Starting phenix.real_space_refine on Mon Aug 5 21:06:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/08_2024/7s9v_24938.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/08_2024/7s9v_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/08_2024/7s9v_24938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/08_2024/7s9v_24938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/08_2024/7s9v_24938.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9v_24938/08_2024/7s9v_24938.cif" } resolution = 3.3 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= 0.005 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 Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 635": "OD1" <-> "OD2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ASP 948": "OD1" <-> "OD2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A TYR 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1155": "OE1" <-> "OE2" Residue "A TYR 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1196": "OE1" <-> "OE2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A GLU 1230": "OE1" <-> "OE2" Residue "A GLU 1239": "OE1" <-> "OE2" Residue "A ASP 1285": "OD1" <-> "OD2" Residue "A PHE 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1314": "OD1" <-> "OD2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: {'GLU:plan': 3, 'ASN:plan1': 1, '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: 8.03, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.82 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.70 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: 4.76 Time building geometry restraints manager: 5.34 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: 98.01 - 105.59: 382 105.59 - 113.18: 7823 113.18 - 120.77: 6597 120.77 - 128.35: 4860 128.35 - 135.94: 130 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: 1.540 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.190 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- 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= 0.451 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 (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: -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 TRP 0.035 0.003 TRP A 892 HIS 0.014 0.001 HIS B 482 PHE 0.048 0.003 PHE A 843 TYR 0.025 0.003 TYR B 171 ARG 0.012 0.001 ARG B 95 *********************** 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 fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.691 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: 0.2866 time to fit residues: 60.5222 Evaluate side-chains 84 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14593 Z= 0.222 Angle : 0.591 10.325 19792 Z= 0.303 Chirality : 0.045 0.156 2186 Planarity : 0.005 0.055 2599 Dihedral : 5.169 41.843 2000 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.72 % Allowed : 5.52 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.35 (0.19), residues: 1813 helix: 0.38 (0.23), residues: 533 sheet: -1.16 (0.32), residues: 262 loop : -1.55 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 603 HIS 0.004 0.001 HIS A1158 PHE 0.014 0.001 PHE A1161 TYR 0.022 0.001 TYR A 614 ARG 0.007 0.000 ARG A 550 *********************** 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 95 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5478 (tt0) cc_final: 0.4654 (mm-40) outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 0.2716 time to fit residues: 39.3081 Evaluate side-chains 86 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 420 THR 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 A residue 1298 SER 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 91 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14593 Z= 0.237 Angle : 0.564 7.661 19792 Z= 0.287 Chirality : 0.045 0.158 2186 Planarity : 0.005 0.044 2599 Dihedral : 4.738 31.306 2000 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.25 % Allowed : 8.15 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.16 (0.19), residues: 1813 helix: 0.63 (0.24), residues: 533 sheet: -1.12 (0.30), residues: 289 loop : -1.47 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 892 HIS 0.003 0.001 HIS A1158 PHE 0.016 0.001 PHE A1161 TYR 0.021 0.001 TYR A 614 ARG 0.005 0.000 ARG A 550 *********************** 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 102 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5666 (tt0) cc_final: 0.4827 (mm-40) REVERT: A 964 