " (cutoff:3.500A) Processing helix chain 'G' and resid 1056 through 1073 removed outlier: 4.353A pdb=" N GLU G1060 " --> pdb=" O GLU G1056 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL G1061 " --> pdb=" O GLY G1057 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET G1062 " --> pdb=" O GLU G1058 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN G1066 " --> pdb=" O MET G1062 " (cutoff:3.500A) Processing helix chain 'G' and resid 1076 through 1078 No H-bonds generated for 'chain 'G' and resid 1076 through 1078' Processing helix chain 'G' and resid 1079 through 1091 removed outlier: 3.620A pdb=" N VAL G1088 " --> pdb=" O CYS G1084 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU G1089 " --> pdb=" O MET G1085 " (cutoff:3.500A) Processing helix chain 'G' and resid 1094 through 1099 removed outlier: 3.928A pdb=" N LYS G1098 " --> pdb=" O LYS G1094 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN G1099 " --> pdb=" O ILE G1095 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1094 through 1099' Processing helix chain 'G' and resid 1100 through 1114 removed outlier: 3.590A pdb=" N HIS G1107 " --> pdb=" O ASN G1103 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G1108 " --> pdb=" O PHE G1104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G1109 " --> pdb=" O MET G1105 " (cutoff:3.500A) Processing helix chain 'G' and resid 1118 through 1130 removed outlier: 3.824A pdb=" N ILE G1122 " --> pdb=" O SER G1118 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP G1123 " --> pdb=" O ILE G1119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS G1124 " --> pdb=" O MET G1120 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 418 removed outlier: 3.618A pdb=" N LEU F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 470 No H-bonds generated for 'chain 'F' and resid 468 through 470' Processing helix chain 'F' and resid 481 through 486 removed outlier: 4.334A pdb=" N LEU F 486 " --> pdb=" O LYS F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 489 No H-bonds generated for 'chain 'F' and resid 487 through 489' Processing helix chain 'H' and resid 414 through 434 Processing helix chain 'H' and resid 435 through 437 No H-bonds generated for 'chain 'H' and resid 435 through 437' Processing helix chain 'H' and resid 738 through 743 removed outlier: 4.349A pdb=" N ASP H 742 " --> pdb=" O GLU H 738 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 6.466A pdb=" N LYS A 99 " --> pdb=" O VAL D 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.904A pdb=" N SER A 114 " --> pdb=" O GLY A 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.811A pdb=" N PHE A 120 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N SER A 647 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 669 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 614 through 618 Processing sheet with id=AA5, first strand: chain 'A' and resid 639 through 641 removed outlier: 4.135A pdb=" N SER A 639 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 708 " --> pdb=" O TYR A 641 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 82 through 89 removed outlier: 6.332A pdb=" N CYS D 84 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP D 438 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN D 86 " --> pdb=" O ARG D 436 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 436 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 428 " --> pdb=" O GLN D 415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN D 415 " --> pdb=" O VAL D 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.357A pdb=" N LEU D 111 " --> pdb=" O CYS D 126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE D 113 " --> pdb=" O TYR D 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154 removed outlier: 3.537A pdb=" N THR D 149 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 166 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 174 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 193 through 198 removed outlier: 6.595A pdb=" N VAL D 209 " --> pdb=" O ASN D 194 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU D 196 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU D 207 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE D 198 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU D 205 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 219 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU D 225 " --> pdb=" O ASN D 219 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N GLN D 292 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D 226 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE D 294 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 228 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.748A pdb=" N SER D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 309 through 315 removed outlier: 4.490A pdb=" N CYS D 311 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER D 323 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS D 332 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE D 352 " --> pdb=" O