Starting phenix.real_space_refine on Mon Aug 5 14:07:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/08_2024/6uen_20754.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/08_2024/6uen_20754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/08_2024/6uen_20754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/08_2024/6uen_20754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/08_2024/6uen_20754.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/08_2024/6uen_20754.cif" } resolution = 3.67 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= 0.014 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 75 5.16 5 C 8726 2.51 5 N 2342 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 581": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A ARG 747": "NH1" <-> "NH2" Residue "A ASP 759": "OD1" <-> "OD2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 816": "OD1" <-> "OD2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 864": "NH1" <-> "NH2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A ARG 918": "NH1" <-> "NH2" Residue "A TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A ASP 989": "OD1" <-> "OD2" Residue "A TYR 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ASP 1023": "OD1" <-> "OD2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A ASP 1033": "OD1" <-> "OD2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1067": "OE1" <-> "OE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "A TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ASP 1106": "OD1" <-> "OD2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A GLU 1244": "OE1" <-> "OE2" Residue "A TYR 1246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1253": "NH1" <-> "NH2" Residue "A ARG 1256": "NH1" <-> "NH2" Residue "A GLU 1269": "OE1" <-> "OE2" Residue "A ASP 1287": "OD1" <-> "OD2" Residue "A ASP 1290": "OD1" <-> "OD2" Residue "A ASP 1296": "OD1" <-> "OD2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1364": "OD1" <-> "OD2" Residue "A ASP 1378": "OD1" <-> "OD2" Residue "A GLU 1379": "OE1" <-> "OE2" Residue "A GLU 1418": "OE1" <-> "OE2" Residue "A TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E ASP 235": "OD1" <-> "OD2" Residue "E PHE 241": "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: 13705 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1392, 11352 Classifications: {'peptide': 1392} Link IDs: {'PTRANS': 47, 'TRANS': 1344} Chain breaks: 2 Chain: "B" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 460 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 423 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "D" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Time building chain proxies: 7.49, per 1000 atoms: 0.55 Number of scatterers: 13705 At special positions: 0 Unit cell: (109.398, 140.422, 102.867, 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 75 16.00 O 2562 8.00 N 2342 7.00 C 8726 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: 5.71 Conformation dependent library (CDL) restraints added in 2.6 seconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 62.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.887A pdb=" N TYR A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.041A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.576A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.669A pdb=" N GLN A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.580A pdb=" N PHE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 120 removed outlier: 3.840A pdb=" N GLN A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.818A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 228 removed outlier: 3.711A pdb=" N ILE A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.984A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.129A pdb=" N ILE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 379 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.567A pdb=" N ASP A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.331A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 