Starting phenix.real_space_refine on Tue Dec 31 09:13:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uy7_26866/12_2024/7uy7_26866.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy7_26866/12_2024/7uy7_26866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uy7_26866/12_2024/7uy7_26866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy7_26866/12_2024/7uy7_26866.map" model { file = "/net/cci-nas-00/data/ceres_data/7uy7_26866/12_2024/7uy7_26866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy7_26866/12_2024/7uy7_26866.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 52 5.16 5 C 9774 2.51 5 N 2483 2.21 5 O 2841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15161 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4634 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 13, 'TRANS': 538} Chain breaks: 3 Chain: "B" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2378 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 284} Chain breaks: 2 Chain: "C" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1315 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "E" Number of atoms: 6408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6408 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 27, 'TRANS': 755} Chain breaks: 6 Chain: "F" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2906 SG CYS A 398 64.316 80.845 59.373 1.00108.69 S ATOM 2928 SG CYS A 401 66.766 81.052 62.374 1.00107.51 S ATOM 3018 SG CYS A 412 63.667 83.058 62.401 1.00125.64 S ATOM 3040 SG CYS A 415 66.495 83.823 59.787 1.00129.44 S Time building chain proxies: 9.16, per 1000 atoms: 0.60 Number of scatterers: 15161 At special positions: 0 Unit cell: (138.6, 144.1, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 52 16.00 P 10 15.00 O 2841 8.00 N 2483 7.00 C 9774 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: 4.01 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 900 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 398 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 415 " pdb="ZN ZN A 900 " - pdb=" SG CYS A 412 " Number of angles added : 6 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 21 sheets defined 44.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.279A pdb=" N LEU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.587A pdb=" N LEU A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.591A pdb=" N GLN A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.926A pdb=" N LEU A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.789A pdb=" N ASP A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.640A pdb=" N PHE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 485 through 497 removed outlier: 3.788A pdb=" N ILE A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 496 " --> pdb=" O LYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 4.048A pdb=" N ILE A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 Processing helix chain 'A' and resid 599 through 622 Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.525A pdb=" N GLU B 12 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 13' Processing helix chain 'B' and resid 108 through 136 removed outlier: 4.381A pdb=" N GLU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.642A pdb=" N LEU B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.840A pdb=" N ILE B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 254 through 272 removed outlier: 5.233A pdb=" N ASP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 306 removed outlier: 3.774A pdb=" N PHE B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 314 through 327 removed outlier: 3.848A pdb=" N ASN B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 352 Processing helix chain 'C' and resid 15 through 23 removed outlier: 4.527A pdb=" N ASP C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 48 through 61 removed outlier: 4.007A pdb=" N ASN C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 87 removed outlier: 3.501A pdb=" N ALA C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.750A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 164 removed outlier: 3.508A pdb=" N ASN C 164 " --> pdb=" O ILE C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'D' and resid 186 through 197 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.771A pdb=" N ASP E 250 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 251 " --> pdb=" O ILE E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 251' Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 390 through 400 removed outlier: 3.733A pdb=" N THR E 398 " --> pdb=" O THR E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 498 removed