Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 12:00:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/08_2023/6l53_0836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/08_2023/6l53_0836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/08_2023/6l53_0836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/08_2023/6l53_0836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/08_2023/6l53_0836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l53_0836/08_2023/6l53_0836.pdb" } resolution = 3.63 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= 1.000 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8824 2.51 5 N 2394 2.21 5 O 2701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1308": "OE1" <-> "OE2" Residue "A PHE 2142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2374": "NH1" <-> "NH2" Residue "A PHE 2417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13991 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1935, 13991 Classifications: {'peptide': 1935} Incomplete info: {'truncation_to_alanine': 304} Link IDs: {'CIS': 63, 'PCIS': 4, 'PTRANS': 63, 'TRANS': 1804} Chain breaks: 27 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1471 Unresolved non-hydrogen angles: 1868 Unresolved non-hydrogen dihedrals: 1327 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 10, 'TYR:plan': 20, 'ASN:plan1': 11, 'TRP:plan': 19, 'HIS:plan': 12, 'PHE:plan': 15, 'GLU:plan': 28, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 975 Time building chain proxies: 7.64, per 1000 atoms: 0.55 Number of scatterers: 13991 At special positions: 0 Unit cell: (130, 180.96, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2701 8.00 N 2394 7.00 C 8824 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: 5.32 Conformation dependent library (CDL) restraints added in 2.1 seconds 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 2 sheets defined 58.8% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.737A pdb=" N ASP A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.031A pdb=" N GLU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.759A pdb=" N ALA A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.512A pdb=" N THR A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.574A pdb=" N ASN A 181 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.103A pdb=" N SER A 204 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.885A pdb=" N GLU A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 229 through 246 removed outlier: 3.695A pdb=" N PHE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 271 removed outlier: 3.987A pdb=" N ALA A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 293 removed outlier: 4.217A pdb=" N SER A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.829A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.560A pdb=" N CYS A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.864A pdb=" N ILE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 342 through 356 Proline residue: A 348 - end of helix removed outlier: 3.592A pdb=" N ALA A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.658A pdb=" N GLU A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.668A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 415 removed outlier: 3.560A pdb=" N LEU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 444 through 457 removed outlier: 4.177A pdb=" N PHE A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.630A pdb=" N VAL A 462 " --> pdb=" O CYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.731A pdb=" N MET A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 removed outlier: 4.400A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 5.433A pdb=" N GLN A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 582 removed outlier: 4.380A pdb=" N LYS A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.650A pdb=" N ASP A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.511A pdb=" N MET A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 removed outlier: 3.835A pdb=" N SER A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 670 removed outlier: 3.628A pdb=" N TYR A 662 " --> pdb=" O PRO A 658 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 removed outlier: 3.862A pdb=" N LEU A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 739 through 747 removed outlier: 3.721A pdb=" N LYS A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 4.018A pdb=" N VAL A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.615A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 removed outlier: 3.964A pdb=" N GLN A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS A 848 " --> pdb=" O ALA A 844 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 937 through 948 removed outlier: 3.843A pdb=" N ILE A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 947 " --> pdb=" O ILE A 943 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 985 removed outlier: 3.702A pdb=" N ASN A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 981 " --> pdb=" O GLN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.649A pdb=" N TYR A 995 " --> pdb=" O LYS A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1016 removed outlier: 3.708A pdb=" N THR A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1073 through 1078 removed