4.155A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.517A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.569A pdb=" N MET A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 removed outlier: 4.023A pdb=" N TYR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 removed outlier: 4.105A pdb=" N LEU A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.924A pdb=" N ILE A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 removed outlier: 5.403A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 553 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 604 removed outlier: 4.029A pdb=" N VAL A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 709 through 724 removed outlier: 3.553A pdb=" N SER A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 removed outlier: 3.509A pdb=" N LEU A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.557A pdb=" N ASN A 762 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 801 removed outlier: 3.819A pdb=" N TRP A 785 " --> pdb=" O CYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.784A pdb=" N LYS A 886 " --> pdb=" O ALA A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 922 through 939 removed outlier: 3.786A pdb=" N TRP A 932 " --> pdb=" O PHE A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1034 through 1045 removed outlier: 3.562A pdb=" N THR A1045 " --> pdb=" O THR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.507A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1111 removed outlier: 3.828A pdb=" N THR A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A1104 " --> pdb=" O TYR A1100 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1131 through 1142 removed outlier: 3.630A pdb=" N ILE A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 Processing helix chain 'A' and resid 1158 through 1180 removed outlier: 3.712A pdb=" N ILE A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A1176 " --> pdb=" O ASN A1172 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A1178 " --> pdb=" O THR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1212 removed outlier: 3.864A pdb=" N TRP A1211 " --> pdb=" O ARG A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 3.733A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1359 removed outlier: 3.916A pdb=" N THR A1358 " --> pdb=" O PRO A1354 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A1359 " --> pdb=" O ALA A1355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1354 through 1359' Processing helix chain 'A' and resid 1365 through 1375 removed outlier: 3.677A pdb=" N ASN A1369 " --> pdb=" O THR A1365 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1404 removed outlier: 3.758A pdb=" N ILE A1389 " --> pdb=" O PHE A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 removed outlier: 3.599A pdb=" N GLN A1443 " --> pdb=" O VAL A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 4.089A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.630A pdb=" N SER B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.807A pdb=" N ILE B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.774A pdb=" N ALA C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 182 removed outlier: 4.726A pdb=" N ASP C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 167 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 171 through 202 removed outlier: 3.507A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 191 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.596A pdb=" N LEU E 152 " --> pdb=" O MET E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.527A pdb=" N MET E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.512A pdb=" N ALA E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 210 removed outlier: 3.740A pdb=" N ALA E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.670A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 808 Processing sheet with id=AA5, first strand: chain 'A' and resid 867 through 869 removed outlier: 4.879A pdb=" N GLN A 867 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN A 874 " --> pdb=" O GLN A 867 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 