LYS D 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AB4, first strand: chain 'G' and resid 605 through 608 removed outlier: 3.880A pdb=" N GLN G 606 " --> pdb=" O ARG G 808 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG G 808 " --> pdb=" O GLN G 606 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR G 608 " --> pdb=" O THR G 806 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR G 806 " --> pdb=" O THR G 608 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY G 761 " --> pdb=" O LEU G 807 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 885 through 891 removed outlier: 6.798A pdb=" N PHE G 880 " --> pdb=" O ARG G 887 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN G 889 " --> pdb=" O TYR G 878 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR G 878 " --> pdb=" O GLN G 889 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU G 891 " --> pdb=" O ILE G 876 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE G 876 " --> pdb=" O GLU G 891 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE G 877 " --> pdb=" O ILE G 935 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL G 937 " --> pdb=" O PHE G 877 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN G 879 " --> pdb=" O VAL G 937 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE G 939 " --> pdb=" O GLN G 879 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LEU G 881 " --> pdb=" O ILE G 939 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 974 through 979 removed outlier: 6.669A pdb=" N VAL H 442 " --> pdb=" O LEU G 977 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS G 979 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASP H 440 " --> pdb=" O CYS G 979 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 441 " --> pdb=" O GLN H 784 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE H 779 " --> pdb=" O SER H 775 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 427 through 431 Processing sheet with id=AB8, first strand: chain 'F' and resid 433 through 439 removed outlier: 6.624A pdb=" N LEU F 448 " --> pdb=" O ILE F 435 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS F 437 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS F 446 " --> pdb=" O LYS F 437 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL F 460 " --> pdb=" O LEU F 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 455 through 457 removed outlier: 4.235A pdb=" N ARG H 472 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS H 471 " --> pdb=" O VAL H 491 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 511 through 513 removed outlier: 6.017A pdb=" N ARG H 553 " --> pdb=" O VAL H 598 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 561 through 566 removed outlier: 3.535A pdb=" N GLY H 563 " --> pdb=" O ALA H 577 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 611 through 614 removed outlier: 3.751A pdb=" N ASP H 613 " --> pdb=" O VAL H 627 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 661 through 662 Processing sheet with id=AC5, first strand: chain 'H' and resid 701 through 706 removed outlier: 3.956A pdb=" N GLN H 703 " --> pdb=" O SER H 717 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER H 717 " --> pdb=" O GLN H 703 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE H 749 " --> pdb=" O VAL H 725 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 909 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: 2.26 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 4779 1.38 - 1.53: 7770 1.53 - 1.68: 881 1.68 - 1.84: 113 1.84 - 1.99: 9 Bond restraints: 13552 Sorted by residual: bond pdb=" CB CYS A 573 " pdb=" SG CYS A 573 " ideal model delta sigma weight residual 1.808 1.992 -0.184 3.30e-02 9.18e+02 3.10e+01 bond pdb=" CB PRO G1021 " pdb=" CG PRO G1021 " ideal model delta sigma weight residual 1.492 1.661 -0.169 5.00e-02 4.00e+02 1.14e+01 bond pdb=" C2 SAH A 801 " pdb=" N3 SAH A 801 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.38e+00 bond pdb=" CA CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sigma weight residual 1.529 1.573 -0.044 1.53e-02 4.27e+03 8.11e+00 bond pdb=" C8 SAH A 801 " pdb=" N7 SAH A 801 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.68e+00 ... (remaining 13547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 18316 4.35 - 8.70: 56 8.70 - 13.04: 5 13.04 - 17.39: 1 17.39 - 21.74: 2 Bond angle restraints: 18380 Sorted by residual: angle pdb=" CA PRO G1021 " pdb=" N PRO G1021 " pdb=" CD PRO G1021 " ideal model delta sigma weight residual 112.00 97.49 14.51 1.40e+00 5.10e-01 1.07e+02 angle pdb=" CA CYS A 573 " pdb=" CB CYS A 573 " pdb=" SG CYS A 573 " ideal model delta sigma weight residual 114.40 136.14 -21.74 2.30e+00 1.89e-01 8.93e+01 angle pdb=" CA CYS A 604 " pdb=" CB CYS A 604 " pdb=" SG CYS A 604 " ideal model delta sigma weight residual 114.40 133.15 -18.75 2.30e+00 1.89e-01 6.65e+01 angle pdb=" CA CYS A 580 " pdb=" CB CYS A 580 " pdb=" SG CYS A 580 " ideal model delta sigma weight residual 114.40 127.13 -12.73 2.30e+00 1.89e-01 3.06e+01 angle pdb=" CA CYS