outlier: 3.966A pdb=" N ASN E 496 " --> pdb=" O ASP E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 removed outlier: 4.044A pdb=" N SER E 515 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 547 Processing helix chain 'E' and resid 559 through 567 removed outlier: 3.580A pdb=" N ILE E 563 " --> pdb=" O THR E 559 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 564 " --> pdb=" O VAL E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 574 No H-bonds generated for 'chain 'E' and resid 573 through 574' Processing helix chain 'E' and resid 575 through 580 removed outlier: 4.096A pdb=" N LEU E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 580 " --> pdb=" O TRP E 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 575 through 580' Processing helix chain 'E' and resid 595 through 604 removed outlier: 3.580A pdb=" N MET E 602 " --> pdb=" O PHE E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 620 removed outlier: 3.537A pdb=" N GLU E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE E 619 " --> pdb=" O SER E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 635 Processing helix chain 'E' and resid 643 through 652 removed outlier: 4.353A pdb=" N GLN E 648 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 652 " --> pdb=" O GLN E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 679 removed outlier: 3.714A pdb=" N LEU E 657 " --> pdb=" O THR E 653 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET E 675 " --> pdb=" O ALA E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 692 Processing helix chain 'E' and resid 694 through 701 removed outlier: 4.155A pdb=" N SER E 698 " --> pdb=" O ILE E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 718 removed outlier: 3.534A pdb=" N ARG E 706 " --> pdb=" O GLN E 702 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 711 " --> pdb=" O ASN E 707 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 714 " --> pdb=" O LEU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 749 removed outlier: 3.522A pdb=" N GLN E 745 " --> pdb=" O GLN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 790 through 800 removed outlier: 3.785A pdb=" N ILE E 796 " --> pdb=" O TYR E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 818 Processing helix chain 'E' and resid 819 through 822 removed outlier: 3.811A pdb=" N GLY E 822 " --> pdb=" O PRO E 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 819 through 822' Processing helix chain 'E' and resid 871 through 893 removed outlier: 3.519A pdb=" N SER E 875 " --> pdb=" O ALA E 871 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 887 " --> pdb=" O GLN E 883 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 888 " --> pdb=" O ARG E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 923 removed outlier: 3.732A pdb=" N THR E 902 " --> pdb=" O GLN E 898 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 910 " --> pdb=" O LYS E 906 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS E 911 " --> pdb=" O GLN E 907 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR E 918 " --> pdb=" O ALA E 914 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 919 " --> pdb=" O ASN E 915 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 921 " --> pdb=" O MET E 917 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 922 " --> pdb=" O TYR E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 930 through 955 removed outlier: 3.813A pdb=" N GLU E 953 " --> pdb=" O LYS E 949 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E 955 " --> pdb=" O ILE E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 994 Processing helix chain 'E' and resid 1054 through 1067 Processing helix chain 'E' and resid 1072 through 1080 removed outlier: 3.817A pdb=" N ASP E1077 " --> pdb=" O ASN E1073 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E1078 " --> pdb=" O MET E1074 " (cutoff:3.500A) Processing helix chain 'E' and resid 1082 through 1087 removed outlier: 3.589A pdb=" N ASP E1087 " --> pdb=" O GLN E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1192 removed outlier: 4.212A pdb=" N ILE E1188 " --> pdb=" O LEU E1184 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E1189 " --> pdb=" O PHE E1185 " (cutoff:3.500A) Processing helix chain 'E' and resid 1193 through 1195 No H-bonds generated for 'chain 'E' and resid 1193 through 1195' Processing helix chain 'E' and resid 1199 through 1207 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.763A pdb=" N ILE A 67 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 73 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.715A pdb=" N TYR A 82 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.852A pdb=" N