869 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 3.533A pdb=" N ILE A1413 " --> pdb=" O ASP A1229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AA8, first strand: chain 'E' and resid 158 through 159 removed outlier: 3.836A pdb=" N GLY E 158 " --> pdb=" O ARG E 167 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2118 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: 4.55 Time building geometry restraints manager: 6.29 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: 4468 1.34 - 1.46: 2345 1.46 - 1.58: 7007 1.58 - 1.69: 0 1.69 - 1.81: 127 Bond restraints: 13947 Sorted by residual: bond pdb=" C GLY A 430 " pdb=" N HIS A 431 " ideal model delta sigma weight residual 1.331 1.301 0.030 2.07e-02 2.33e+03 2.11e+00 bond pdb=" CB ILE A 428 " pdb=" CG2 ILE A 428 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU A 131 " pdb=" CD1 LEU A 131 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB ILE A 787 " pdb=" CG2 ILE A 787 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB LEU A 313 " pdb=" CG LEU A 313 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 13942 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.53: 307 106.53 - 113.42: 7982 113.42 - 120.30: 5205 120.30 - 127.19: 5230 127.19 - 134.07: 120 Bond angle restraints: 18844 Sorted by residual: angle pdb=" C MET A 628 " pdb=" N PHE A 629 " pdb=" CA PHE A 629 " ideal model delta sigma weight residual 122.74 117.49 5.25 1.82e+00 3.02e-01 8.33e+00 angle pdb=" CA TRP A 287 " pdb=" CB TRP A 287 " pdb=" CG TRP A 287 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.11e+00 angle pdb=" N GLN A 831 " pdb=" CA GLN A 831 " pdb=" C GLN A 831 " ideal model delta sigma weight residual 113.72 109.61 4.11 1.52e+00 4.33e-01 7.32e+00 angle pdb=" N GLN A 831 " pdb=" CA GLN A 831 " pdb=" CB GLN A 831 " ideal model delta sigma weight residual 113.65 109.91 3.74 1.47e+00 4.63e-01 6.48e+00 angle pdb=" C ASN A1113 " pdb=" N ILE A1114 " pdb=" CA ILE A1114 " ideal model delta sigma weight residual 120.69 124.18 -3.49 1.46e+00 4.69e-01 5.70e+00 ... (remaining 18839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7639 17.92 - 35.84: 758 35.84 - 53.76: 118 53.76 - 71.68: 18 71.68 - 89.60: 11 Dihedral angle restraints: 8544 sinusoidal: 3538 harmonic: 5006 Sorted by residual: dihedral pdb=" CA PHE A 244 " pdb=" C PHE A 244 " pdb=" N ILE A 245 " pdb=" CA ILE A 245 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN A1139 " pdb=" C ASN A1139 " pdb=" N LEU A1140 " pdb=" CA LEU A1140 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN A 831 " pdb=" C GLN A 831 " pdb=" N ALA A 832 " pdb=" CA ALA A 832 " ideal model delta harmonic sigma weight residual 180.00 162.58 17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1419 0.037 - 0.074: 566 0.074 - 0.112: 157 0.112 - 0.149: 30 0.149 - 0.186: 3 Chirality restraints: 2175 Sorted by residual: chirality pdb=" CB VAL A 379 " pdb=" CA VAL A 379 " pdb=" CG1 VAL A 379 " pdb=" CG2 VAL A 379 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CB THR A 745 " pdb=" CA THR A 745 " pdb=" OG1 THR A 745 " pdb=" CG2 THR A 745 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE A 817 " pdb=" N ILE A 817 " pdb=" C ILE A 817 " pdb=" CB ILE A 817 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2172 not shown) Planarity restraints: 2381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 632 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 633 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1001 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A1002 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1002 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1002 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 737 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 738 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " -0.022 5.00e-02 4.00e+02 ... (remaining 2378 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 220 2.67 - 3.23: 13904 3.23 - 3.78: 19770 3.78 - 4.34: 26248 4.34 - 4.90: 44239 Nonbonded interactions: 104381 Sorted by model