outlier: 3.614A pdb=" N VAL A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1085 removed outlier: 3.766A pdb=" N LEU A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 Processing helix chain 'A' and resid 1091 through 1106 removed outlier: 3.697A pdb=" N TRP A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER A1097 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1105 " --> pdb=" O GLY A1101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A1106 " --> pdb=" O LYS A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1120 removed outlier: 3.873A pdb=" N LYS A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1133 removed outlier: 4.057A pdb=" N LEU A1129 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1215 removed outlier: 3.561A pdb=" N ASP A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1297 removed outlier: 3.811A pdb=" N LYS A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER A1288 " --> pdb=" O GLU A1284 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1295 " --> pdb=" O VAL A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1316 through 1331 removed outlier: 3.538A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 removed outlier: 3.739A pdb=" N LEU A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 3.609A pdb=" N VAL A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1368 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1411 removed outlier: 3.705A pdb=" N ASN A1404 " --> pdb=" O THR A1400 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1406 " --> pdb=" O TYR A1402 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1411 " --> pdb=" O LEU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1420 Processing helix chain 'A' and resid 1421 through 1428 removed outlier: 3.705A pdb=" N ALA A1428 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1442 Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 4.107A pdb=" N THR A1456 " --> pdb=" O GLN A1452 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A1458 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A1459 " --> pdb=" O LYS A1455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A1460 " --> pdb=" O THR A1456 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 4.134A pdb=" N THR A1471 " --> pdb=" O LYS A1467 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A1472 " --> pdb=" O LYS A1468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1484 removed outlier: 3.876A pdb=" N LEU A1483 " --> pdb=" O GLY A1480 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A1484 " --> pdb=" O PRO A1481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1480 through 1484' Processing helix chain 'A' and resid 1488 through 1497 removed outlier: 4.148A pdb=" N THR A1493 " --> pdb=" O LYS A1489 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A1494 " --> pdb=" O LEU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 3.578A pdb=" N THR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1533 " --> pdb=" O ALA A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1538 removed outlier: 4.117A pdb=" N LYS A1537 " --> pdb=" O ALA A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 3.704A pdb=" N GLN A1603 " --> pdb=" O PHE A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1632 removed outlier: 4.163A pdb=" N ALA A1621 " --> pdb=" O LYS A1617 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A1625 " --> pdb=" O ALA A1621 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1628 " --> pdb=" O SER A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1638 Processing helix chain 'A' and resid 1644 through 1655 removed outlier: 3.799A pdb=" N LYS A1650 " --> pdb=" O LEU A1646 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A1651 " --> pdb=" O PRO A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1675 removed outlier: 3.860A pdb=" N GLU A1665 " --> pdb=" O ILE A1661 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1668 " --> pdb=" O GLU A1664 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A1675 " --> pdb=" O GLY A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1708 removed outlier: 3.548A pdb=" N ILE A1707 " --> pdb=" O MET A1703 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A1708 " --> pdb=" O VAL A1704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1703 through 1708' Processing helix chain 'A' and resid 1708 through 1713 removed outlier: 4.239A pdb=" N ILE A1712 " --> pdb=" O TRP A1708 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A1713 " --> pdb=" O ARG A1709 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1708 through 1713' Processing helix chain 'A' and resid 1729 through 1738 removed outlier: 3.842A pdb=" N LYS A1735 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A1736 " --> pdb=" O VAL A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1759 removed outlier: 3.575A pdb=" N SER A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1797 removed outlier: 3.594A pdb=" N VAL A1797 " --> pdb=" O LEU A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1812 removed outlier: 4.197A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A1812 " --> pdb=" O GLU A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1825 through 1830 Processing helix chain 'A' and resid 1837 through 1851 removed outlier: 3.985A pdb=" N ILE A1841 " --> pdb=" O VAL A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1866 Processing helix chain 'A' and resid 1927 through 1940 removed outlier: 4.042A pdb=" N SER A1931 " --> pdb=" O GLN A1927 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A1932 " --> pdb=" O ASP A1928 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A1936 " --> pdb=" O LYS A1932 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A1940 " --> pdb=" O LYS A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1958 removed outlier: 3.526A pdb=" N VAL A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1948 " --> pdb=" O MET A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1971 removed outlier: 3.715A pdb=" N VAL A1969 " --> pdb=" O LEU A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1991 removed outlier: 3.801A pdb=" N ARG A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A1980 " --> pdb=" O TYR A1976 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A1981 " --> pdb=" O VAL A1977 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A1986 " --> pdb=" O GLN A1982 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A1989 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1991 " --> pdb=" O GLU A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2027 removed outlier: 3.542A pdb=" N PHE A2019 " --> pdb=" O LYS A2015 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A2020 " --> pdb=" O PRO A2016 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A2025 " --> pdb=" O LEU A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2072 through 2080 removed outlier: 3.653A pdb=" N LEU A2078 " --> pdb=" O ILE A2074 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A2079 " --> pdb=" O MET A2075 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A2080 " --> pdb=" O LEU A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2101 removed outlier: 3.935A pdb=" N LEU A2099 " --> pdb=" O SER A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 removed outlier: 3.559A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2180 removed outlier: 3.941A pdb=" N THR A2179 " --> pdb=" O MET A2176 " (cutoff:3.500A) Processing helix chain 'A' and resid 2215 through 2231 Processing helix chain 'A' and resid 2252 through 2258 removed outlier: 3.842A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A2258 " --> pdb=" O TYR A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2289 removed outlier: 3.991A pdb=" N GLU A2285 " --> pdb=" O LYS A2281 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A2286 " --> pdb=" O ALA A2282 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2287 " --> pdb=" O VAL A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2301 Processing helix chain 'A' and resid 2308 through 2331 removed outlier: 3.541A pdb=" N ARG A2319 " --> pdb=" O GLN A2315 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A2330 " --> pdb=" O MET A2326 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A2331 " --> pdb=" O VAL A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2360 through 2364 removed outlier: 3.744A pdb=" N LYS A2363 " --> pdb=" O GLU A2360 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 3.955A pdb=" N ALA A2382 " --> pdb=" O ASN A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2396 removed outlier: 3.537A pdb=" N SER A2395 " --> pdb=" O VAL A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2396 through 2406 removed outlier: 3.892A pdb=" N LEU A2400 " --> pdb=" O CYS A2396 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A2401 " --> pdb=" O GLU A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2419 removed outlier: 3.780A pdb=" N LEU A2411 " --> pdb=" O ARG A2407 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A2414 " --> pdb=" O LEU A2410 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A2417 " --> pdb=" O LEU A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3621 removed outlier: 3.554A pdb=" N VAL A3612 " --> pdb=" O TYR A3608 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A3613 " --> pdb=" O ALA A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3645 Processing helix chain 'A' and resid 3654 through 3658 removed outlier: 3.734A pdb=" N THR A3658 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2138 through 2140 removed outlier: 3.786A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A2154 " --> pdb=" O LYS A2138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2212 through 2213 505 hydrogen bonds defined for protein. 1449 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: 5.32 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4661 1.34 - 1.46: 2767 1.46 - 1.58: 6647 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14180 Sorted by residual: bond pdb=" N GLN A 490 " pdb=" CA GLN A 490 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" C CYS A 489 " pdb=" N GLN A 490 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.41e+00 bond pdb=" C HIS A 675 " pdb=" N ASP A 676 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.32e+00 bond pdb=" N ARG A2366 " pdb=" CA ARG A2366 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.07e+00 bond pdb=" N HIS A2278 " pdb=" CA HIS A2278 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.00e+00 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.75: 437 107.75 - 114.85: 8809 114.85 - 