Starting phenix.real_space_refine on Fri Feb 16 21:58:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/02_2024/6uxv_20933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/02_2024/6uxv_20933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/02_2024/6uxv_20933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/02_2024/6uxv_20933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/02_2024/6uxv_20933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/02_2024/6uxv_20933.pdb" } resolution = 4.7 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= 0.003 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 49 5.16 5 C 10539 2.51 5 N 2901 2.21 5 O 3160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "B GLU 721": "OE1" <-> "OE2" Residue "B ARG 926": "NH1" <-> "NH2" Residue "B GLU 1256": "OE1" <-> "OE2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 573": "OE1" <-> "OE2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F GLU 530": "OE1" <-> "OE2" Residue "F GLU 692": "OE1" <-> "OE2" Residue "G GLU 530": "OE1" <-> "OE2" Residue "G GLU 685": "OE1" <-> "OE2" Residue "H TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 533": "OE1" <-> "OE2" Residue "H ARG 541": "NH1" <-> "NH2" Residue "H ARG 554": "NH1" <-> "NH2" Residue "I GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16649 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1133 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain: "B" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3890 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain breaks: 6 Chain: "C" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2005 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1322 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "F" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1583 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1435 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2085 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 3 Chain: "I" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 336 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 66} Unresolved non-hydrogen planarities: 66 Chain: "K" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 141 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 91 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 416 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 1, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'UNK:plan-1': 82} Unresolved non-hydrogen planarities: 82 Chain: "N" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 151 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "O" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 91 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 8.79, per 1000 atoms: 0.53 Number of scatterers: 16649 At special positions: 0 Unit cell: (137.76, 154.56, 151.2, 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 49 16.00 O 3160 8.00 N 2901 7.00 C 10539 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: 7.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 5 sheets defined 68.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 490 through 518 removed outlier: 3.585A pdb=" N ALA A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 557 Proline residue: A 540 - end of helix removed outlier: 3.785A pdb=" N GLN A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 597 removed outlier: 3.683A pdb=" N ALA A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 715 Processing helix chain 'B' and resid 717 through 734 removed outlier: 3.660A pdb=" N ASN B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 765 Processing helix chain 'B' and resid 792 through 805 removed outlier: 4.087A pdb=" N VAL B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 798 " --> pdb=" O LYS B 794 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 805 " --> pdb=" O GLU B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 895 removed outlier: 3.770A pdb=" N LYS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 929 removed outlier: 3.729A pdb=" N LEU B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 957 removed outlier: 3.502A pdb=" N ILE B 957 " --> pdb=" O TRP B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 981 Processing helix chain 'B' and resid 989 through 1003 removed outlier: 4.135A pdb=" N ASP B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1046 removed outlier: 3.886A pdb=" N PHE B1038 " --> pdb=" O LYS B1034 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B1040 " --> pdb=" O GLN B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1061 Processing helix chain 'B' and resid 1079 through 1090 removed outlier: 3.749A pdb=" N LYS B1083 " --> pdb=" O HIS B1079 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B1086 " --> pdb=" O LYS B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1093 