PHE A 123 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 152 " --> pdb=" O PHE A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 163 removed outlier: 4.024A pdb=" N GLU A 163 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG D 203 " --> pdb=" O GLU A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.640A pdb=" N SER A 297 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 266 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 311 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 268 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.640A pdb=" N SER A 297 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 266 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 311 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 268 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 380 through 397 removed outlier: 6.352A pdb=" N LYS A 387 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLN A 431 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 389 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU A 429 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU A 589 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A 591 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR A 443 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N TYR A 593 " --> pdb=" O TYR A 443 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 505 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL A 594 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS A 503 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 569 through 575 removed outlier: 3.753A pdb=" N TYR A 575 " --> pdb=" O LYS A 580 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 580 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 28 removed outlier: 3.819A pdb=" N LEU B 27 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N GLU B 58 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N CYS B 96 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 100 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 82 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE B 103 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR B 80 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.689A pdb=" N LYS B 276 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 288 " --> pdb=" O LYS B 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 removed outlier: 5.102A pdb=" N LEU C 137 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 139 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN C 107 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR C 94 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE C 46 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR C 96 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 127 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 39 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 261 through 262 removed outlier: 4.123A pdb=" N LEU E 262 " --> pdb=" O SER E 405 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER E 405 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 264 through 266 removed outlier: 3.742A pdb=" N ASP E 264 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 280 " --> pdb=" O CYS E 293 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 282 " --> pdb=" O ASP E 291 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE E 426 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 294 " --> pdb=" O PHE E 426 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL E 428 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN E 296 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 307 through 308 removed outlier: 6.701A pdb=" N TYR E 307 " --> pdb=" O SER E 382 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 356 through 362 removed outlier: 3.762A pdb=" N GLY E 356 " --> pdb=" O TYR E 347 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR E 347 " --> pdb=" O GLY E 356 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 358 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS E 345 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 341 " --> pdb=" O GLN E 362 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL E 721 " --> pdb=" O ASP E 344 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 346 " --> pdb=" O VAL E 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 526 through 528 removed outlier: 7.062A pdb=" N LYS E 456 " --> pdb=" O PHE E 475 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU E 477 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER E 454 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET E 479 " --> pdb=" O CYS E 452 