121.94: 7100 121.94 - 129.04: 2868 129.04 - 136.13: 112 Bond angle restraints: 19326 Sorted by residual: angle pdb=" C CYS A 489 " pdb=" N GLN A 490 " pdb=" CA GLN A 490 " ideal model delta sigma weight residual 121.70 136.13 -14.43 1.80e+00 3.09e-01 6.43e+01 angle pdb=" C LEU A2277 " pdb=" N HIS A2278 " pdb=" CA HIS A2278 " ideal model delta sigma weight residual 121.70 133.67 -11.97 1.80e+00 3.09e-01 4.42e+01 angle pdb=" C HIS A 675 " pdb=" N ASP A 676 " pdb=" CA ASP A 676 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" N PRO A3627 " pdb=" CA PRO A3627 " pdb=" CB PRO A3627 " ideal model delta sigma weight residual 102.60 110.03 -7.43 1.17e+00 7.31e-01 4.03e+01 angle pdb=" C ASN A1019 " pdb=" N ARG A1020 " pdb=" CA ARG A1020 " ideal model delta sigma weight residual 121.70 132.28 -10.58 1.80e+00 3.09e-01 3.45e+01 ... (remaining 19321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8194 17.07 - 34.15: 310 34.15 - 51.22: 50 51.22 - 68.30: 12 68.30 - 85.37: 5 Dihedral angle restraints: 8571 sinusoidal: 2929 harmonic: 5642 Sorted by residual: dihedral pdb=" CA ILE A 901 " pdb=" C ILE A 901 " pdb=" N PRO A 902 " pdb=" CA PRO A 902 " ideal model delta harmonic sigma weight residual 180.00 128.38 51.62 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA LEU A1657 " pdb=" C LEU A1657 " pdb=" N PRO A1658 " pdb=" CA PRO A1658 " ideal model delta harmonic sigma weight residual -180.00 -146.56 -33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA ILE A1089 " pdb=" C ILE A1089 " pdb=" N GLN A1090 " pdb=" CA GLN A1090 " ideal model delta harmonic sigma weight residual -180.00 -147.02 -32.98 0 5.00e+00 4.00e-02 4.35e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2023 0.051 - 0.103: 351 0.103 - 0.154: 35 0.154 - 0.205: 7 0.205 - 0.257: 1 Chirality restraints: 2417 Sorted by residual: chirality pdb=" CA PRO A3627 " pdb=" N PRO A3627 " pdb=" C PRO A3627 " pdb=" CB PRO A3627 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLN A 490 " pdb=" N GLN A 490 " pdb=" C GLN A 490 " pdb=" CB GLN A 490 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PRO A2276 " pdb=" N PRO A2276 " pdb=" C PRO A2276 " pdb=" CB PRO A2276 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 2414 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 901 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO A 902 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A2275 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A2276 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2276 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2276 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1346 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO A1347 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1347 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1347 " 0.024 5.00e-02 4.00e+02 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 801 2.73 - 3.28: 14768 3.28 - 3.82: 20909 3.82 - 4.36: 25364 4.36 - 4.90: 41180 Nonbonded interactions: 103022 Sorted by model distance: nonbonded pdb=" O VAL A1094 " pdb=" OG SER A1097 " model vdw 2.193 2.440 nonbonded pdb=" O CYS A 492 " pdb=" OH TYR A 565 " model vdw 2.199 2.440 nonbonded pdb=" O ALA A 259 " pdb=" OG1 THR A 262 " model vdw 2.200 2.440 nonbonded pdb=" O SER A1608 " pdb=" OG SER A1618 " model vdw 2.233 2.440 nonbonded pdb=" O ASN A 111 " pdb=" OG SER A 115 " model vdw 2.250 2.440 ... (remaining 103017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.740 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 39.220 Find NCS groups from input model: 0.430 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 0.047 14180 Z= 0.151 Angle : 0.688 14.431 19326 Z= 0.387 Chirality : 0.040 0.257 2417 Planarity : 0.004 0.078 2459 Dihedral : 9.711 85.375 4875 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.85 % Favored : 89.89 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.05 % 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: -4.90 (0.16), residues: 1879 helix: -2.77 (0.13), residues: 917 sheet: -3.39 (0.85), residues: 29 loop : -3.83 (0.17), residues: 933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 402 time to evaluate : 1.730 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: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 16 residues processed: 444 average time/residue: 0.2729 time to fit residues: 173.9506 Evaluate side-chains 278 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1528 time to fit residues: 6.9068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.0170 chunk 175 optimal weight: 6.