Starting phenix.real_space_refine on Thu Sep 18 05:39:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s9v_24938/09_2025/7s9v_24938.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s9v_24938/09_2025/7s9v_24938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s9v_24938/09_2025/7s9v_24938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s9v_24938/09_2025/7s9v_24938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s9v_24938/09_2025/7s9v_24938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s9v_24938/09_2025/7s9v_24938.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 73 5.16 5 C 8981 2.51 5 N 2558 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14286 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1296, 10121 Classifications: {'peptide': 1296} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1227} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 4138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4138 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 491} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.37, per 1000 atoms: 0.24 Number of scatterers: 14286 At special positions: 0 Unit cell: (95.7, 125.4, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 2 15.00 O 2672 8.00 N 2558 7.00 C 8981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 653.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 35.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.711A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.949A pdb=" N ASP A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 133 through 149 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.534A pdb=" N ARG A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 168' Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.581A pdb=" N GLU A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.559A pdb=" N ILE A 192 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.728A pdb=" N HIS A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.006A pdb=" N ALA A 346 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 440 through 450 removed outlier: 3.508A pdb=" N ARG A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.515A pdb=" N ALA A 458 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 484 removed outlier: 4.139A pdb=" N VAL A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 521 removed outlier: 4.004A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 551 removed outlier: 4.438A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.528A pdb=" N LYS A 559 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 560 " --> pdb=" O LEU A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 569 through 584 Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.656A pdb=" N VAL A 592 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 626 removed outlier: 3.862A pdb=" N GLY A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 618 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.781A pdb=" N GLY A 633 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 675 removed outlier: 3.788A pdb=" N LEU A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.617A pdb=" N ILE A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 4.447A pdb=" N THR A 774 " --> pdb=" O LYS A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 790 Processing helix chain 'A' and resid 802 through 809 removed outlier: 3.532A pdb=" N ALA A 805 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 807 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 808 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 816 removed outlier: 4.085A pdb=" N VAL A 813 " --> pdb=" O ARG A 810 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 814 " --> pdb=" O GLY A 811 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 815 " --> pdb=" O GLN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 872 through 890 removed outlier: 3.574A pdb=" N GLY A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 890 " --> pdb=" O VAL A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.522A pdb=" N GLN A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 987 removed outlier: 3.695A pdb=" N HIS A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 994 Proline residue: A 992 - end of helix Processing helix chain 'A' and resid 1002 through 1023 removed outlier: 3.739A pdb=" N ARG A1011 " --> pdb=" O GLY A1007 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN A1018 " --> pdb=" O GLU A1014 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A1019 " --> pdb=" O ASP A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1061 Processing helix chain 'A' and resid 1117 through 1126 removed outlier: 3.509A pdb=" N TYR A1121 " --> pdb=" O GLY A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1153 removed outlier: 3.687A pdb=" N THR A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1160 through 1165 removed outlier: 4.010A pdb=" N VAL A1165 " --> pdb=" O TYR A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1192 removed outlier: 3.974A pdb=" N ARG A1180 " --> pdb=" O ARG A1176 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR A1183 " --> pdb=" O ASP A1179 