A 530 " pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " ideal model delta sigma weight residual 114.40 125.31 -10.91 2.30e+00 1.89e-01 2.25e+01 ... (remaining 18375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6895 17.95 - 35.91: 918 35.91 - 53.86: 266 53.86 - 71.81: 55 71.81 - 89.77: 33 Dihedral angle restraints: 8167 sinusoidal: 3247 harmonic: 4920 Sorted by residual: dihedral pdb=" CA CYS A 534 " pdb=" C CYS A 534 " pdb=" N PRO A 535 " pdb=" CA PRO A 535 " ideal model delta harmonic sigma weight residual 180.00 -127.01 -52.99 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CB CYS A 523 " pdb=" SG CYS A 523 " pdb=" SG CYS A 549 " pdb=" CB CYS A 549 " ideal model delta sinusoidal sigma weight residual 93.00 -177.94 -89.06 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CB CYS A 547 " pdb=" SG CYS A 547 " pdb=" SG CYS A 549 " pdb=" CB CYS A 549 " ideal model delta sinusoidal sigma weight residual 93.00 4.04 88.96 1 1.00e+01 1.00e-02 9.43e+01 ... (remaining 8164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1205 0.032 - 0.064: 536 0.064 - 0.097: 176 0.097 - 0.129: 83 0.129 - 0.161: 9 Chirality restraints: 2009 Sorted by residual: chirality pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" C PRO A 535 " pdb=" CB PRO A 535 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CG LEU G 911 " pdb=" CB LEU G 911 " pdb=" CD1 LEU G 911 " pdb=" CD2 LEU G 911 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CG LEU H 552 " pdb=" CB LEU H 552 " pdb=" CD1 LEU H 552 " pdb=" CD2 LEU H 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 2006 not shown) Planarity restraints: 2363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G1020 " 0.094 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO G1021 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO G1021 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO G1021 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 534 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C CYS A 534 " 0.064 2.00e-02 2.50e+03 pdb=" O CYS A 534 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 535 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 541 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO H 542 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 542 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 542 " 0.026 5.00e-02 4.00e+02 ... (remaining 2360 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 282 2.67 - 3.23: 12293 3.23 - 3.78: 20426 3.78 - 4.34: 28126 4.34 - 4.90: 45596 Nonbonded interactions: 106723 Sorted by model distance: nonbonded pdb=" O CYS A 534 " pdb=" N CYS A 536 " model vdw 2.109 3.120 nonbonded pdb=" O ILE A 131 " pdb=" OH TYR D 308 " model vdw 2.134 3.040 nonbonded pdb=" O ALA A 687 " pdb=" OH TYR A 726 " model vdw 2.156 3.040 nonbonded pdb=" NZ LYS A 99 " pdb=" O MET D 180 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR H 525 " pdb=" O ASP H 529 " model vdw 2.205 3.040 ... (remaining 106718 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.315 13585 Z= 0.386 Angle : 1.330 42.060 18446 Z= 0.652 Chirality : 0.043 0.161 2009 Planarity : 0.005 0.130 2363 Dihedral : 17.830 89.767 4854 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.00 % Favored : 90.32 % Rotamer: Outliers : 0.36 % Allowed : 31.84 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.20), residues: 1633 helix: -0.80 (0.32), residues: 259 sheet: -1.01 (0.28), residues: 347 loop : -1.92 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 409 TYR 0.020 0.001 TYR A 728 PHE 0.018 0.001 PHE F 413 TRP 0.024 0.001 TRP H 586 HIS 0.005 0.001 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (13552) covalent geometry : angle 0.76147 / 0.39 (18380) SS BOND : bond 0.14343 / 10.83 ( 33) SS BOND : angle 18.24355 / 14.84 ( 66) hydrogen bonds : bond 0.25644 / 16.92 ( 331) hydrogen bonds : angle 9.48340 / 6.45 ( 909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.5401 (tmm) cc_final: 0.4195 (tpt) REVERT: G 585 MET cc_start: 0.4438 (ptm) cc_final: 0.4193 (ptm) REVERT: G 755 ARG cc_start: 0.7405 (tpp-160) cc_final: 0.7190 (tpt170) outliers start: 5 outliers final: 5 residues processed: 162 average time/residue: 0.1258 time to fit residues: 29.7673 Evaluate side-chains 146 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 608 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 525 HIS ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 648 GLN A 688 ASN G 568 HIS G 691 HIS G 757 GLN G 929 HIS G 940 ASN G 955 HIS H 503 ASN H 517 ASN H 617 HIS H 658 ASN H 754 HIS ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.190019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.129738 restraints weight = 18215.280| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.24 r_work: 0.3853 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.325 13585 Z= 0.418 Angle : 1.329 40.283 18446 Z= 0.651 Chirality : 0.047 0.198 2009 Planarity : 0.005 0.067 2363 Dihedral : 6.219 61.076 1804 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.17 % Favored : 89.16 % Rotamer: Outliers : 4.99 % Allowed : 27.28 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.19), residues: 1633 helix: -0.92 (0.30), residues: 279 sheet: -1.46 (0.26), residues: 347 loop : -2.07 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 409 TYR 0.023 0.002 TYR A 728 PHE 0.023 0.002 PHE D 113 TRP 0.024 0.002 TRP H 586 HIS 0.008 0.001 HIS G 975 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (13552) covalent geometry : angle 0.76664 / 0.40 (18380) SS BOND : bond 0.14326 / 10.81 ( 33) SS BOND : angle 18.16276 / 14.77 ( 66) hydrogen bonds : bond 0.04280 / 2.90 ( 331) hydrogen bonds : angle 6.52585 / 4.50 ( 909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 146 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6482 (mt) REVERT: A 644 GLU cc_start: 0.6289 (mt-10) cc_final: 0.6075 (mt-10) REVERT: G 542 THR cc_start: 0.7521 (m) cc_final: 0.7227 (p) REVERT: G 755 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.7456 (tpt170) REVERT: G 1045 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6798 (tt) REVERT: H 429 LYS cc_start: 0.8150 (tptp) cc_final: 0.6968 (mmtm) REVERT: H 482 GLU cc_start: 0.4529 (OUTLIER) cc_final: 0.4191 (tm-30) REVERT: H 541 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7139 (tmmt) REVERT: H 639 ARG cc_start: 0.6915 (ptt-90) cc_final: 0.6579 (pmt-80) REVERT: H 681 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7308 (mt) outliers start: 70 outliers final: 36 residues processed: 204 average time/residue: 0.1171 time to fit residues: 35.5795 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 929 HIS Chi-restraints excluded: chain G residue 936 ASP Chi-restraints excluded: chain G residue 976 ILE Chi-restraints excluded: chain G residue 1023 ARG Chi-restraints excluded: chain G residue 1045 ILE Chi-restraints excluded: chain G residue 1088 VAL Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 430 ILE Chi-restraints excluded: chain H residue 482 GLU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 585 LEU Chi-restraints excluded: chain H residue 608 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 630 ASP Chi-restraints excluded: chain H residue 681 LEU Chi-restraints excluded: chain H residue 770 VAL Chi-restraints excluded: chain H residue 772 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 11 optimal weight: 0.0270 chunk 94 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 140 optimal weight: 0.0370 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN ** G 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1068 HIS ** H 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.194933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.144176 restraints weight = 18115.139| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.12 r_work: 0.3953 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.323 13585 Z= 0.381 Angle : 1.273 40.210 18446 Z= 0.619 Chirality : 0.044 0.198 2009 Planarity : 0.004 0.047 2363 Dihedral : 5.673 60.175 1801 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.76 % Favored : 90.63 % Rotamer: Outliers : 4.56 % Allowed : 26.71 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.20), residues: 1633 helix: -0.78 (0.31), residues: 280 sheet: -1.34 (0.27), residues: 344 loop : -1.98 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 409 TYR 0.021 0.001 TYR A 728 PHE 0.015 0.001 PHE H 624 TRP 0.022 0.002 TRP H 586 HIS 0.009 0.001 HIS G 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (13552) covalent geometry : angle 0.68000 / 0.35 (18380) SS BOND : bond 0.14521 / 10.98 ( 33) SS BOND : angle 18.00859 / 14.63 ( 66) hydrogen bonds : bond 0.03447 / 2.29 ( 331) hydrogen bonds : angle 5.92166 / 4.09 ( 909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.2490 (tt) REVERT: A 149 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6474 (mt) REVERT: A 701 MET cc_start: 0.5930 (mtp) cc_final: 0.5158 (mtm) REVERT: D 101 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7164 (t80) REVERT: D 317 ASP cc_start: 0.8122 (m-30) cc_final: 0.7912 (m-30) REVERT: D 336 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: D 406 HIS cc_start: 0.4860 (OUTLIER) cc_final: 0.4056 (t-90) REVERT: G 900 TRP cc_start: 0.7134 (m-90) cc_final: 0.6918 (m-90) REVERT: G 975 HIS cc_start: 0.5413 (OUTLIER) cc_final: 0.4482 (m-70) REVERT: G 1011 ARG cc_start: 0.4896 (OUTLIER) cc_final: 0.4477 (mtt-85) REVERT: G 1045 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6620 (tt) REVERT: G 1062 MET cc_start: 0.6475 (tpp) cc_final: 0.6198 (tpp) REVERT: H 541 LYS cc_start: 0.7577 (tmtt) cc_final: 0.7028 (tmmt) REVERT: H 589 SER cc_start: 0.1986 (OUTLIER) cc_final: 0.1754 (p) REVERT: H 639 ARG cc_start: 0.6806 (ptt-90) cc_final: 0.6360 (ptt-90) outliers start: 64 outliers final: 29 residues processed: 207 average time/residue: 0.1152 time to fit residues: 35.5554 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1011 ARG Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1045 ILE Chi-restraints excluded: chain G residue 1088 VAL Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 589 