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 123 HIS A 171 GLN A 178 GLN A 191 ASN A 309 HIS A 326 HIS A 490 GLN A 510 GLN A 671 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 GLN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 GLN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 ASN ** A1472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1825 GLN A1832 HIS ** A2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2229 GLN A2337 HIS A2352 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 14180 Z= 0.230 Angle : 0.804 14.517 19326 Z= 0.409 Chirality : 0.044 0.228 2417 Planarity : 0.005 0.075 2459 Dihedral : 4.729 50.811 2001 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.66 % Favored : 88.24 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.05 % 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: -3.96 (0.17), residues: 1879 helix: -1.86 (0.15), residues: 962 sheet: -2.80 (0.95), residues: 29 loop : -3.58 (0.19), residues: 888 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 259 time to evaluate : 1.638 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: symmetry clash outliers start: 56 outliers final: 24 residues processed: 300 average time/residue: 0.2650 time to fit residues: 116.4662 Evaluate side-chains 250 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1333 time to fit residues: 8.1444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 175 optimal weight: 0.0040 chunk 189 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 174 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 ASN A1472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14180 Z= 0.208 Angle : 0.794 14.431 19326 Z= 0.402 Chirality : 0.044 0.225 2417 Planarity : 0.005 0.074 2459 Dihedral : 4.850 51.186 2001 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.07 % Favored : 88.77 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -3.49 (0.18), residues: 1879 helix: -1.37 (0.16), residues: 977 sheet: -2.48 (1.03), residues: 29 loop : -3.51 (0.19), residues: 873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 251 time to evaluate : 1.606 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 outliers start: 46 outliers final: 19 residues processed: 281 average time/residue: 0.2550 time to fit residues: 107.1034 Evaluate side-chains 250 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1285 time to fit residues: 6.9633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 0.3980 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 chunk 176 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 chunk 167 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 557 ASN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1362 ASN A2192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 14180 Z= 0.195 Angle : 0.778 14.406 19326 Z= 0.395 Chirality : 0.043 0.225 2417 Planarity : 0.005 0.074 2459 Dihedral : 4.833 50.254 2001 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.34 % Favored : 88.56 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -3.20 (0.19), residues: 1879 helix: -1.05 (0.17), residues: 988 sheet: -2.17 (1.11), residues: 29 loop : -3.51 (0.19), residues: 862 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 249 time to evaluate : 1.466 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 outliers start: 35 outliers final: 10 residues processed: 273 average time/residue: 0.2518 time to fit residues: 102.6883 Evaluate side-chains 241 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1282 time to fit residues: 4.5893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 138 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 197 HIS A 309 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 671 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN A1362 ASN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 GLN A2192 HIS A2356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 14180 Z= 0.304 Angle : 0.861 14.665 19326 Z= 0.438 Chirality : 0.046 0.231 2417 Planarity : 0.005 0.072 2459 Dihedral : 5.419 49.593 2001 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.35 % Favored : 87.39 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.16 % 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: -3.14 (0.19), residues: 1879 helix: -1.03 (0.16), residues: 1007 sheet: -2.56 (1.02), residues: 29 loop : -3.47 (0.20), residues: 843 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 243 time to evaluate : 1.689 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 outliers start: 49 outliers final: 29 residues processed: 277 average time/residue: 0.2565 time to fit residues: 106.1255 Evaluate side-chains 253 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1491 time to fit residues: 9.7557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 109 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.0170 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 309 HIS A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 GLN A2356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 14180 Z= 0.207 Angle : 0.810 14.565 19326 Z= 0.410 Chirality : 0.044 0.245 2417 Planarity : 0.005 0.078 2459 Dihedral : 5.279 50.813 2001 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.39 % Favored : 88.45 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.16 % 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: -2.95 (0.19), residues: 1879 helix: -0.87 (0.17), residues: 1009 sheet: -2.56 (1.00), residues: 29 loop : -3.40 (0.21), residues: 841 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 1.757 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: symmetry clash outliers start: 25 outliers final: 8 residues processed: 268 average time/residue: 0.2542 time to fit residues: 101.7373 Evaluate side-chains 244 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1252 time to fit residues: 4.