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A1184 " --> pdb=" O ARG A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 removed outlier: 4.003A pdb=" N GLY A1204 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A1206 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1230 Processing helix chain 'A' and resid 1231 through 1254 removed outlier: 3.581A pdb=" N LYS A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A1252 " --> pdb=" O GLU A1248 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1253 " --> pdb=" O TRP A1249 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.533A pdb=" N ARG B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.514A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.985A pdb=" N ALA B 126 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 212 through 220 removed outlier: 6.765A pdb=" N GLY B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS B 217 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA B 218 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 220 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 346 removed outlier: 4.470A pdb=" N GLU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.846A pdb=" N SER B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.852A pdb=" N SER B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 497 removed outlier: 4.092A pdb=" N ALA B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 480 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.607A pdb=" N ASP B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 539' Processing helix chain 'B' and resid 541 through 556 removed outlier: 4.073A pdb=" N GLY B 546 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 569 through 574 removed outlier: 4.200A pdb=" N ASP B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 6.871A pdb=" N THR A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER A 70 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 76 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE A 68 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE A 78 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG A 64 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET A 82 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 62 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN A 84 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR A 60 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N LYS A 86 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 12.544A pdb=" N ASN A 58 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 50 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TRP A 14 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 53 " --> pdb=" O TRP A 14 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 16 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 105 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 160 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 158 through 160 current: chain 'A' and resid 280 through 293 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 280 through 293 current: chain 'A' and resid 414 through 420 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 202 through 203 current: chain 'B' and resid 108 through 111 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 108 through 111 current: chain 'B' and resid 130 through 136 removed outlier: 4.587A pdb=" N PHE B 131 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 148 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS B 146 " --> pdb=" O GLY B 135 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 146 through 152 current: chain 'B' and resid 199 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 4.738A pdb=" N LEU A 327 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS A 320 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP A 325 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 330 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 427 removed outlier: 3.510A pdb=" N TYR A 425 " --> pdb=" O TYR A 954 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG A 953 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR A1138 " --> pdb=" O ARG A 953 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 955 " --> pdb=" O THR A1138 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A1140 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 957 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA7, first strand: chain 'A' and resid 782 through 783 removed outlier: 6.782A pdb=" N GLY A 689 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR A 800 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TRP A 691 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR A 598 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ALA A 905 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP A 600 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR A 907 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 602 " --> pdb=" O THR A 907 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 599 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE A 928 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 601 " --> pdb=" O PHE A 928 