SER Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 630 ASP Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 771 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 0.0030 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 929 HIS G1047 GLN ** G1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.196195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.142080 restraints weight = 18110.024| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.39 r_work: 0.3967 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3970 r_free = 0.3970 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.323 13585 Z= 0.379 Angle : 1.268 41.099 18446 Z= 0.613 Chirality : 0.044 0.289 2009 Planarity : 0.004 0.046 2363 Dihedral : 5.322 60.570 1798 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.76 % Favored : 90.69 % Rotamer: Outliers : 3.85 % Allowed : 26.99 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.20), residues: 1633 helix: -0.60 (0.32), residues: 273 sheet: -1.25 (0.26), residues: 357 loop : -1.88 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 409 TYR 0.019 0.001 TYR A 728 PHE 0.012 0.001 PHE D 113 TRP 0.016 0.001 TRP H 682 HIS 0.003 0.001 HIS G 975 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 (13552) covalent geometry : angle 0.67113 / 0.34 (18380) SS BOND : bond 0.14543 / 11.00 ( 33) SS BOND : angle 17.99941 / 14.61 ( 66) hydrogen bonds : bond 0.03053 / 2.03 ( 331) hydrogen bonds : angle 5.60316 / 3.87 ( 909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5533 (mt-10) REVERT: A 701 MET cc_start: 0.6249 (mtp) cc_final: 0.5523 (mtm) REVERT: D 101 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7235 (t80) REVERT: D 317 ASP cc_start: 0.8035 (m-30) cc_final: 0.7791 (m-30) REVERT: D 336 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6878 (tpp) REVERT: D 406 HIS cc_start: 0.4902 (OUTLIER) cc_final: 0.4084 (t-90) REVERT: G 747 MET cc_start: 0.4194 (pmm) cc_final: 0.3939 (pmm) REVERT: G 975 HIS cc_start: 0.5287 (OUTLIER) cc_final: 0.4283 (m-70) REVERT: G 1011 ARG cc_start: 0.4998 (OUTLIER) cc_final: 0.4477 (mtt-85) REVERT: G 1045 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6782 (tt) REVERT: G 1058 GLU cc_start: 0.4335 (OUTLIER) cc_final: 0.4033 (pt0) REVERT: H 589 SER cc_start: 0.2117 (OUTLIER) cc_final: 0.1831 (p) REVERT: H 639 ARG cc_start: 0.6687 (ptt-90) cc_final: 0.6288 (ptt-90) outliers start: 54 outliers final: 32 residues processed: 194 average time/residue: 0.1073 time to fit residues: 31.5115 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain G residue 582 VAL Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 929 HIS Chi-restraints excluded: chain G residue 936 ASP Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1011 ARG Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1045 ILE Chi-restraints excluded: chain G residue 1058 GLU Chi-restraints excluded: chain G residue 1088 VAL Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 589 SER Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 634 MET Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 771 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.192200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.137934 restraints weight = 18262.120| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.53 r_work: 0.3882 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.325 13585 Z= 0.397 Angle : 1.286 40.648 18446 Z= 0.625 Chirality : 0.046 0.203 2009 Planarity : 0.004 0.047 2363 Dihedral : 5.586 60.869 1798 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.23 % Favored : 89.28 % Rotamer: Outliers : 4.27 % Allowed : 26.21 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.20), residues: 1633 helix: -0.76 (0.30), residues: 285 sheet: -1.23 (0.26), residues: 379 loop : -1.97 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 409 TYR 0.026 0.002 TYR H 513 PHE 0.019 0.002 PHE D 113 TRP 0.023 0.002 TRP H 682 HIS 0.013 0.001 HIS G 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (13552) covalent geometry : angle 0.70622 / 0.36 (18380) SS BOND : bond 0.14495 / 10.95 ( 33) SS BOND : angle 17.97277 / 14.60 ( 66) hydrogen bonds : bond 0.03344 / 2.24 ( 331) hydrogen bonds : angle 5.60684 / 3.86 ( 909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 101 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7264 (t80) REVERT: D 140 ASP cc_start: 0.6423 (t70) cc_final: 0.5742 (t70) REVERT: D 173 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7521 (mtt-85) REVERT: D 195 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: D 336 MET cc_start: 0.7340 (tpp) cc_final: 0.7115 (tpp) REVERT: D 406 HIS cc_start: 0.4797 (OUTLIER) cc_final: 0.3764 (t-170) REVERT: G 747 MET cc_start: 0.4499 (pmm) cc_final: 0.4244 (pmm) REVERT: G 900 TRP cc_start: 0.6801 (m-90) cc_final: 0.6221 (m-90) REVERT: G 975 HIS cc_start: 0.5490 (OUTLIER) cc_final: 0.4542 (m-70) REVERT: G 1033 ASP cc_start: 0.5821 (OUTLIER) cc_final: 0.5262 (m-30) REVERT: G 1045 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6271 (pt) REVERT: G 1062 MET cc_start: 0.6558 (tpp) cc_final: 0.6211 (tpp) REVERT: H 417 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: H 429 LYS cc_start: 0.8147 (tptp) cc_final: 0.6953 (mmtm) REVERT: H 514 MET cc_start: 0.6263 (ttp) cc_final: 0.5834 (ttp) REVERT: H 589 SER cc_start: 0.2405 (OUTLIER) cc_final: 0.2205 (p) REVERT: H 639 ARG cc_start: 0.6761 (ptt-90) cc_final: 0.6291 (ptt-90) outliers start: 60 outliers final: 38 residues processed: 192 average time/residue: 0.1135 time to fit residues: 32.7248 Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 694 ASN Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 929 HIS Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1045 ILE Chi-restraints excluded: chain G residue 1088 VAL Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 585 LEU Chi-restraints excluded: chain H residue 589 SER Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 630 ASP Chi-restraints excluded: chain H residue 634 MET Chi-restraints excluded: chain H residue 687 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 137 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 132 optimal weight: 0.0980 chunk 134 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** G 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 929 HIS H 686 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.193876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.138289 restraints weight = 18078.289| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 3.32 r_work: 0.3914 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.328 13585 Z= 0.384 Angle : 1.266 41.981 18446 Z= 0.614 Chirality : 0.044 0.201 2009 Planarity : 0.004 0.047 2363 Dihedral : 5.390 60.884 1798 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.37 % Favored : 90.20 % Rotamer: Outliers : 3.85 % Allowed : 26.92 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.20), residues: 1633 helix: -0.68 (0.30), residues: 283 sheet: -1.21 (0.26), residues: 379 loop : -1.92 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 409 TYR 0.020 0.001 TYR H 513 PHE 0.016 0.001 PHE D 113 TRP 0.017 0.002 TRP H 682 HIS 0.005 0.001 HIS G 975 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (13552) covalent geometry : angle 0.66890 / 0.34 (18380) SS BOND : bond 0.14552 / 10.99 ( 33) SS BOND : angle 17.97499 / 14.58 ( 66) hydrogen bonds : bond 0.03000 / 1.99 ( 331) hydrogen bonds : angle 5.41007 / 3.72 ( 909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 MET cc_start: 0.6327 (mtp) cc_final: 0.5523 (mtm) REVERT: D 101 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7258 (t80) REVERT: D 317 ASP cc_start: 0.8078 (m-30) cc_final: 0.7861 (m-30) REVERT: D 406 HIS cc_start: 0.4861 (OUTLIER) cc_final: 0.3931 (t-90) REVERT: G 747 MET cc_start: 0.4485 (pmm) cc_final: 0.4273 (pmm) REVERT: G 763 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.5382 (m-80) REVERT: G 900 TRP cc_start: 0.7209 (m-90) cc_final: 0.6968 (m-90) REVERT: G 975 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.4137 (m-70) REVERT: G 1045 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6743 (tt) REVERT: H 417 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: H 429 LYS cc_start: 0.8052 (tptp) cc_final: 0.6879 (mmtm) REVERT: H 639 ARG cc_start: 0.6734 (ptt-90) cc_final: 0.6325 (ptt-90) outliers start: 54 outliers final: 35 residues processed: 187 average time/residue: 0.1234 time to fit residues: 34.2043 Evaluate side-chains 175 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 954 ILE Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1045 ILE Chi-restraints excluded: chain G residue 1088 VAL Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 585 LEU Chi-restraints excluded: chain H residue 608 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 634 MET Chi-restraints excluded: chain H residue 687 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 0.0980 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN D 258 HIS G 552 ASN G 614 HIS G 804 GLN ** G 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.188913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.128997 restraints weight = 18180.583| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.16 r_work: 0.3842 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.329 13585 Z= 0.421 Angle : 1.309 41.460 18446 Z= 0.638 Chirality : 0.047 0.203 2009 Planarity : 0.005 0.047 2363 Dihedral : 5.836 61.359 1798 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.15 % Favored : 88.36 % Rotamer: Outliers : 3.99 % Allowed : 27.14 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.20), residues: 1633 helix: -0.66 (0.30), residues: 282 sheet: -1.35 (0.26), residues: 385 loop : -2.07 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 409 TYR 0.025 0.002 TYR H 665 PHE 0.024 0.002 PHE D 113 TRP 0.024 0.002 TRP H 682 HIS 0.011 0.001 HIS D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (13552) covalent geometry : angle 0.74967 / 0.38 (18380) SS BOND : bond 0.14542 / 10.97 ( 33) SS BOND : angle 17.95642 / 14.57 ( 66) hydrogen bonds : bond 0.03569 / 2.41 ( 331) hydrogen