Starting phenix.real_space_refine on Sun Dec 10 06:59:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/12_2023/6uen_20754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/12_2023/6uen_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_20754/12_2023/6uen_20754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/12_2023/6uen_20754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/12_2023/6uen_20754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uen_20754/12_2023/6uen_20754.pdb" } 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-1.21rc1-5172/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: 7.63, per 1000 atoms: 0.56 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: 5.18 Conformation dependent library (CDL) restraints added in 2.4 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: 1.43 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: 4.79 Time building geometry restraints manager: 5.64 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 2.440 nonbonded pdb=" OH TYR A 917 " pdb=" O ARG A 995 " model vdw 2.116 2.440 nonbonded pdb=" O TYR A 752 " pdb=" NE2 GLN A 766 " model vdw 2.195 2.520 nonbonded pdb=" O ARG A 555 " pdb=" NE2 GLN A 563 " model vdw 2.219 2.520 nonbonded pdb=" OG1 THR B 160 " pdb=" OD1 ASP E 168 " model vdw 2.241 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 1.320 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.430 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- 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 : 1.636 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.2777 time to fit residues: 118.5610 Evaluate side-chains 232 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1190 time to fit residues: 2.4795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 168 GLN A 170 HIS A 199 HIS A 228 ASN A 363 ASN A 381 HIS A 556 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 773 HIS A 930 ASN A 980 ASN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS C 150 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13947 Z= 0.180 Angle : 0.535 7.554 18844 Z= 0.282 Chirality : 0.039 0.151 2175 Planarity : 0.004 0.058 2381 Dihedral : 4.447 17.804 1847 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.80 % Allowed : 15.14 % Favored : 83.05 % 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: -0.50 (0.20), residues: 1682 helix: 0.66 (0.16), residues: 965 sheet: -0.36 (0.55), residues: 73 loop : -1.87 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 287 HIS 0.006 0.001 HIS A 229 PHE 0.016 0.001 PHE A1328 TYR 0.014 0.001 TYR A1456 ARG 0.004 0.000 ARG E 174 *********************** 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 303 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 275 time to evaluate : 1.592 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 283 average time/residue: 0.2446 time to fit residues: 104.1474 Evaluate side-chains 253 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 238 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1314 time to fit residues: 5.8052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 215 ASN A 448 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13947 Z= 0.349 Angle : 0.630 9.195 18844 Z= 0.328 Chirality : 0.043 0.199 2175 Planarity : 0.004 0.063 2381 Dihedral : 4.661 18.181 1847 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.00 % Allowed : 19.14 % Favored : 78.87 % 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: -0.33 (0.20), residues: 1682 helix: 0.86 (0.16), residues: 957 sheet: -0.73 (0.54), residues: 80 loop : -1.82 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 932 HIS 0.008 0.001 HIS A 229 PHE 0.020 0.002 PHE A 25 TYR 0.019 0.002 TYR A1226 ARG 0.003 0.000 ARG A 929 *********************** 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 273 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.654 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 260 average time/residue: 0.2512 time to fit residues: 97.6344 Evaluate side-chains 239 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1339 time to fit residues: 6.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 0.0870 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 0.0060 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.0776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 448 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** 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: 0.8023 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13947 Z= 0.149 Angle : 0.520 12.855 18844 Z= 0.268 Chirality : 0.038 0.160 2175 Planarity : 0.003 0.055 2381 Dihedral : 4.205 17.802 1847 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.42 % Allowed : 20.49 % Favored : 78.09 % 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: 0.38 (0.20), residues: 1682 helix: 1.45 (0.17), residues: 968 sheet: -0.32 (0.57), residues: 74 loop : -1.59 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 287 HIS 0.004 0.001 HIS A 853 PHE 0.014 0.001 PHE A 868 TYR 0.012 0.001 TYR A 13 ARG 0.006 0.000 ARG A 995 *********************** 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 279 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 1.517 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 266 average time/residue: 0.2604 time to fit residues: 106.1962 Evaluate side-chains 244 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 234 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1330 time to fit residues: 4.9247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 603 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13947 Z= 0.276 Angle : 0.565 12.805 18844 Z= 0.292 Chirality : 0.040 0.149 2175 Planarity : 0.004 0.058 2381 Dihedral : 4.338 17.485 1847 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.06 % Allowed : 22.04 % Favored : 75.90 % 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: 0.33 (0.20), residues: 1682 helix: 1.37 (0.17), residues: 968 sheet: -0.38 (0.57), residues: 74 loop : -1.55 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.006 0.001 HIS A 229 PHE 0.015 0.002 PHE A 25 TYR 0.016 0.001 TYR A 998 ARG 0.003 0.000 ARG A 995 *********************** 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 268 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.479 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 254 average time/residue: 0.2511 time to fit residues: 95.3016 Evaluate side-chains 237 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1466 time to fit residues: 5.5023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 561 HIS A 599 ASN A 604 GLN A 611 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13947 Z= 0.152 Angle : 