distance: nonbonded pdb=" OH TYR A 606 " pdb=" O SER A 728 " model vdw 2.112 3.040 nonbonded pdb=" OH TYR A 917 " pdb=" O ARG A 995 " model vdw 2.116 3.040 nonbonded pdb=" O TYR A 752 " pdb=" NE2 GLN A 766 " model vdw 2.195 3.120 nonbonded pdb=" O ARG A 555 " pdb=" NE2 GLN A 563 " model vdw 2.219 3.120 nonbonded pdb=" OG1 THR B 160 " pdb=" OD1 ASP E 168 " model vdw 2.241 3.040 ... (remaining 104376 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 128 through 182) selection = chain 'C' } 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: 1.670 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 38.250 Find NCS groups from input model: 0.290 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: 0.010 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: 43.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.006 0.039 13947 Z= 0.364 Angle : 0.654 7.531 18844 Z= 0.361 Chirality : 0.043 0.186 2175 Planarity : 0.004 0.052 2381 Dihedral : 14.230 89.605 5294 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.13 % Allowed : 7.35 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.18), residues: 1682 helix: -0.96 (0.15), residues: 947 sheet: -0.92 (0.59), residues: 59 loop : -2.28 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 480 HIS 0.007 0.001 HIS A 255 PHE 0.020 0.002 PHE A 25 TYR 0.018 0.002 TYR A 998 ARG 0.004 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7093 (m-80) cc_final: 0.6079 (m-10) REVERT: A 197 MET cc_start: 0.9018 (mtp) cc_final: 0.8653 (mtm) REVERT: A 438 GLN cc_start: 0.8104 (mp10) cc_final: 0.7666 (tm-30) REVERT: A 580 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7786 (mtt90) REVERT: A 721 ASP cc_start: 0.8232 (t0) cc_final: 0.7810 (t0) REVERT: A 824 MET cc_start: 0.5857 (mmm) cc_final: 0.5484 (mpp) REVERT: A 887 VAL cc_start: 0.9311 (m) cc_final: 0.9062 (p) REVERT: A 959 LEU cc_start: 0.9128 (mt) cc_final: 0.8870 (mp) REVERT: A 1017 SER cc_start: 0.9083 (m) cc_final: 0.8852 (p) REVERT: A 1169 MET cc_start: 0.8778 (mtm) cc_final: 0.8384 (mtm) REVERT: A 1290 ASP cc_start: 0.7293 (t70) cc_final: 0.6947 (t0) REVERT: B 161 SER cc_start: 0.8324 (p) cc_final: 0.8079 (p) REVERT: B 175 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 141 LYS cc_start: 0.7335 (mttp) cc_final: 0.7021 (mttp) REVERT: D 150 HIS cc_start: 0.6946 (m-70) cc_final: 0.6585 (m-70) REVERT: D 195 MET cc_start: 0.6872 (ttm) cc_final: 0.6272 (ttm) REVERT: E 148 MET cc_start: 0.7261 (ttt) cc_final: 0.7010 (ttm) REVERT: E 175 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6440 (mm-30) outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.2713 time to fit residues: 115.7176 Evaluate side-chains 236 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 743 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 199 HIS A 215 ASN A 228 ASN A 363 ASN A 381 HIS A 556 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 773 HIS A 930 ASN A 980 ASN A1022 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS E 150 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13947 Z= 0.278 Angle : 0.595 7.612 18844 Z= 0.314 Chirality : 0.041 0.161 2175 Planarity : 0.004 0.059 2381 Dihedral : 4.748 37.363 1849 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.87 % Allowed : 14.50 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.19), residues: 1682 helix: 0.39 (0.16), residues: 964 sheet: -0.72 (0.53), residues: 79 loop : -1.96 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 932 HIS 0.006 0.001 HIS A 853 PHE 0.019 0.002 PHE A1328 TYR 0.017 0.001 TYR A 998 ARG 0.004 0.000 ARG A1339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7011 (m-80) cc_final: 0.6033 (m-10) REVERT: A 197 MET cc_start: 0.8880 (mtp) cc_final: 0.8442 (mtm) REVERT: A 374 ASN cc_start: 0.8434 (t0) cc_final: 0.7892 (m110) REVERT: A 511 ARG cc_start: 0.7102 (ptt90) cc_final: 0.6833 (ptt90) REVERT: A 568 HIS cc_start: 0.7277 (t70) cc_final: 0.6791 (m-70) REVERT: A 580 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7799 (mtt90) REVERT: A 721 ASP cc_start: 0.7999 (t0) cc_final: 0.7552 (t0) REVERT: A 959 LEU cc_start: 0.9191 (mt) cc_final: 0.8983 (mp) REVERT: A 1226 TYR cc_start: 0.9088 (t80) cc_final: 0.8886 (t80) REVERT: A 1290 ASP cc_start: 0.7529 (t70) cc_final: 0.7124 (t0) REVERT: A 1319 LEU cc_start: 0.8595 (mt) cc_final: 0.8338 (mt) REVERT: A 1348 GLU cc_start: 0.7853 (mp0) cc_final: 0.7248 (mp0) REVERT: A 1404 ASN cc_start: 0.8304 (t0) cc_final: 0.7938 (t0) REVERT: B 148 MET cc_start: 0.8408 (ttm) cc_final: 0.7988 (ttp) REVERT: B 161 SER cc_start: 0.8484 (p) cc_final: 0.8245 (p) REVERT: C 141 LYS cc_start: 0.7350 (mttp) cc_final: 0.7081 (mttt) REVERT: C 167 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5704 (ptt180) REVERT: D 145 ILE cc_start: 0.7827 (mt) cc_final: 0.7625 (mt) REVERT: D 150 HIS cc_start: 0.7034 (m-70) cc_final: 0.6583 (m-70) REVERT: E 142 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6536 (mt) REVERT: E 146 LEU cc_start: 0.8360 (tt) cc_final: 0.8127 (mm) REVERT: E 148 MET cc_start: 0.7266 (ttt) cc_final: 0.7054 (ttm) REVERT: E 175 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6432 (pm20) REVERT: E 180 LYS cc_start: 0.6455 (mtpp) cc_final: 0.6116 (mttt) REVERT: E 191 ARG cc_start: 0.7114 (ptm160) cc_final: 0.6845 (tmm-80) outliers start: 29 outliers final: 18 residues processed: 268 average time/residue: 0.2462 time to fit residues: 99.5314 Evaluate side-chains 251 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 232 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 766 GLN B 150 HIS C 150 HIS E 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13947 Z= 0.184 Angle : 0.528 7.546 18844 Z= 0.278 Chirality : 0.039 0.141 2175 Planarity : 0.004 0.058 2381 Dihedral : 4.457 37.628 1849 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.51 % Allowed : 16.17 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.20), residues: 1682 helix: 1.06 (0.17), residues: 966 sheet: -0.19 (0.57), residues: 74 loop : -1.74 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 287 HIS 0.015 0.001 HIS E 150 PHE 0.013 0.001 PHE A 87 TYR 0.013 0.001 TYR A 998 ARG 0.004 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 257 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6985 (m-80) cc_final: 0.6039 (m-10) REVERT: A 197 MET cc_start: 0.8847 (mtp) cc_final: 0.8451 (mtm) REVERT: A 204 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7931 (tt) REVERT: A 264 THR cc_start: 0.8941 (p) cc_final: 0.8729 (t) REVERT: A 374 ASN cc_start: 0.8274 (t0) cc_final: 0.8015 (m110) REVERT: A 427 ARG cc_start: 0.7625 (mmt180) cc_final: 0.7345 (mmm160) REVERT: A 512 ASP cc_start: 0.8346 (m-30) cc_final: 0.8109 (m-30) REVERT: A 568 HIS cc_start: 0.7266 (t70) cc_final: 0.6838 (m-70) REVERT: A 580 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7780 (mtt90) REVERT: A 816 ASP cc_start: 0.7548 (p0) cc_final: 0.7222 (p0) REVERT: A 1269 GLU cc_start: 0.7532 (pt0) cc_final: 0.7185 (pt0) REVERT: A 1290 ASP cc_start: 0.7563 (t70) cc_final: 0.7244 (t0) REVERT: A 1348 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: A 1458 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7574 (mp0) REVERT: B 148 MET cc_start: 0.8306 (ttm) cc_final: 0.8037 (ttp) REVERT: B 173 LEU cc_start: 0.8569 (tp) cc_final: 0.8278 (tp) REVERT: C 167 ARG cc_start: 0.6380 (ptm-80) cc_final: 0.5982 (ptt180) REVERT: D 150 HIS cc_start: 0.6909 (m-70) cc_final: 0.6419 (m-70) REVERT: E 142 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6650 (mt) REVERT: E 146 LEU cc_start: 0.8288 (tt) cc_final: 0.8049 (mm) REVERT: E 148 MET cc_start: 0.7606 (ttt) cc_final: 0.7250 (ttm) REVERT: E 175 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6396 (pm20) REVERT: E 180 LYS cc_start: 0.6629 (mtpp) cc_final: 0.6183 (mttt) REVERT: E 191 ARG cc_start: 0.7048 (ptm160) cc_final: 0.6773 (tmm-80) outliers start: 39 outliers final: 20 residues processed: 273 average time/residue: 0.2398 time to fit residues: 98.7704 Evaluate side-chains 259 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 236 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 949 ASN Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.1980 