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 743 through 745 Processing sheet with id=AA9, first strand: chain 'A' and resid 822 through 823 removed outlier: 3.652A pdb=" N LYS A 852 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 894 removed outlier: 3.506A pdb=" N TRP A 892 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.325A pdb=" N MET A 996 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA A1093 " --> pdb=" O MET A 996 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY A 998 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 997 " --> pdb=" O ALA A1110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1068 through 1070 Processing sheet with id=AB4, first strand: chain 'A' and resid 1259 through 1261 removed outlier: 6.483A pdb=" N ILE A1259 " --> pdb=" O VAL A1273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 12 removed outlier: 3.700A pdb=" N THR B 7 " --> pdb=" O MET A1304 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A1302 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU B 11 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A1300 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A1305 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 69 through 71 current: chain 'B' and resid 372 through 391 removed outlier: 3.904A pdb=" N ARG B 374 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG B 380 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 426 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG B 382 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 424 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 384 " --> pdb=" O ASN B 422 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN B 422 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA B 386 " --> pdb=" O PRO B 420 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LEU B 388 " --> pdb=" O TRP B 418 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N TRP B 418 " --> pdb=" O LEU B 388 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 418 through 433 current: chain 'B' and resid 519 through 524 Processing sheet with id=AB7, first strand: chain 'B' and resid 164 through 166 407 hydrogen bonds defined for protein. 1128 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: 2.62 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4771 1.34 - 1.46: 2178 1.46 - 1.57: 7525 1.57 - 1.69: 3 1.69 - 1.81: 116 Bond restraints: 14593 Sorted by residual: bond pdb=" CB PRO A 929 " pdb=" CG PRO A 929 " ideal model delta sigma weight residual 1.506 1.410 0.096 3.90e-02 6.57e+02 6.00e+00 bond pdb=" C TRP B 19 " pdb=" N THR B 20 " ideal model delta sigma weight residual 1.333 1.302 0.031 1.34e-02 5.57e+03 5.37e+00 bond pdb=" CB ARG A 418 " pdb=" CG ARG A 418 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.07e+00 bond pdb=" CB ILE B 431 " pdb=" CG2 ILE B 431 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.65e+00 bond pdb=" CA TYR A 168 " pdb=" CB TYR A 168 " ideal model delta sigma weight residual 1.534 1.497 0.037 2.33e-02 1.84e+03 2.53e+00 ... (remaining 14588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19124 2.05 - 4.09: 572 4.09 - 6.14: 72 6.14 - 8.19: 20 8.19 - 10.24: 4 Bond angle restraints: 19792 Sorted by residual: angle pdb=" N PRO A 211 " pdb=" CA PRO A 211 " pdb=" CB PRO A 211 " ideal model delta sigma weight residual 103.44 109.92 -6.48 1.12e+00 7.97e-01 3.35e+01 angle pdb=" C ARG B 71 " pdb=" N MET B 72 " pdb=" CA MET B 72 " ideal model delta sigma weight residual 121.03 129.07 -8.04 1.60e+00 3.91e-01 2.52e+01 angle pdb=" N ASP B 562 " pdb=" CA ASP B 562 " pdb=" C ASP B 562 " ideal model delta sigma weight residual 109.81 118.90 -9.09 2.21e+00 2.05e-01 1.69e+01 angle pdb=" N GLU A 482 " pdb=" CA GLU A 482 " pdb=" CB GLU A 482 " ideal model delta sigma weight residual 110.41 116.79 -6.38 1.68e+00 3.54e-01 1.44e+01 angle pdb=" N GLU A 988 " pdb=" CA GLU A 988 " pdb=" C GLU A 988 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 ... (remaining 19787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 7950 17.08 - 34.15: 726 34.15 - 51.23: 131 51.23 - 68.30: 29 68.30 - 85.37: 14 Dihedral angle restraints: 8850 sinusoidal: 3599 harmonic: 5251 Sorted by residual: dihedral pdb=" CA SER B 561 " pdb=" C SER B 561 " pdb=" N ASP B 562 " pdb=" CA ASP B 562 " ideal model delta harmonic sigma weight residual -180.00 -146.34 -33.66 0 5.00e+00 4.00e-02 4.53e+01 dihedral pdb=" CA ILE B 362 " pdb=" C ILE B 362 " pdb=" N GLY B 363 " pdb=" CA GLY B 363 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASP B 113 " pdb=" C ASP B 113 " pdb=" N ASP B 114 " pdb=" CA ASP B 114 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 8847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1478 0.048 - 0.097: 525 0.097 - 0.145: 154 0.145 - 0.194: 25 0.194 - 0.242: 4 Chirality restraints: 2186 Sorted by residual: chirality pdb=" CA ASP B 562 " pdb=" N ASP B 562 " pdb=" C ASP B 562 " pdb=" CB ASP B 562 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PRO A 211 " pdb=" N PRO A 211 " pdb=" C PRO A 211 " pdb=" CB PRO A 211 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2183 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 843 " 0.024 