No H-bonds generated for 'chain 'B' and resid 1091 through 1093' Processing helix chain 'B' and resid 1105 through 1114 removed outlier: 3.774A pdb=" N VAL B1109 " --> pdb=" O LEU B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1137 removed outlier: 4.402A pdb=" N ILE B1133 " --> pdb=" O PRO B1129 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B1136 " --> pdb=" O LEU B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1149 removed outlier: 3.764A pdb=" N SER B1141 " --> pdb=" O SER B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1232 through 1259 Processing helix chain 'B' and resid 1263 through 1270 removed outlier: 3.927A pdb=" N LYS B1267 " --> pdb=" O PRO B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1286 Processing helix chain 'B' and resid 1292 through 1314 removed outlier: 4.041A pdb=" N GLU B1314 " --> pdb=" O LEU B1310 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 450 Processing helix chain 'C' and resid 487 through 499 Processing helix chain 'C' and resid 510 through 522 Processing helix chain 'C' and resid 528 through 533 Processing helix chain 'C' and resid 571 through 580 removed outlier: 4.557A pdb=" N PHE C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 610 removed outlier: 4.139A pdb=" N THR C 591 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C 604 " --> pdb=" O GLN C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 649 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 320 through 327 Processing helix chain 'D' and resid 328 through 332 removed outlier: 3.996A pdb=" N THR D 332 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 357 removed outlier: 3.880A pdb=" N ASN D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.507A pdb=" N SER D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 436 through 442 removed outlier: 4.152A pdb=" N LEU D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 320 through 327 removed outlier: 3.707A pdb=" N VAL E 324 " --> pdb=" O HIS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 339 through 357 removed outlier: 3.948A pdb=" N ASN E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.642A pdb=" N ALA E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 388 Processing helix chain 'E' and resid 429 through 434 Processing helix chain 'F' and resid 528 through 542 Processing helix chain 'F' and resid 545 through 552 Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.592A pdb=" N PHE F 565 " --> pdb=" O CYS F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 624 Proline residue: F 620 - end of helix removed outlier: 4.072A pdb=" N GLN F 624 " --> pdb=" O PRO F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 647 removed outlier: 4.047A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 749 Processing helix chain 'F' and resid 766 through 780 Proline residue: F 777 - end of helix removed outlier: 4.306A pdb=" N LEU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 541 removed outlier: 3.694A pdb=" N GLU G 541 " --> pdb=" O LYS G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 552 Processing helix chain 'G' and resid 557 through 567 Processing helix chain 'G' and resid 625 through 630 removed outlier: 3.760A pdb=" N ARG G 629 " --> pdb=" O SER G 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 655 Proline residue: G 649 - end of helix removed outlier: 3.566A pdb=" N GLU G 655 " --> pdb=" O GLU G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 680 through 747 Processing helix chain 'G' and resid 764 through 779 Proline residue: G 777 - end of helix Processing helix chain 'H' and resid 82 through 114 removed outlier: 3.959A pdb=" N LEU H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR H 114 " --> pdb=" O GLN H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 117 No H-bonds generated for 'chain 'H' and resid 115 through 117' Processing helix chain 'H' and resid 311 through 318 Processing helix chain 'H' and resid 324 through 340 Processing helix chain 'H' and resid 382 through 387 Processing helix chain 'H' and resid 393 through 397 Processing helix chain 'H' and resid 403 through 410 Processing helix chain 'H' and resid 450 through 456 removed outlier: 4.563A pdb=" N ASN H 453 " --> pdb=" O LEU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 510 Proline residue: H 478 - end of helix removed outlier: 3.950A pdb=" N ASP H 510 " --> pdb=" O LYS H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 529 removed outlier: 3.577A pdb=" N ALA H 514 " --> pdb=" O ASP H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 547 removed outlier: 4.074A pdb=" N ASN H 544 " --> pdb=" O VAL H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 562 removed outlier: 3.693A pdb=" N LEU H 553 " --> pdb=" O ASN H 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 