bonds : angle 5.71081 / 3.93 ( 909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 101 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7326 (t80) REVERT: D 173 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (mtt-85) REVERT: D 195 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: D 406 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.4097 (t-90) REVERT: G 546 ARG cc_start: 0.5350 (mmm160) cc_final: 0.4939 (mmm160) REVERT: G 975 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.4970 (m-70) REVERT: H 639 ARG cc_start: 0.6868 (ptt-90) cc_final: 0.6443 (ptt-90) outliers start: 56 outliers final: 37 residues processed: 189 average time/residue: 0.1227 time to fit residues: 33.9770 Evaluate side-chains 172 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 936 ASP Chi-restraints excluded: chain G residue 954 ILE Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1088 VAL Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 608 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 704 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 95 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 157 optimal weight: 0.9980 chunk 152 optimal weight: 0.0270 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN G 614 HIS ** G1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.190026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.132604 restraints weight = 18143.484| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.49 r_work: 0.3836 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.326 13585 Z= 0.409 Angle : 1.298 41.255 18446 Z= 0.632 Chirality : 0.046 0.201 2009 Planarity : 0.005 0.078 2363 Dihedral : 5.801 61.102 1798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.47 % Favored : 89.10 % Rotamer: Outliers : 3.77 % Allowed : 28.28 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.20), residues: 1633 helix: -0.67 (0.30), residues: 282 sheet: -1.40 (0.26), residues: 385 loop : -2.11 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 409 TYR 0.023 0.002 TYR A 728 PHE 0.022 0.002 PHE D 113 TRP 0.026 0.002 TRP H 616 HIS 0.009 0.001 HIS D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (13552) covalent geometry : angle 0.73190 / 0.37 (18380) SS BOND : bond 0.14536 / 10.98 ( 33) SS BOND : angle 17.94231 / 14.57 ( 66) hydrogen bonds : bond 0.03406 / 2.29 ( 331) hydrogen bonds : angle 5.63490 / 3.89 ( 909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.497 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 128 LEU cc_start: 0.3319 (OUTLIER) cc_final: 0.2802 (tt) REVERT: D 101 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7348 (t80) REVERT: D 173 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7593 (mtt-85) REVERT: D 195 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: D 406 HIS cc_start: 0.4740 (OUTLIER) cc_final: 0.4044 (t-90) REVERT: G 975 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.5375 (m-70) REVERT: F 409 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7314 (tmm-80) REVERT: H 585 LEU cc_start: 0.8442 (tp) cc_final: 0.8056 (pp) REVERT: H 639 ARG cc_start: 0.6906 (ptt-90) cc_final: 0.6477 (ptt-90) outliers start: 53 outliers final: 41 residues processed: 188 average time/residue: 0.0901 time to fit residues: 25.2169 Evaluate side-chains 180 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 954 ILE Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 608 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 704 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 614 HIS ** G1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.192380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135754 restraints weight = 18120.092| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.27 r_work: 0.3898 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.325 13585 Z= 0.383 Angle : 1.271 41.296 18446 Z= 0.616 Chirality : 0.045 0.206 2009 Planarity : 0.004 0.055 2363 Dihedral : 5.476 60.729 1798 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.12 % Favored : 90.45 % Rotamer: Outliers : 3.77 % Allowed : 27.85 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.20), residues: 1633 helix: -0.54 (0.30), residues: 281 sheet: -1.39 (0.25), residues: 391 loop : -1.94 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 409 TYR 0.020 0.001 TYR A 728 PHE 0.015 0.001 PHE D 113 TRP 0.023 0.002 TRP H 682 HIS 0.007 0.001 HIS H 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (13552) covalent geometry : angle 0.68247 / 0.34 (18380) SS BOND : bond 0.14514 / 10.97 ( 33) SS BOND : angle 17.94682 / 14.57 ( 66) hydrogen bonds : bond 0.02964 / 1.97 ( 331) hydrogen bonds : angle 5.37181 / 3.72 ( 909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.3347 (OUTLIER) cc_final: 0.2811 (tt) REVERT: A 603 ASN cc_start: 0.5804 (OUTLIER) cc_final: 0.5580 (m-40) REVERT: D 101 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7242 (t80) REVERT: D 173 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7473 (mtt-85) REVERT: D 195 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: G 