2.00e-02 2.50e+03 2.13e-02 7.94e+00 pdb=" CG PHE A 843 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 843 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 843 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 843 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 72 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO B 73 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 588 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 589 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.035 5.00e-02 4.00e+02 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3064 2.79 - 3.31: 11797 3.31 - 3.84: 20752 3.84 - 4.37: 23447 4.37 - 4.90: 43065 Nonbonded interactions: 102125 Sorted by model distance: nonbonded pdb=" OG1 THR A 611 " pdb=" O1B ADP A1401 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR B 183 " pdb=" OD2 ASP B 203 " model vdw 2.260 3.040 nonbonded pdb=" NH2 ARG A 370 " pdb=" OE2 GLU A 394 " model vdw 2.297 3.120 nonbonded pdb=" NH1 ARG A 814 " pdb=" O ASN A1194 " model vdw 2.303 3.120 nonbonded pdb=" OE1 GLU B 341 " pdb=" OH TYR B 508 " model vdw 2.306 3.040 ... (remaining 102120 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.007 0.096 14593 Z= 0.290 Angle : 0.859 10.235 19792 Z= 0.476 Chirality : 0.054 0.242 2186 Planarity : 0.007 0.068 2599 Dihedral : 13.957 85.375 5456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.18), residues: 1813 helix: -0.30 (0.22), residues: 500 sheet: -1.06 (0.31), residues: 287 loop : -1.66 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 95 TYR 0.025 0.003 TYR B 171 PHE 0.048 0.003 PHE A 843 TRP 0.035 0.003 TRP A 892 HIS 0.014 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00674 (14593) covalent geometry : angle 0.85924 (19792) hydrogen bonds : bond 0.23378 ( 407) hydrogen bonds : angle 6.93247 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5661 (tt0) cc_final: 0.4916 (mm110) REVERT: B 453 MET cc_start: 0.7948 (ttm) cc_final: 0.7713 (ttm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1362 time to fit residues: 28.7360 Evaluate side-chains 84 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0870 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088396 restraints weight = 27742.513| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.80 r_work: 0.3189 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14593 Z= 0.103 Angle : 0.551 10.508 19792 Z= 0.279 Chirality : 0.043 0.151 2186 Planarity : 0.005 0.049 2599 Dihedral : 4.815 41.256 2000 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.46 % Allowed : 4.80 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.19), residues: 1813 helix: 0.57 (0.24), residues: 528 sheet: -0.99 (0.32), residues: 261 loop : -1.47 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 550 TYR 0.021 0.001 TYR A 614 PHE 0.010 0.001 PHE B 186 TRP 0.010 0.001 TRP A 603 HIS 0.005 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00204 (14593) covalent geometry : angle 0.55060 (19792) hydrogen bonds : bond 0.04931 ( 407) hydrogen bonds : angle 4.74415 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5055 (tt0) cc_final: 0.4147 (mm-40) REVERT: A 843 PHE cc_start: 0.7718 (t80) cc_final: 0.7471 (t80) REVERT: A 1208 MET cc_start: 0.7509 (tpt) cc_final: 0.7206 (tpp) REVERT: B 383 GLU cc_start: 0.7491 (pm20) cc_final: 0.7167 (pm20) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 0.1215 time to fit residues: 17.8073 Evaluate side-chains 89 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 238 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 125 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 123 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.086743 restraints weight = 28010.482| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.78 r_work: 0.3168 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14593 Z= 0.109 Angle : 0.517 7.500 19792 Z= 0.261 Chirality : 0.043 0.149 2186 Planarity : 0.004 0.040 2599 Dihedral : 4.337 30.486 2000 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.92 % Allowed : 6.64 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.19), residues: 1813 helix: 0.91 (0.24), residues: 531 sheet: -0.86 (0.31), residues: 269 loop : -1.27 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 550 TYR 0.019 0.001 TYR A 614 PHE 0.013 0.001 PHE A1161 TRP 0.010 0.001 TRP A 892 HIS 0.002 0.001 HIS A1158 Details of bonding type rmsd covalent geometry : bond 0.00246 (14593) covalent geometry : angle 0.51709 (19792) hydrogen bonds : bond 0.04894 ( 407) hydrogen bonds : angle 4.35127 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5206 (tt0) cc_final: 0.4304 (mm-40) REVERT: A 649 ARG cc_start: 0.7707 (tmm160) cc_final: 0.7484 (tmm160) REVERT: B 383 GLU cc_start: 0.7446 (pm20) cc_final: 0.7090 (pm20) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.1168 time to fit residues: 17.6619 Evaluate side-chains 88 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 143 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS A1112 ASN A1164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082486 restraints weight = 28326.726| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.11 r_work: 0.3078 