0.517 14.628 18844 Z= 0.264 Chirality : 0.038 0.157 2175 Planarity : 0.003 0.055 2381 Dihedral : 4.080 16.964 1847 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.74 % Allowed : 21.71 % Favored : 76.55 % 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: 0.71 (0.20), residues: 1682 helix: 1.71 (0.17), residues: 972 sheet: -0.24 (0.55), residues: 85 loop : -1.47 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 287 HIS 0.005 0.001 HIS D 150 PHE 0.013 0.001 PHE A 868 TYR 0.010 0.001 TYR A 917 ARG 0.007 0.000 ARG A 918 *********************** 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 276 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 1.701 Fit side-chains outliers start: 27 outliers final: 11 residues processed: 261 average time/residue: 0.2443 time to fit residues: 98.9011 Evaluate side-chains 240 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2036 time to fit residues: 6.0630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 611 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 940 GLN ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 ASN C 150 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13947 Z= 0.359 Angle : 0.640 13.506 18844 Z= 0.330 Chirality : 0.042 0.156 2175 Planarity : 0.004 0.061 2381 Dihedral : 4.447 18.097 1847 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.87 % Allowed : 23.45 % Favored : 74.68 % 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: 0.27 (0.20), residues: 1682 helix: 1.34 (0.17), residues: 967 sheet: -0.83 (0.62), residues: 66 loop : -1.52 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 480 HIS 0.007 0.001 HIS A 612 PHE 0.019 0.002 PHE A 25 TYR 0.018 0.002 TYR A 998 ARG 0.006 0.001 ARG A1253 *********************** 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 245 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.660 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 236 average time/residue: 0.2375 time to fit residues: 85.5439 Evaluate side-chains 226 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1339 time to fit residues: 6.7188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN C 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13947 Z= 0.206 Angle : 0.579 15.021 18844 Z= 0.293 Chirality : 0.039 0.170 2175 Planarity : 0.004 0.059 2381 Dihedral : 4.253 17.510 1847 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.10 % Allowed : 23.78 % Favored : 75.13 % 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: 0.50 (0.20), residues: 1682 helix: 1.52 (0.17), residues: 967 sheet: -0.48 (0.60), residues: 71 loop : -1.45 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 287 HIS 0.005 0.001 HIS A 612 PHE 0.015 0.002 PHE A 868 TYR 0.013 0.001 TYR A 998 ARG 0.012 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 8 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 246 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 1.665 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 232 average time/residue: 0.2419 time to fit residues: 84.9572 Evaluate side-chains 225 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1353 time to fit residues: 4.7896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 0.0000 chunk 136 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS D 150 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13947 Z= 0.216 Angle : 0.575 14.346 18844 Z= 0.292 Chirality : 0.040 0.161 2175 Planarity : 0.004 0.059 2381 Dihedral : 4.210 17.289 1847 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.64 % Allowed : 24.48 % Favored : 74.87 % 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: 0.52 (0.20), residues: 1682 helix: 1.53 (0.17), residues: 967 sheet: -0.47 (0.60), residues: 71 loop : -1.44 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.004 0.001 HIS A 612 PHE 0.017 0.002 PHE A 868 TYR 0.013 0.001 TYR A 998 ARG 0.007 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 9 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 232 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 222 time to evaluate : 1.462 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 225 average time/residue: 0.2493 time to fit residues: 84.6861 Evaluate side-chains 224 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1393 time to fit residues: 4.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 167 optimal weight: 0.4980 chunk 154 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1360 ASN ** 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: 0.7976 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13947 Z= 0.138 Angle : 0.542 15.635 18844 Z= 0.272 Chirality : 0.038 0.152 2175 Planarity : 0.003 0.055 2381 Dihedral : 3.969 16.646 1847 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.19 % Allowed : 25.13 % Favored : 74.68 % 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: 0.87 (0.21), residues: 1682 helix: 1.86 (0.17), residues: 967 sheet: -0.32 (0.54), residues: 85 loop : -1.39 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 287 HIS 0.010 0.001 HIS D 150 PHE 0.013 0.001 PHE A 87 TYR 0.012 0.001 TYR A 330 ARG 0.005 0.000 ARG A 918 ********************** REFINEMENT MACRO_CYCLE 10 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 242 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.725 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 239 average time/residue: 0.2434 time to fit residues: 88.8181 Evaluate side-chains 221 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1233 time to fit residues: 2.7475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.0370 chunk 137 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 GLN D 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124686 restraints weight = 19877.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126192 restraints weight = 14411.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127519 restraints weight = 11165.537| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3152 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= 0.138 Angle : 0.534 15.282 18844 Z= 0.268 Chirality : 0.038 0.153 2175 Planarity : 0.003 0.054 2381 Dihedral : 3.881 16.025 1847 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.45 % Allowed : 25.97 % Favored : 73.58 % 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: 1.03 (0.21), residues: 1682 helix: 2.00 (0.17), residues: 967 sheet: -0.38 (0.54), residues: 85 loop : -1.33 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 287 HIS 0.004 0.001 HIS A 853 PHE 0.019 0.001 PHE A 329 TYR 0.021 0.001 TYR A 598 ARG 0.005 0.000 ARG A 918 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.49 seconds wall clock time: 49 minutes 40.95 seconds (2980.95 seconds total)