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS E 452 " --> pdb=" O MET E 479 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR E 481 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 450 " --> pdb=" O TYR E 481 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 453 " --> pdb=" O VAL E 552 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 551 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 778 through 779 removed outlier: 3.714A pdb=" N ASN E1007 " --> pdb=" O LEU E1019 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 783 through 784 Processing sheet with id=AC2, first strand: chain 'E' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'E' and resid 962 through 963 642 hydrogen bonds defined for protein. 1809 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: 5.59 Time building geometry restraints manager: 4.59 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: 4586 1.34 - 1.46: 2377 1.46 - 1.58: 8400 1.58 - 1.70: 20 1.70 - 1.82: 81 Bond restraints: 15464 Sorted by residual: bond pdb=" CA THR E 964 " pdb=" CB THR E 964 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.58e-02 4.01e+03 3.62e+00 bond pdb=" C3' DT F 9 " pdb=" O3' DT F 9 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" CA LYS A 494 " pdb=" C LYS A 494 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.27e-02 6.20e+03 1.84e+00 bond pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" N LYS A 494 " pdb=" CA LYS A 494 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.19e-02 7.06e+03 1.32e+00 ... (remaining 15459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 20561 1.88 - 3.76: 246 3.76 - 5.64: 42 5.64 - 7.52: 11 7.52 - 9.40: 2 Bond angle restraints: 20862 Sorted by residual: angle pdb=" N LYS A 494 " pdb=" CA LYS A 494 " pdb=" C LYS A 494 " ideal model delta sigma weight residual 111.07 120.47 -9.40 1.07e+00 8.73e-01 7.71e+01 angle pdb=" C ILE A 495 " pdb=" N PHE A 496 " pdb=" CA PHE A 496 " ideal model delta sigma weight residual 120.28 126.65 -6.37 1.34e+00 5.57e-01 2.26e+01 angle pdb=" CA ILE A 495 " pdb=" C ILE A 495 " pdb=" N PHE A 496 " ideal model delta sigma weight residual 117.15 112.76 4.39 1.14e+00 7.69e-01 1.48e+01 angle pdb=" N GLN B 349 " pdb=" CA GLN B 349 " pdb=" CB GLN B 349 " ideal model delta sigma weight residual 110.28 115.52 -5.24 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 111.36 114.61 -3.25 1.09e+00 8.42e-01 8.91e+00 ... (remaining 20857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 9160 32.78 - 65.55: 231 65.55 - 98.32: 23 98.32 - 131.10: 0 131.10 - 163.87: 1 Dihedral angle restraints: 9415 sinusoidal: 4013 harmonic: 5402 Sorted by residual: dihedral pdb=" C THR E 964 " pdb=" N THR E 964 " pdb=" CA THR E 964 " pdb=" CB THR E 964 " ideal model delta harmonic sigma weight residual -122.00 -132.47 10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C4' DT F 9 " pdb=" C3' DT F 9 " pdb=" O3' DT F 9 " pdb=" P DG F 10 " ideal model delta sinusoidal sigma weight residual 220.00 56.13 163.87 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA PHE A 473 " pdb=" C PHE A 473 " pdb=" N ILE A 474 " pdb=" CA ILE A 474 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2058 0.069 - 0.137: 257 0.137 - 0.206: 9 0.206 - 0.275: 0 0.275 - 0.343: 2 Chirality restraints: 2326 Sorted by residual: chirality pdb=" CA THR E 964 " pdb=" N THR E 964 " pdb=" C THR E 964 " pdb=" CB THR E 964 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA LYS A 494 " pdb=" N LYS A 494 " pdb=" C LYS A 494 " pdb=" CB LYS A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 2323 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 970 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO E 971 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 971 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 971 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 191 " 0.142 9.50e-02 1.11e+02 6.39e-02 2.85e+00 pdb=" NE ARG B 191 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 191 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 191 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 191 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 792 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO E 793 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 793 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 793 " -0.020 5.00e-02 4.00e+02 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1242 2.74 - 3.28: 16562 3.28 - 3.82: 25942 3.82 - 4.36: 30353 4.36 - 4.90: 49034 Nonbonded interactions: 123133 Sorted by model distance: nonbonded pdb=" O SER E 390 " pdb=" OG1 THR E 394 " model vdw 2.203 3.040 nonbonded pdb=" O SER C 116 " pdb=" OH TYR C 123 " model vdw 2.207 3.040 nonbonded pdb=" O SER B 342 " pdb=" ND1 HIS B 346 " model vdw 2.217 3.120 nonbonded pdb=" O TYR A 242 " pdb=" ND2 ASN A 324 " model vdw 2.236 3.120 nonbonded pdb=" O GLU A 534 " pdb=" NE2 GLN A 538 " model vdw 2.258 3.120 ... (remaining 123128 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 15464 Z= 0.142 Angle : 0.557 9.396 20862 Z= 0.307 Chirality : 0.043 0.343 2326 Planarity : 0.003 0.064 2602 Dihedral : 15.121 163.875 5905 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1776 helix: 0.98 (0.21), residues: 670 sheet: -0.59 (0.35), residues: 250 loop : -1.36 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 576 HIS 0.011 0.001 HIS B 194 PHE 0.013 0.001 PHE A 473 TYR 0.015 0.001 TYR B 116 ARG 0.010 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6445 (mpp) cc_final: 0.6167 (mpp) REVERT: A 454 ASN cc_start: 0.8879 (t0) cc_final: 0.8614 (t0) REVERT: B 192 ILE cc_start: 0.9019 (tp) cc_final: 0.8528 (tp) REVERT: B 289 VAL cc_start: 0.8220 (p) cc_final: 0.7957 (m) REVERT: E 531 ASN cc_start: 0.7352 (p0) cc_final: 0.6696 (t0) REVERT: E 639 ILE cc_start: 0.8655 (mp) cc_final: 0.8423 (tt) REVERT: E 811 ILE cc_start: 0.7482 (mp) cc_final: 0.7113 (mt) REVERT: E 815 MET cc_start: 0.7817 (pmm) cc_final: 0.7601 (mpp) REVERT: E 877 LEU cc_start: 0.8509 (pp) cc_final: 0.8164 (mm) REVERT: E 1074 MET cc_start: 0.8468 (mpp) cc_final: 0.8222 (mpp) REVERT: E 1191 MET cc_start: 0.8419 (ptp) cc_final: 0.8061 (mpp) outliers start: 3 outliers final: 1 residues processed: 177 average time/residue: 0.2815 time to fit residues: 74.9699 Evaluate side-chains 101 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.0370 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 464 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN A 562 GLN A 567 ASN B 89 ASN B 94 GLN B 346 HIS B 360 HIS E 716 ASN ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15464 Z= 0.162 Angle : 0.554 6.917 20862 Z= 0.296 Chirality : 0.044 0.174 2326 Planarity : 0.004 0.055 2602 Dihedral : 9.067 163.561 2033 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1776 helix: 0.97 (0.20), residues: 701 sheet: -0.34 (0.37), residues: 225 loop : -1.38 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 695 HIS 0.008 0.001 HIS B 346 PHE 0.028 0.001 PHE C 73 TYR 0.022 0.001 TYR C 96 ARG 0.007 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6487 (mpp) cc_final: 0.6148 (mmm) REVERT: A 375 MET cc_start: 0.2916 (mmt) cc_final: 0.2700 (mmt) REVERT: A 477 TYR cc_start: 0.6488 (p90) cc_final: 0.6262 (p90) REVERT: C 73 PHE cc_start: 0.8778 (m-80) cc_final: 0.8541 (m-80) REVERT: E 531 ASN cc_start: 0.7553 (p0) cc_final: 0.7056 (t0) REVERT: E 602 MET cc_start: 0.7730 (ppp) cc_final: 0.7484 (ppp) REVERT: E 604 MET cc_start: 0.8933 (tmm) cc_final: 0.8259 (tmm) REVERT: E 811 ILE cc_start: 0.7217 (mp) cc_final: 0.6869 (mt) REVERT: E 877 LEU cc_start: 0.8526 (pp) cc_final: 0.8214 (mm) REVERT: E 1078 ILE cc_start: 0.8936 (mm) cc_final: 0.8734 (mm) REVERT: E 1191 MET cc_start: 0.8137 (ptp) cc_final: 0.7850 (mpp) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.2774 time to fit residues: 63.8726 Evaluate side-chains 93 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 0.0040 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN B 120 GLN B 346 HIS C 80 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15464 Z= 0.242 Angle : 0.583 7.049 20862 Z= 0.313 Chirality : 0.044 0.181 2326 Planarity : 0.004 0.059 2602 Dihedral : 9.170 165.435 2033 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1776 helix: 0.91 (0.20), residues: 691 sheet: -0.65 (0.36), residues: 230 loop : -1.51 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 695 HIS 0.008 0.001 HIS B 346 PHE 0.023 0.002 PHE B 348 TYR 0.018 0.002 TYR E 367 ARG 0.008 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6391 (mpp) cc_final: 0.6160 (mpp) REVERT: A 375 MET cc_start: 0.3390 (mmt) cc_final: 0.3099 (mmm) REVERT: A 477 TYR cc_start: 0.6659 (p90) cc_final: 0.6427 (p90) REVERT: B 346 HIS cc_start: 0.8585 (m90) cc_final: 0.8359 (m90) REVERT: C 73 PHE cc_start: 0.8800 (m-80) cc_final: 0.8546 (m-80) REVERT: E 639 ILE cc_start: 0.8699 (mp) cc_final: 0.8457 (tt) REVERT: E 1191 MET cc_start: 0.8219 (ptp) cc_final: 0.7970 (mpp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2863 time to fit residues: 59.2544 Evaluate side-chains 81 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN A 464 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15464 Z= 0.153 Angle : 0.555 9.019 20862 Z= 0.291 Chirality : 0.043 0.189 2326 Planarity : 0.004 0.050 2602 Dihedral : 9.115 165.236 2033 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1776 helix: 