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14593 Z= 0.232 Angle : 0.642 7.399 19792 Z= 0.328 Chirality : 0.048 0.205 2186 Planarity : 0.005 0.042 2599 Dihedral : 4.894 27.642 2000 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.38 % Allowed : 9.01 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.19), residues: 1813 helix: 0.56 (0.23), residues: 531 sheet: -1.20 (0.29), residues: 298 loop : -1.43 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 645 TYR 0.021 0.002 TYR A 614 PHE 0.021 0.002 PHE A1161 TRP 0.014 0.002 TRP A 281 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00564 (14593) covalent geometry : angle 0.64199 (19792) hydrogen bonds : bond 0.07187 ( 407) hydrogen bonds : angle 4.74676 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.626 Fit side-chains REVERT: A 25 GLN cc_start: 0.5288 (tt0) cc_final: 0.4300 (mm-40) REVERT: A 964 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7272 (mtp-110) REVERT: B 600 ASP cc_start: 0.8094 (t70) cc_final: 0.7837 (t0) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.1169 time to fit residues: 17.3838 Evaluate side-chains 90 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 122 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085554 restraints weight = 28005.580| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.05 r_work: 0.3136 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14593 Z= 0.102 Angle : 0.510 7.612 19792 Z= 0.258 Chirality : 0.043 0.153 2186 Planarity : 0.004 0.038 2599 Dihedral : 4.307 24.013 2000 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.31 % Allowed : 10.32 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1813 helix: 0.96 (0.24), residues: 534 sheet: -1.04 (0.30), residues: 298 loop : -1.28 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 550 TYR 0.022 0.001 TYR A 614 PHE 0.011 0.001 PHE A 571 TRP 0.008 0.001 TRP A 691 HIS 0.003 0.001 HIS A1158 Details of bonding type rmsd covalent geometry : bond 0.00228 (14593) covalent geometry : angle 0.51001 (19792) hydrogen bonds : bond 0.04727 ( 407) hydrogen bonds : angle 4.27258 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.565 Fit side-chains REVERT: A 25 GLN cc_start: 0.5383 (tt0) cc_final: 0.4432 (mm-40) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 0.1036 time to fit residues: 16.0364 Evaluate side-chains 88 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 90 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084010 restraints weight = 28198.767| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.13 r_work: 0.3097 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14593 Z= 0.126 Angle : 0.519 7.104 19792 Z= 0.261 Chirality : 0.044 0.154 2186 Planarity : 0.004 0.038 2599 Dihedral : 4.245 22.792 2000 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.38 % Allowed : 10.91 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.20), residues: 1813 helix: 1.05 (0.24), residues: 533 sheet: -1.01 (0.30), residues: 298 loop : -1.25 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.020 0.001 TYR A 614 PHE 0.012 0.001 PHE A 571 TRP 0.010 0.001 TRP A 691 HIS 0.003 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00298 (14593) covalent geometry : angle 0.51908 (19792) hydrogen bonds : bond 0.05024 ( 407) hydrogen bonds : angle 4.25739 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.577 Fit side-chains REVERT: A 25 GLN cc_start: 0.5360 (tt0) cc_final: 0.4404 (mm-40) REVERT: A 964 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7159 (mtp-110) outliers start: 21 outliers final: 17 residues processed: 97 average time/residue: 0.1125 time to fit residues: 17.2039 Evaluate side-chains 94 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084610 restraints weight = 27889.756| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.06 r_work: 0.3116 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14593 Z= 0.130 Angle : 0.520 7.035 19792 Z= 0.262 Chirality : 0.044 0.156 2186 Planarity : 0.004 0.038 2599 Dihedral : 4.214 21.451 2000 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.51 % Allowed : 11.05 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1813 helix: 1.08 (0.24), residues: 533 sheet: -0.98 (0.30), residues: 305 loop : -1.24 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.020 0.001 TYR A 614 PHE 0.013 0.001 PHE A 571 TRP 0.009 0.001 TRP A 281 HIS 0.004 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00309 (14593) covalent geometry : angle 0.52043 (19792) hydrogen bonds : bond 0.05027 ( 407) hydrogen bonds : angle 4.22610 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.506 Fit side-chains REVERT: A 25 GLN cc_start: 0.5315 (tt0) cc_final: 0.4381 (mm-40) REVERT: A 964 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7160 (mtp-110) outliers start: 23 outliers final: 18 residues processed: 98 average time/residue: 0.1014 time to fit residues: 16.0896 Evaluate side-chains 97 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1164 HIS B 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084654 restraints weight = 27851.180| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.15 r_work: 0.3117 