chunk 162 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 0.0770 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 448 ASN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13947 Z= 0.167 Angle : 0.518 9.346 18844 Z= 0.270 Chirality : 0.038 0.138 2175 Planarity : 0.003 0.056 2381 Dihedral : 4.275 36.735 1849 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.64 % Allowed : 17.72 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.20), residues: 1682 helix: 1.41 (0.17), residues: 971 sheet: -0.10 (0.58), residues: 74 loop : -1.61 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 287 HIS 0.015 0.001 HIS E 150 PHE 0.011 0.001 PHE A 338 TYR 0.011 0.001 TYR A 998 ARG 0.003 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6971 (m-80) cc_final: 0.6048 (m-10) REVERT: A 197 MET cc_start: 0.8732 (mtp) cc_final: 0.8505 (mtm) REVERT: A 204 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 327 GLU cc_start: 0.8099 (mp0) cc_final: 0.7779 (mm-30) REVERT: A 453 TYR cc_start: 0.8225 (m-80) cc_final: 0.7954 (m-10) REVERT: A 460 MET cc_start: 0.8120 (mtm) cc_final: 0.7742 (mtm) REVERT: A 512 ASP cc_start: 0.8231 (m-30) cc_final: 0.8027 (m-30) REVERT: A 568 HIS cc_start: 0.7250 (t70) cc_final: 0.6828 (m-70) REVERT: A 580 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7723 (mtt90) REVERT: A 646 MET cc_start: 0.8666 (mmm) cc_final: 0.8279 (mmm) REVERT: A 816 ASP cc_start: 0.7543 (p0) cc_final: 0.7223 (p0) REVERT: A 868 PHE cc_start: 0.6922 (m-10) cc_final: 0.6668 (m-10) REVERT: A 1182 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7626 (pp) REVERT: A 1309 MET cc_start: 0.8705 (tpp) cc_final: 0.8416 (mmt) REVERT: A 1348 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: A 1359 THR cc_start: 0.9054 (p) cc_final: 0.8627 (p) REVERT: B 152 LEU cc_start: 0.8689 (tt) cc_final: 0.8380 (tp) REVERT: C 167 ARG cc_start: 0.6421 (ptm-80) cc_final: 0.5987 (ptt180) REVERT: E 148 MET cc_start: 0.7680 (ttt) cc_final: 0.7472 (ttm) REVERT: E 175 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6322 (pm20) REVERT: E 180 LYS cc_start: 0.6551 (mtpp) cc_final: 0.6181 (mttt) REVERT: E 191 ARG cc_start: 0.7034 (ptm160) cc_final: 0.6700 (tmm-80) outliers start: 41 outliers final: 19 residues processed: 279 average time/residue: 0.2272 time to fit residues: 95.4135 Evaluate side-chains 261 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0030 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 HIS A 604 GLN A 727 GLN C 150 HIS D 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13947 Z= 0.152 Angle : 0.512 12.020 18844 Z= 0.263 Chirality : 0.038 0.194 2175 Planarity : 0.003 0.054 2381 Dihedral : 4.112 34.464 1849 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.32 % Allowed : 19.20 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.20), residues: 1682 helix: 1.60 (0.17), residues: 974 sheet: -0.06 (0.59), residues: 70 loop : -1.50 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 287 HIS 0.005 0.001 HIS A 853 PHE 0.010 0.001 PHE A 87 TYR 0.012 0.001 TYR A 917 ARG 0.003 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6967 (m-80) cc_final: 0.6037 (m-10) REVERT: A 197 MET cc_start: 0.8708 (mtp) cc_final: 0.8501 (mtm) REVERT: A 204 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 327 GLU cc_start: 0.8125 (mp0) cc_final: 0.7782 (mm-30) REVERT: A 453 TYR cc_start: 0.8173 (m-80) cc_final: 0.7893 (m-10) REVERT: A 568 HIS cc_start: 0.7213 (t70) cc_final: 0.6793 (m-70) REVERT: A 580 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7669 (mtt90) REVERT: A 816 ASP cc_start: 0.7532 (p0) cc_final: 0.7178 (p0) REVERT: A 898 LEU cc_start: 0.7418 (tp) cc_final: 0.7002 (tt) REVERT: A 1182 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7691 (pp) REVERT: A 1309 MET cc_start: 0.8761 (tpp) cc_final: 0.8289 (mmt) REVERT: A 1348 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 1359 THR cc_start: 0.9081 (p) cc_final: 0.8814 (p) REVERT: A 1436 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8941 (tt) REVERT: B 152 LEU cc_start: 0.8644 (tt) cc_final: 0.8404 (tp) REVERT: B 161 SER cc_start: 0.9109 (t) cc_final: 0.8778 (p) REVERT: C 167 ARG cc_start: 0.6336 (ptm-80) cc_final: 0.5867 (ptt180) REVERT: E 148 MET cc_start: 0.7844 (ttt) cc_final: 0.7539 (ttm) REVERT: E 175 GLU cc_start: 0.6632 (mm-30) cc_final: 0.5717 (pm20) REVERT: E 180 LYS cc_start: 0.6582 (mtpp) cc_final: 0.6069 (mttt) REVERT: E 187 MET cc_start: 0.7949 (ppp) cc_final: 0.7420 (ppp) outliers start: 36 outliers final: 21 residues processed: 281 average time/residue: 0.2372 time to fit residues: 101.9597 Evaluate side-chains 260 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 150 HIS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 134 optimal weight: 0.0770 chunk 75 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 448 ASN C 150 HIS D 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13947 Z= 0.149 Angle : 0.513 9.886 18844 Z= 0.264 Chirality : 0.038 0.197 2175 Planarity : 0.003 0.052 2381 Dihedral : 4.006 32.518 1849 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 20.88 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1682 helix: 1.72 (0.17), residues: 972 sheet: -0.02 (0.57), residues: 72 loop : -1.42 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.012 0.001 HIS D 150 PHE 0.016 0.001 PHE A 868 TYR 0.010 0.001 TYR A 917 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7090 (m-80) cc_final: 0.5989 (m-10) REVERT: A 204 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 327 GLU cc_start: 0.8100 (mp0) cc_final: 0.7796 (mm-30) REVERT: A 403 LYS cc_start: 0.8109 (tptt) cc_final: 0.7800 (ttmm) REVERT: A 453 TYR cc_start: 0.8144 (m-80) cc_final: 0.7904 (m-10) REVERT: A 460 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6884 (mtt) REVERT: A 568 HIS cc_start: 0.7110 (t70) cc_final: 0.6697 (m-70) REVERT: A 580 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7641 (mtt90) REVERT: A 646 MET cc_start: 0.8641 (mmm) cc_final: 0.8328 (mmm) REVERT: A 700 ASP cc_start: 0.8391 (t0) cc_final: 0.8134 (t0) REVERT: A 816 ASP cc_start: 0.7525 (p0) cc_final: 0.7197 (p0) REVERT: A 898 LEU cc_start: 0.7448 (tp) cc_final: 0.7148 (tt) REVERT: A 1182 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7746 (pp) REVERT: A 1309 MET cc_start: 0.8766 (tpp) cc_final: 0.8292 (mmt) REVERT: A 1348 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 1359 THR cc_start: 0.9093 (p) cc_final: 0.8629 (p) REVERT: A 1436 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8961 (tt) REVERT: A 1449 ASP cc_start: 0.8504 (t0) cc_final: 0.7974 (t0) REVERT: B 161 SER cc_start: 0.9134 (t) cc_final: 0.8747 (p) REVERT: B 180 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8312 (ttmm) REVERT: C 137 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6663 (mtp85) REVERT: C 141 LYS cc_start: 0.7184 (mtpt) cc_final: 0.6907 (mttt) REVERT: C 149 LEU cc_start: 0.8627 (mm) cc_final: 0.8340 (mm) REVERT: C 167 ARG cc_start: 0.6324 (ptm-80) cc_final: 0.5806 (ptt180) REVERT: E 175 GLU cc_start: 0.6744 (mm-30) cc_final: 0.5927 (pm20) REVERT: E 180 LYS cc_start: 0.6543 (mtpp) cc_final: 0.6024 (mttt) REVERT: E 187 MET cc_start: 0.8025 (ppp) cc_final: 0.7659 (ppp) REVERT: E 193 GLU cc_start: 0.7375 (tp30) cc_final: 0.7161 (tp30) outliers start: 36 outliers final: 25 residues processed: 273 average time/residue: 0.2308 time to fit residues: 96.5307 Evaluate side-chains 267 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 237 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 74 optimal weight: 9.