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7236 (mtp-110) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.2532 time to fit residues: 38.5627 Evaluate side-chains 89 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.5980 chunk 123 optimal weight: 0.0020 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN A1164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14593 Z= 0.210 Angle : 0.541 7.829 19792 Z= 0.273 Chirality : 0.044 0.157 2186 Planarity : 0.004 0.040 2599 Dihedral : 4.511 27.507 2000 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.45 % Allowed : 9.73 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.98 (0.19), residues: 1813 helix: 0.81 (0.24), residues: 533 sheet: -1.00 (0.30), residues: 297 loop : -1.38 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.012 0.001 HIS A 705 PHE 0.013 0.001 PHE A1161 TYR 0.021 0.001 TYR A 614 ARG 0.004 0.000 ARG A 550 *********************** 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 102 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5683 (tt0) cc_final: 0.4897 (mm-40) REVERT: A 964 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7136 (mtp-110) outliers start: 22 outliers final: 13 residues processed: 100 average time/residue: 0.2437 time to fit residues: 38.2829 Evaluate side-chains 90 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 964 ARG 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 189 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 6.9990 chunk 99 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN A1164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14593 Z= 0.209 Angle : 0.529 7.755 19792 Z= 0.267 Chirality : 0.044 0.156 2186 Planarity : 0.004 0.039 2599 Dihedral : 4.385 24.794 2000 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.91 % Allowed : 10.78 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1813 helix: 0.92 (0.24), residues: 534 sheet: -0.97 (0.30), residues: 290 loop : -1.33 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.003 0.001 HIS A 705 PHE 0.014 0.001 PHE A1161 TYR 0.020 0.001 TYR A 614 ARG 0.004 0.000 ARG A 550 *********************** 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 107 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5800 (tt0) cc_final: 0.4969 (mm-40) REVERT: A 422 MET cc_start: 0.7861 (ptp) cc_final: 0.7577 (mtm) REVERT: A 964 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7080 (mtp-110) outliers start: 29 outliers final: 22 residues processed: 102 average time/residue: 0.2395 time to fit residues: 39.0737 Evaluate side-chains 98 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 340 ASP 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 943 GLN Chi-restraints excluded: chain A residue 964 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 175 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14593 Z= 0.121 Angle : 0.481 7.965 19792 Z= 0.240 Chirality : 0.042 0.145 2186 Planarity : 0.004 0.036 2599 Dihedral : 4.001 23.075 2000 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.38 % Allowed : 11.77 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.58 (0.20), residues: 1813 helix: 1.18 (0.24), residues: 536 sheet: -0.79 (0.31), residues: 283 loop : -1.15 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS A1158 PHE 0.009 0.001 PHE A 843 TYR 0.020 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 *********************** 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 109 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5694 (tt0) cc_final: 0.4905 (mm-40) REVERT: A 843 PHE cc_start: 0.6771 (t80) cc_final: 0.6553 (t80) outliers start: 21 outliers final: 14 residues processed: 107 average time/residue: 0.2342 time to fit residues: 38.9827 Evaluate side-chains 96 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 910 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 32 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 106 optimal weight: 0.0370 chunk 80 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS A1112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14593 Z= 0.176 Angle : 0.506 7.699 19792 Z= 0.254 Chirality : 0.043 0.150 2186 Planarity : 0.004 0.037 2599 Dihedral : 4.005 21.281 2000 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.64 % Allowed : 12.23 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.56 (0.20), residues: 1813 helix: 1.19 (0.24), residues: 536 sheet: -0.76 (0.31), residues: 283 loop : -1.14 