1.01 (0.20), residues: 693 sheet: -0.50 (0.36), residues: 224 loop : -1.43 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 695 HIS 0.007 0.001 HIS A 464 PHE 0.017 0.001 PHE B 348 TYR 0.016 0.001 TYR C 96 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6322 (mpp) cc_final: 0.6059 (mpp) REVERT: A 477 TYR cc_start: 0.6422 (p90) cc_final: 0.6213 (p90) REVERT: E 531 ASN cc_start: 0.7472 (p0) cc_final: 0.6924 (t0) REVERT: E 604 MET cc_start: 0.9045 (tmm) cc_final: 0.8220 (tmm) REVERT: E 639 ILE cc_start: 0.8645 (mp) cc_final: 0.8418 (tt) REVERT: E 1076 ASP cc_start: 0.9270 (m-30) cc_final: 0.8444 (p0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2678 time to fit residues: 63.0832 Evaluate side-chains 88 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 0.0170 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN B 346 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15464 Z= 0.162 Angle : 0.542 7.086 20862 Z= 0.286 Chirality : 0.043 0.168 2326 Planarity : 0.003 0.056 2602 Dihedral : 9.090 165.324 2033 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1776 helix: 0.97 (0.20), residues: 703 sheet: -0.52 (0.36), residues: 228 loop : -1.49 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 695 HIS 0.007 0.001 HIS B 346 PHE 0.019 0.001 PHE B 348 TYR 0.015 0.001 TYR C 96 ARG 0.003 0.000 ARG E 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6302 (mpp) cc_final: 0.6041 (mpp) REVERT: A 380 MET cc_start: 0.8088 (pmm) cc_final: 0.7631 (ptp) REVERT: A 592 MET cc_start: 0.7333 (mmp) cc_final: 0.7013 (mmp) REVERT: B 346 HIS cc_start: 0.8560 (m90) cc_final: 0.8326 (m90) REVERT: E 531 ASN cc_start: 0.7354 (p0) cc_final: 0.7124 (p0) REVERT: E 604 MET cc_start: 0.9140 (tmm) cc_final: 0.8394 (tmm) REVERT: E 639 ILE cc_start: 0.8669 (mp) cc_final: 0.8454 (tt) REVERT: E 1076 ASP cc_start: 0.9267 (m-30) cc_final: 0.8494 (p0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2564 time to fit residues: 57.2974 Evaluate side-chains 88 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.0370 chunk 156 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15464 Z= 0.225 Angle : 0.579 7.187 20862 Z= 0.307 Chirality : 0.044 0.182 2326 Planarity : 0.004 0.046 2602 Dihedral : 9.177 166.348 2033 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1776 helix: 0.90 (0.20), residues: 707 sheet: -0.64 (0.36), residues: 231 loop : -1.55 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E1024 HIS 0.004 0.001 HIS A 466 PHE 0.026 0.002 PHE E 539 TYR 0.016 0.001 TYR A 507 ARG 0.005 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6353 (mpp) cc_final: 0.6112 (mpp) REVERT: A 477 TYR cc_start: 0.6927 (p90) cc_final: 0.6558 (p90) REVERT: B 346 HIS cc_start: 0.8549 (m90) cc_final: 0.8315 (m90) REVERT: E 531 ASN cc_start: 0.7412 (p0) cc_final: 0.7192 (p0) REVERT: E 604 MET cc_start: 0.9102 (tmm) cc_final: 0.8505 (tmm) REVERT: E 1076 ASP cc_start: 0.9289 (m-30) cc_final: 0.8692 (p0) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2717 time to fit residues: 58.2597 Evaluate side-chains 88 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 464 HIS A 567 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15464 Z= 0.190 Angle : 0.570 9.463 20862 Z= 0.300 Chirality : 0.044 0.235 2326 Planarity : 0.003 0.045 2602 Dihedral : 9.164 166.870 2033 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1776 helix: 0.96 (0.20), residues: 707 sheet: -0.57 (0.36), residues: 230 loop : -1.64 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1024 HIS 0.009 0.001 HIS A 464 PHE 0.036 0.001 PHE C 73 TYR 0.017 0.001 TYR D 193 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.857 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 198 MET cc_start: 0.6295 (mpp) cc_final: 0.6061 (mpp) REVERT: A 380 MET cc_start: 0.8057 (pmm) cc_final: 0.7692 (ptp) REVERT: C 73 PHE cc_start: 0.8781 (m-80) cc_final: 0.8530 (m-80) REVERT: E 531 ASN cc_start: 0.7351 (p0) cc_final: 0.7146 (p0) REVERT: E 604 MET cc_start: 0.8867 (tmm) cc_final: 0.8667 (tmm) REVERT: E 639 ILE cc_start: 0.8760 (mp) cc_final: 0.8482 (tt) REVERT: E 1076 ASP cc_start: 0.9150 (m-30) cc_final: 0.8551 (p0) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2560 time to fit residues: 55.8624 Evaluate side-chains 89 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 346 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1183 GLN ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15464 Z= 0.254 Angle : 0.623 8.958 20862 Z= 0.329 Chirality : 0.045 0.167 2326 Planarity : 0.004 0.047 2602 Dihedral : 9.290 168.005 2033 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1776 helix: 0.84 (0.20), residues: 707 sheet: -0.91 (0.36), residues: 