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13947 Z= 0.197 Angle : 0.537 12.900 18844 Z= 0.278 Chirality : 0.039 0.223 2175 Planarity : 0.003 0.055 2381 Dihedral : 4.082 35.535 1849 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.03 % Allowed : 20.49 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.20), residues: 1682 helix: 1.68 (0.17), residues: 972 sheet: -0.02 (0.58), residues: 70 loop : -1.39 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 932 HIS 0.004 0.001 HIS A 612 PHE 0.015 0.001 PHE A 868 TYR 0.013 0.001 TYR A 917 ARG 0.003 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 249 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7101 (m-80) cc_final: 0.5968 (m-10) REVERT: A 204 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8044 (tt) REVERT: A 327 GLU cc_start: 0.8158 (mp0) cc_final: 0.7906 (mm-30) REVERT: A 343 ILE cc_start: 0.8523 (mt) cc_final: 0.8078 (mt) REVERT: A 453 TYR cc_start: 0.8214 (m-80) cc_final: 0.7952 (m-10) REVERT: A 568 HIS cc_start: 0.7104 (t70) cc_final: 0.6702 (m-70) REVERT: A 580 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7678 (mtt90) REVERT: A 619 LYS cc_start: 0.6610 (ttmt) cc_final: 0.5892 (tttm) REVERT: A 646 MET cc_start: 0.8699 (mmm) cc_final: 0.8369 (mmm) REVERT: A 700 ASP cc_start: 0.8270 (t0) cc_final: 0.8063 (t0) REVERT: A 816 ASP cc_start: 0.7523 (p0) cc_final: 0.7228 (p0) REVERT: A 1109 ASP cc_start: 0.6818 (m-30) cc_final: 0.6523 (m-30) REVERT: A 1182 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7588 (pp) REVERT: A 1242 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 1309 MET cc_start: 0.8749 (tpp) cc_final: 0.8287 (mmt) REVERT: A 1436 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8978 (tt) REVERT: A 1449 ASP cc_start: 0.8513 (t0) cc_final: 0.7990 (t0) REVERT: C 141 LYS cc_start: 0.7497 (mtpt) cc_final: 0.7089 (mttt) REVERT: C 149 LEU cc_start: 0.8593 (mm) cc_final: 0.8341 (mm) REVERT: C 167 ARG cc_start: 0.6356 (ptm-80) cc_final: 0.5901 (ptt180) REVERT: E 148 MET cc_start: 0.7900 (ttm) cc_final: 0.7538 (ttm) REVERT: E 150 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7366 (t-90) REVERT: E 175 GLU cc_start: 0.6795 (mm-30) cc_final: 0.5969 (pm20) REVERT: E 180 LYS cc_start: 0.6578 (mtpp) cc_final: 0.6031 (mttt) REVERT: E 206 MET cc_start: 0.6989 (tpt) cc_final: 0.6578 (tpt) outliers start: 47 outliers final: 34 residues processed: 273 average time/residue: 0.2318 time to fit residues: 96.0093 Evaluate side-chains 276 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 51.6924 > 50: distance: 81 - 88: 4.512 distance: 88 - 89: 13.453 distance: 89 - 90: 10.990 distance: 89 - 92: 7.682 distance: 90 - 91: 15.335 distance: 90 - 99: 8.284 distance: 92 - 93: 13.817 distance: 93 - 94: 9.419 distance: 94 - 95: 9.097 distance: 95 - 96: 3.564 distance: 96 - 97: 7.883 distance: 96 - 98: 14.196 distance: 99 - 100: 5.279 distance: 100 - 101: 19.832 distance: 100 - 103: 5.267 distance: 101 - 102: 15.435 distance: 101 - 107: 5.097 distance: 103 - 104: 3.113 distance: 104 - 105: 20.568 distance: 104 - 106: 22.896 distance: 107 - 108: 8.999 distance: 108 - 109: 13.142 distance: 108 - 111: 3.273 distance: 109 - 110: 9.858 distance: 109 - 114: 11.274 distance: 111 - 112: 7.993 distance: 111 - 113: 11.499 distance: 114 - 115: 9.183 distance: 115 - 116: 4.705 distance: 116 - 121: 16.300 distance: 118 - 119: 9.335 distance: 118 - 120: 19.732 distance: 121 - 122: 9.905 distance: 122 - 123: 18.659 distance: 122 - 125: 11.787 distance: 123 - 124: 12.582 distance: 123 - 127: 20.726 distance: 125 - 126: 26.755 distance: 127 - 128: 16.675 distance: 128 - 129: 30.750 distance: 128 - 131: 10.334 distance: 129 - 130: 27.633 distance: 129 - 133: 32.592 distance: 131 - 132: 11.944 distance: 133 - 134: 41.042 distance: 134 - 135: 21.747 distance: 134 - 137: 16.618 distance: 135 - 136: 19.211 distance: 135 - 144: 5.986 distance: 137 - 138: 3.674 distance: 138 - 139: 10.055 distance: 139 - 140: 12.417 distance: 140 - 141: 10.684 distance: 141 - 142: 8.231 distance: 141 - 143: 9.708 distance: 144 - 145: 8.692 distance: 144 - 150: 15.672 distance: 145 - 146: 9.032 distance: 145 - 148: 11.595 distance: 146 - 147: 4.634 distance: 146 - 151: 8.191 distance: 148 - 149: 9.839 distance: 149 - 150: 10.579 distance: 151 - 152: 10.071 distance: 152 - 153: 13.649 distance: 152 - 155: 10.085 distance: 153 - 154: 8.948 distance: 153 - 157: 25.545 distance: 155 - 156: 28.246 distance: 157 - 158: 24.029 distance: 158 - 159: 7.898 distance: 158 - 161: 17.410 distance: 159 - 160: 31.426 distance: 159 - 166: 10.870 distance: 161 - 162: 10.771 distance: 162 - 163: 18.409 distance: 163 - 164: 22.693 distance: 163 - 165: 20.380