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14593 Z= 0.107 Angle : 0.502 7.705 19792 Z= 0.252 Chirality : 0.043 0.151 2186 Planarity : 0.004 0.037 2599 Dihedral : 4.077 21.306 2000 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.78 % Allowed : 11.11 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.20), residues: 1813 helix: 1.17 (0.24), residues: 533 sheet: -0.94 (0.31), residues: 291 loop : -1.19 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 550 TYR 0.020 0.001 TYR A 614 PHE 0.011 0.001 PHE A 571 TRP 0.009 0.001 TRP A 691 HIS 0.007 0.001 HIS A 705 Details of bonding type rmsd covalent geometry : bond 0.00247 (14593) covalent geometry : angle 0.50201 (19792) hydrogen bonds : bond 0.04576 ( 407) hydrogen bonds : angle 4.11776 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.565 Fit side-chains REVERT: A 25 GLN cc_start: 0.5269 (tt0) cc_final: 0.4350 (mm-40) REVERT: A 964 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7096 (mtp-110) REVERT: A 1190 MET cc_start: 0.8601 (tpp) cc_final: 0.8366 (tpp) outliers start: 27 outliers final: 23 residues processed: 102 average time/residue: 0.1026 time to fit residues: 16.8448 Evaluate side-chains 100 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.0570 chunk 138 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.109374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086358 restraints weight = 27796.459| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.08 r_work: 0.3143 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14593 Z= 0.086 Angle : 0.479 7.349 19792 Z= 0.239 Chirality : 0.042 0.145 2186 Planarity : 0.004 0.036 2599 Dihedral : 3.829 20.686 2000 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.58 % Allowed : 11.44 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.20), residues: 1813 helix: 1.32 (0.24), residues: 535 sheet: -0.74 (0.31), residues: 298 loop : -1.06 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 67 TYR 0.019 0.001 TYR A 614 PHE 0.009 0.001 PHE A 571 TRP 0.008 0.001 TRP B 19 HIS 0.002 0.000 HIS A1158 Details of bonding type rmsd covalent geometry : bond 0.00192 (14593) covalent geometry : angle 0.47937 (19792) hydrogen bonds : bond 0.03766 ( 407) hydrogen bonds : angle 3.95195 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.589 Fit side-chains REVERT: A 25 GLN cc_start: 0.5333 (tt0) cc_final: 0.4426 (mm110) REVERT: A 964 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7024 (mtp-110) outliers start: 24 outliers final: 22 residues processed: 100 average time/residue: 0.1073 time to fit residues: 17.2578 Evaluate side-chains 99 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085412 restraints weight = 27872.371| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.11 r_work: 0.3123 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14593 Z= 0.107 Angle : 0.500 7.272 19792 Z= 0.249 Chirality : 0.043 0.150 2186 Planarity : 0.004 0.037 2599 Dihedral : 3.894 20.129 2000 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.71 % Allowed : 11.70 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.20), residues: 1813 helix: 1.23 (0.24), residues: 541 sheet: -0.74 (0.31), residues: 296 loop : -1.06 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 550 TYR 0.019 0.001 TYR A 614 PHE 0.012 0.001 PHE A 571 TRP 0.009 0.001 TRP A 892 HIS 0.003 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00253 (14593) covalent geometry : angle 0.50030 (19792) hydrogen bonds : bond 0.04274 ( 407) hydrogen bonds : angle 3.99337 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.511 Fit side-chains REVERT: A 25 GLN cc_start: 0.5351 (tt0) cc_final: 0.4438 (mm110) REVERT: A 964 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7092 (mtp-110) outliers start: 26 outliers final: 22 residues processed: 96 average time/residue: 0.1052 time to fit residues: 16.2043 Evaluate side-chains 96 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 996 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1298 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 144 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 92 optimal weight: 0.0030 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086156 restraints weight = 27869.256| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.10 r_work: 0.3139 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14593 Z= 0.093 Angle : 0.485 7.098 19792 Z= 0.241 Chirality : 0.042 0.147 2186 Planarity : 0.004 0.036 2599 Dihedral : 3.800 20.113 2000 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.58 % Allowed : 11.77 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.20), residues: 1813 helix: 1.31 (0.24), residues: 541 sheet: -0.66 (0.31), residues: 296 loop : -1.01 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 550 TYR 0.019 0.001 TYR A 614 PHE 0.010 0.001 PHE A 571 TRP 0.008 0.001 TRP B 19 HIS 0.003 0.001 HIS A1158 Details of bonding type rmsd covalent geometry : bond 0.00212 (14593) covalent geometry : angle 0.48452 (19792) hydrogen bonds : bond 0.03903 ( 407) hydrogen bonds : angle 3.92865 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.71 seconds wall clock time: 49 minutes 46.43 seconds (2986.43 seconds total)