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 105 optimal weight: 0.0170 chunk 157 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 186 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 85 optimal weight: 0.2980 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 GLN A1326 GLN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 GLN A2192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14180 Z= 0.200 Angle : 0.815 14.386 19326 Z= 0.409 Chirality : 0.044 0.235 2417 Planarity : 0.005 0.094 2459 Dihedral : 5.212 57.155 2001 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.39 % Favored : 88.50 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -2.74 (0.20), residues: 1879 helix: -0.70 (0.17), residues: 999 sheet: -2.46 (1.01), residues: 29 loop : -3.27 (0.21), residues: 851 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 1.604 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: symmetry clash outliers start: 26 outliers final: 8 residues processed: 261 average time/residue: 0.2545 time to fit residues: 100.2799 Evaluate side-chains 238 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 230 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1333 time to fit residues: 4.1434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 0.0060 chunk 146 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN A1326 GLN A1405 GLN A1413 GLN A2356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 14180 Z= 0.259 Angle : 0.855 14.583 19326 Z= 0.430 Chirality : 0.046 0.221 2417 Planarity : 0.006 0.097 2459 Dihedral : 5.418 56.056 2001 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.77 % Favored : 87.07 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -2.80 (0.19), residues: 1879 helix: -0.72 (0.17), residues: 1005 sheet: -2.35 (1.05), residues: 29 loop : -3.37 (0.21), residues: 845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 243 average time/residue: 0.2562 time to fit residues: 93.2578 Evaluate side-chains 231 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1374 time to fit residues: 3.4645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.0010 chunk 162 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 156 optimal weight: 0.4980 chunk 163 optimal weight: 0.5980 chunk 172 optimal weight: 0.0770 chunk 113 optimal weight: 0.6980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 550 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1825 GLN A2168 GLN A2356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14180 Z= 0.200 Angle : 0.840 14.459 19326 Z= 0.423 Chirality : 0.045 0.257 2417 Planarity : 0.006 0.100 2459 Dihedral : 5.319 55.859 2001 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.18 % Favored : 88.66 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -2.65 (0.20), residues: 1879 helix: -0.58 (0.17), residues: 999 sheet: -2.19 (1.07), residues: 29 loop : -3.29 (0.21), residues: 851 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 1.746 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 outliers start: 10 outliers final: 2 residues processed: 242 average time/residue: 0.2597 time to fit residues: 94.6545 Evaluate side-chains 234 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1532 time to fit residues: 2.8155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.0770 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 0.0030 chunk 127 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 0.0870 chunk 121 optimal weight: 7.9990 overall best weight: 0.3326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 GLN ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14180 Z= 0.204 Angle : 0.844 14.409 19326 Z= 0.422 Chirality : 0.045 0.236 2417 Planarity : 0.006 0.100 2459 Dihedral : 5.242 55.237 2001 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.13 % Favored : 87.81 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -2.55 (0.20), residues: 1879 helix: -0.50 (0.17), residues: 996 sheet: -2.21 (1.07), residues: 29 loop : -3.24 (0.21), residues: 854 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 239 average time/residue: 0.2575 time to fit residues: 92.2829 Evaluate side-chains 232 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1293 time to fit residues: 2.7346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 153 optimal weight: 0.2980 chunk 64 optimal weight: 0.0040 chunk 157 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 134 optimal weight: 0.6980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.139920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.118121 restraints weight = 42336.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.119940 restraints weight = 24691.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.121108 restraints weight = 16937.213| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14180 Z= 0.198 Angle : 0.845 14.397 19326 Z= 0.422 Chirality : 0.045 0.239 2417 Planarity : 0.006 0.101 2459 Dihedral : 5.200 55.064 2001 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.44 % Favored : 88.50 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 3.42 % Twisted Proline : 3.12 % Twisted General : 0.11 % 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: -2.47 (0.20), residues: 1879 helix: -0.42 (0.17), residues: 999 sheet: -2.22 (1.06), residues: 29 loop : -3.22 (0.21), residues: 851 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.37 seconds wall clock time: 58 minutes 4.10 seconds (3484.10 seconds total)