763 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.5137 (m-80) REVERT: G 975 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5518 (m-70) REVERT: H 417 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: H 429 LYS cc_start: 0.8040 (tptp) cc_final: 0.6840 (mmtm) REVERT: H 514 MET cc_start: 0.5804 (ttp) cc_final: 0.5437 (ttp) REVERT: H 565 SER cc_start: 0.7233 (t) cc_final: 0.6727 (p) REVERT: H 585 LEU cc_start: 0.8486 (tp) cc_final: 0.8127 (pp) REVERT: H 639 ARG cc_start: 0.6888 (ptt-90) cc_final: 0.6498 (ptt-90) outliers start: 53 outliers final: 36 residues processed: 189 average time/residue: 0.0972 time to fit residues: 27.3907 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 954 ILE Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain G residue 1109 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 608 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 780 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 ASN D 406 HIS G 614 HIS ** G1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.194225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135450 restraints weight = 18024.208| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.58 r_work: 0.3917 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.323 13585 Z= 0.379 Angle : 1.270 41.339 18446 Z= 0.615 Chirality : 0.044 0.220 2009 Planarity : 0.004 0.054 2363 Dihedral : 5.393 60.466 1798 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.94 % Favored : 90.63 % Rotamer: Outliers : 2.64 % Allowed : 29.06 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1633 helix: -0.39 (0.31), residues: 275 sheet: -1.21 (0.27), residues: 355 loop : -1.82 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 409 TYR 0.019 0.001 TYR A 728 PHE 0.020 0.001 PHE H 694 TRP 0.027 0.002 TRP H 616 HIS 0.005 0.001 HIS H 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13552) covalent geometry : angle 0.67960 / 0.34 (18380) SS BOND : bond 0.14494 / 10.96 ( 33) SS BOND : angle 17.94487 / 14.57 ( 66) hydrogen bonds : bond 0.02864 / 1.92 ( 331) hydrogen bonds : angle 5.19367 / 3.59 ( 909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.3213 (OUTLIER) cc_final: 0.2677 (tt) REVERT: A 603 ASN cc_start: 0.5781 (OUTLIER) cc_final: 0.5536 (m110) REVERT: A 644 GLU cc_start: 0.5891 (mt-10) cc_final: 0.5663 (mt-10) REVERT: A 645 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6937 (mp) REVERT: A 675 VAL cc_start: 0.6399 (t) cc_final: 0.4480 (m) REVERT: D 101 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7161 (t80) REVERT: D 173 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7421 (mtt-85) REVERT: D 317 ASP cc_start: 0.8135 (m-30) cc_final: 0.7926 (m-30) REVERT: G 763 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5603 (m-80) REVERT: H 417 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: H 429 LYS cc_start: 0.8059 (tptp) cc_final: 0.6879 (mmtm) REVERT: H 585 LEU cc_start: 0.8530 (tp) cc_final: 0.8291 (pp) REVERT: H 639 ARG cc_start: 0.6859 (ptt-90) cc_final: 0.6480 (ptt-90) outliers start: 37 outliers final: 26 residues processed: 175 average time/residue: 0.0943 time to fit residues: 24.7088 Evaluate side-chains 169 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 728 TYR Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain G residue 763 TYR Chi-restraints excluded: chain G residue 927 VAL Chi-restraints excluded: chain G residue 975 HIS Chi-restraints excluded: chain G residue 1033 ASP Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 495 THR Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 468 PHE Chi-restraints excluded: chain H residue 529 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 608 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 687 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 614 HIS G1103 ASN ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.192516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.136577 restraints weight = 17922.272| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.18 r_work: 0.3911 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.324 13585 Z= 0.385 Angle : 1.276 41.307 18446 Z= 0.618 Chirality : 0.045 0.215 2009 Planarity : 0.004 0.051 2363 Dihedral : 5.457 61.461 1798 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.43 % Favored : 90.14 % Rotamer: Outliers : 2.71 % Allowed : 29.13 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1633 helix: -0.36 (0.31), residues: 277 sheet: -1.24 (0.26), residues: 362 loop : -1.81 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 409 TYR 0.022 0.001 TYR H 665 PHE 0.019 0.001 PHE H 694 TRP 0.037 0.002 TRP H 616 HIS 0.007 0.001 HIS H 607 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (13552) covalent geometry : angle 0.69377 / 0.35 (18380) SS BOND : bond 0.14492 / 10.95 ( 33) SS BOND : angle 17.92064 / 14.56 ( 66) hydrogen bonds : bond 0.02933 / 1.96 ( 331) hydrogen bonds : angle 5.20285 / 3.60 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4367.27 seconds wall clock time: 75 minutes 20.88 seconds (4520.88 seconds total)