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 892 HIS 0.003 0.001 HIS A1158 PHE 0.012 0.001 PHE A 571 TYR 0.018 0.001 TYR A 614 ARG 0.003 0.000 ARG A 137 *********************** 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 110 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5673 (tt0) cc_final: 0.4911 (mm-40) REVERT: A 644 MET cc_start: 0.7612 (mtp) cc_final: 0.7241 (mtp) REVERT: A 964 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7032 (mtp-110) outliers start: 25 outliers final: 17 residues processed: 107 average time/residue: 0.2411 time to fit residues: 40.3158 Evaluate side-chains 96 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 1198 SER Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LEU 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 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.0270 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14593 Z= 0.159 Angle : 0.504 7.274 19792 Z= 0.251 Chirality : 0.043 0.149 2186 Planarity : 0.004 0.036 2599 Dihedral : 3.944 20.744 2000 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.64 % Allowed : 12.43 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.48 (0.20), residues: 1813 helix: 1.27 (0.24), residues: 536 sheet: -0.80 (0.31), residues: 287 loop : -1.07 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 892 HIS 0.005 0.001 HIS A 705 PHE 0.011 0.001 PHE A 571 TYR 0.019 0.001 TYR A 614 ARG 0.003 0.000 ARG A 550 *********************** 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 104 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.656 Fit side-chains REVERT: A 25 GLN cc_start: 0.5675 (tt0) cc_final: 0.4959 (mm110) outliers start: 25 outliers final: 19 residues processed: 101 average time/residue: 0.2275 time to fit residues: 37.0403 Evaluate side-chains 97 residues out of total 1541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 910 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6665 > 50: distance: 60 - 65: 14.231 distance: 65 - 66: 21.000 distance: 66 - 67: 45.823 distance: 66 - 69: 40.673 distance: 67 - 68: 23.940 distance: 67 - 73: 23.627 distance: 69 - 70: 44.471 distance: 70 - 71: 54.176 distance: 70 - 72: 64.153 distance: 73 - 74: 35.932 distance: 74 - 75: 43.162 distance: 74 - 77: 25.486 distance: 75 - 76: 56.686 distance: 75 - 82: 25.068 distance: 77 - 78: 57.494 distance: 78 - 79: 54.120 distance: 79 - 80: 64.367 distance: 79 - 81: 68.666 distance: 82 - 83: 57.437 distance: 83 - 84: 47.301 distance: 83 - 86: 48.808 distance: 84 - 85: 38.950 distance: 84 - 90: 12.746 distance: 86 - 87: 25.809 distance: 87 - 88: 30.632 distance: 87 - 89: 57.981 distance: 90 - 91: 27.373 distance: 91 - 92: 14.358 distance: 91 - 94: 20.818 distance: 92 - 93: 39.422 distance: 92 - 102: 22.240 distance: 94 - 95: 36.497 distance: 95 - 96: 8.193 distance: 95 - 97: 24.325 distance: 96 - 98: 18.300 distance: 97 - 99: 27.695 distance: 98 - 100: 41.568 distance: 99 - 100: 17.778 distance: 100 - 101: 26.782 distance: 102 - 103: 47.231 distance: 102 - 108: 48.081 distance: 103 - 104: 35.887 distance: 103 - 106: 49.605 distance: 104 - 105: 42.537 distance: 104 - 109: 21.094 distance: 106 - 107: 25.198 distance: 107 - 108: 36.213 distance: 109 - 110: 29.380 distance: 110 - 111: 44.498 distance: 111 - 112: 52.508 distance: 111 - 113: 28.860 distance: 113 - 114: 7.885 distance: 114 - 115: 26.671 distance: 114 - 117: 35.277 distance: 115 - 116: 35.788 distance: 115 - 121: 41.397 distance: 117 - 118: 43.217 distance: 117 - 119: 31.130 distance: 118 - 120: 36.328 distance: 121 - 122: 34.145 distance: 122 - 123: 33.711 distance: 122 - 125: 26.586 distance: 123 - 124: 28.976 distance: 123 - 132: 32.708 distance: 124 - 156: 22.925 distance: 125 - 126: 36.437 distance: 126 - 127: 24.613 distance: 127 - 128: 18.052 distance: 128 - 129: 20.831 distance: 129 - 130: 7.160 distance: 129 - 131: 13.372 distance: 132 - 133: 26.719 distance: 133 - 134: 12.908 distance: 133 - 136: 23.103 distance: 134 - 135: 19.652 distance: 134 - 144: 37.759 distance: 135 - 163: 27.006 distance: 136 - 137: 23.251 distance: 137 - 138: 18.040 distance: 137 - 139: 11.326 distance: 138 - 140: 22.309 distance: 139 - 141: 21.342 distance: 140 - 142: 3.575 distance: 141 - 142: 5.065 distance: 142 - 143: 7.812 distance: 144 - 145: 32.538 distance: 145 - 146: 33.508 distance: 145 - 148: 52.791 distance: 146 - 147: 28.798 distance: 146 - 149: 23.034 distance: 147 - 172: 19.036