226 loop : -1.77 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 576 HIS 0.007 0.001 HIS B 346 PHE 0.024 0.002 PHE C 73 TYR 0.017 0.002 TYR E 265 ARG 0.005 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6356 (mpp) cc_final: 0.6115 (mpp) REVERT: A 380 MET cc_start: 0.8040 (pmm) cc_final: 0.7619 (ptp) REVERT: A 477 TYR cc_start: 0.6775 (p90) cc_final: 0.6529 (p90) REVERT: B 113 MET cc_start: 0.8677 (ppp) cc_final: 0.8191 (ppp) REVERT: C 73 PHE cc_start: 0.8833 (m-80) cc_final: 0.8585 (m-80) REVERT: E 531 ASN cc_start: 0.7154 (p0) cc_final: 0.6910 (p0) REVERT: E 604 MET cc_start: 0.8927 (tmm) cc_final: 0.8689 (tmm) REVERT: E 639 ILE cc_start: 0.8820 (mp) cc_final: 0.8535 (tt) REVERT: E 1076 ASP cc_start: 0.9276 (m-30) cc_final: 0.8657 (p0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2564 time to fit residues: 53.3678 Evaluate side-chains 79 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15464 Z= 0.200 Angle : 0.600 8.575 20862 Z= 0.315 Chirality : 0.045 0.192 2326 Planarity : 0.003 0.045 2602 Dihedral : 9.256 168.169 2033 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.06 % Allowed : 0.71 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1776 helix: 0.87 (0.20), residues: 707 sheet: -0.87 (0.35), residues: 243 loop : -1.77 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 695 HIS 0.005 0.001 HIS B 346 PHE 0.029 0.002 PHE B 348 TYR 0.029 0.001 TYR D 193 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6273 (mpp) cc_final: 0.6035 (mmm) REVERT: A 375 MET cc_start: 0.3853 (tpp) cc_final: 0.3091 (tpp) REVERT: A 380 MET cc_start: 0.8053 (pmm) cc_final: 0.7722 (ptp) REVERT: A 499 ASP cc_start: 0.8342 (p0) cc_final: 0.8132 (p0) REVERT: B 113 MET cc_start: 0.8775 (ppp) cc_final: 0.8356 (ppp) REVERT: B 284 ASN cc_start: 0.8369 (t0) cc_final: 0.8162 (t0) REVERT: C 73 PHE cc_start: 0.8831 (m-80) cc_final: 0.8581 (m-80) REVERT: E 531 ASN cc_start: 0.7319 (p0) cc_final: 0.6920 (t0) REVERT: E 604 MET cc_start: 0.8957 (tmm) cc_final: 0.8667 (tmm) REVERT: E 639 ILE cc_start: 0.8774 (mp) cc_final: 0.8490 (tt) REVERT: E 1076 ASP cc_start: 0.9180 (m-30) cc_final: 0.8566 (p0) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2594 time to fit residues: 54.1195 Evaluate side-chains 87 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15464 Z= 0.215 Angle : 0.609 8.811 20862 Z= 0.319 Chirality : 0.044 0.188 2326 Planarity : 0.004 0.046 2602 Dihedral : 9.266 167.747 2033 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1776 helix: 0.87 (0.20), residues: 708 sheet: -0.95 (0.34), residues: 243 loop : -1.84 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 695 HIS 0.004 0.001 HIS A 466 PHE 0.028 0.002 PHE B 348 TYR 0.016 0.001 TYR A 507 ARG 0.005 0.001 ARG B 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.6279 (mpp) cc_final: 0.6042 (mmm) REVERT: A 375 MET cc_start: 0.3796 (tpp) cc_final: 0.3052 (tpp) REVERT: A 380 MET cc_start: 0.8026 (pmm) cc_final: 0.7718 (ptp) REVERT: A 499 ASP cc_start: 0.8335 (p0) cc_final: 0.8057 (p0) REVERT: B 113 MET cc_start: 0.8777 (ppp) cc_final: 0.8371 (ppp) REVERT: B 284 ASN cc_start: 0.8387 (t0) cc_final: 0.8160 (t0) REVERT: C 73 PHE cc_start: 0.8805 (m-80) cc_final: 0.8601 (m-80) REVERT: E 477 LEU cc_start: 0.8940 (tp) cc_final: 0.8668 (tp) REVERT: E 531 ASN cc_start: 0.7296 (p0) cc_final: 0.7046 (p0) REVERT: E 604 MET cc_start: 0.8968 (tmm) cc_final: 0.8633 (tmm) REVERT: E 639 ILE cc_start: 0.8791 (mp) cc_final: 0.8503 (tt) REVERT: E 1076 ASP cc_start: 0.9190 (m-30) cc_final: 0.8597 (p0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2692 time to fit residues: 54.5845 Evaluate side-chains 82 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1199 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 = 0.3720 r_free = 0.3720 target = 0.065065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.053966 restraints weight = 103829.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.054944 restraints weight = 59925.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.055995 restraints weight = 43038.481| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15464 Z= 0.159 Angle : 0.586 9.013 20862 Z= 0.304 Chirality : 0.044 0.200 2326 Planarity : 0.003 0.044 2602 Dihedral : 9.180 167.465 2033 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1776 helix: 0.98 (0.20), residues: 708 sheet: -0.82 (0.34), residues: 252 loop : -1.76 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 695 HIS 0.003 0.001 HIS C 102 PHE 0.027 0.001 PHE B 348 TYR 0.030 0.001 TYR D 193 ARG 0.007 0.000 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.08 seconds wall clock time: 51 minutes 44.62 seconds (3104.62 seconds total)