560 " --> pdb=" O ASN H 556 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU H 561 " --> pdb=" O ILE H 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 102 through 121 removed outlier: 3.645A pdb=" N ASN I 106 " --> pdb=" O SER I 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 147 removed outlier: 4.653A pdb=" N GLU I 139 " --> pdb=" O ARG I 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN I 147 " --> pdb=" O ARG I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 163 removed outlier: 4.000A pdb=" N UNK I 160 " --> pdb=" O UNK I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 175 Processing helix chain 'J' and resid 2 through 57 removed outlier: 3.987A pdb=" N UNK J 6 " --> pdb=" O UNK J 2 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N UNK J 11 " --> pdb=" O UNK J 7 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK J 19 " --> pdb=" O UNK J 15 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N UNK J 27 " --> pdb=" O UNK J 23 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N UNK J 56 " --> pdb=" O UNK J 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'L' and resid 9 through 19 Processing helix chain 'L' and resid 20 through 22 No H-bonds generated for 'chain 'L' and resid 20 through 22' Processing helix chain 'M' and resid 43 through 81 removed outlier: 3.806A pdb=" N UNK M 47 " --> pdb=" O UNK M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'O' and resid 7 through 17 Processing helix chain 'O' and resid 18 through 20 No H-bonds generated for 'chain 'O' and resid 18 through 20' Processing sheet with id=AA1, first strand: chain 'B' and resid 1006 through 1007 removed outlier: 4.134A pdb=" N GLN B1006 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 458 through 461 Processing sheet with id=AA3, first strand: chain 'C' and resid 543 through 552 removed outlier: 3.706A pdb=" N GLN C 556 " --> pdb=" O GLN C 654 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN C 654 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 411 through 412 removed outlier: 6.549A pdb=" N GLN D 411 " --> pdb=" O ILE E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 378 through 380 915 hydrogen bonds defined for protein. 2691 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: 4.20 Time building geometry restraints manager: 8.09 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: 5582 1.34 - 1.46: 2910 1.46 - 1.57: 8333 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 16906 Sorted by residual: bond pdb=" CA ASN H 544 " pdb=" C ASN H 544 " ideal model delta sigma weight residual 1.522 1.436 0.086 1.72e-02 3.38e+03 2.50e+01 bond pdb=" C GLU B1198 " pdb=" N ASN B1199 " ideal model delta sigma weight residual 1.332 1.280 0.052 1.29e-02 6.01e+03 1.59e+01 bond pdb=" CA VAL G 618 " pdb=" CB VAL G 618 " ideal model delta sigma weight residual 1.553 1.531 0.022 7.40e-03 1.83e+04 8.87e+00 bond pdb=" CA LEU B1061 " pdb=" C LEU B1061 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.38e-02 5.25e+03 6.46e+00 bond pdb=" CA ILE C 647 " pdb=" C ILE C 647 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.27e-02 6.20e+03 4.92e+00 ... (remaining 16901 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.52: 377 106.52 - 113.40: 9699 113.40 - 120.28: 5852 120.28 - 127.16: 6855 127.16 - 134.03: 136 Bond angle restraints: 22919 Sorted by residual: angle pdb=" C ARG C 640 " pdb=" N PRO C 641 " pdb=" CA PRO C 641 " ideal model delta sigma weight residual 119.84 133.28 -13.44 1.25e+00 6.40e-01 1.16e+02 angle pdb=" N PRO F 649 " pdb=" CA PRO F 649 " pdb=" CB PRO F 649 " ideal model delta sigma weight residual 103.35 110.58 -7.23 8.70e-01 1.32e+00 6.91e+01 angle pdb=" N PRO F 606 " pdb=" CA PRO F 606 " pdb=" CB PRO F 606 " ideal model delta sigma weight residual 103.25 111.64 -8.39 1.05e+00 9.07e-01 6.38e+01 angle pdb=" N PRO F 599 " pdb=" CA PRO F 599 " pdb=" CB PRO F 599 " ideal model delta sigma weight residual 103.19 110.37 -7.18 1.00e+00 1.00e+00 5.15e+01 angle pdb=" N PRO F 777 " pdb=" CA PRO F 777 " pdb=" CB PRO F 777 " ideal model delta sigma weight residual 103.52 110.16 -6.64 1.06e+00 8.90e-01 3.92e+01 ... (remaining 22914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9279 17.86 - 35.72: 890 35.72 - 53.58: 149 53.58 - 71.44: 31 71.44 - 89.30: 24 Dihedral angle restraints: 10373 sinusoidal: 3857 harmonic: 6516 Sorted by residual: dihedral pdb=" CA ASP B 776 " pdb=" C ASP B 776 " pdb=" N TYR B 777 " pdb=" CA TYR B 777 " ideal model delta harmonic sigma weight residual -180.00 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA ASP B 932 " pdb=" C ASP B 932 " pdb=" N ASN B 933 " pdb=" CA ASN B 933 " ideal model delta harmonic sigma weight residual 180.00 -148.55 -31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA TYR B 745 " pdb=" C TYR B 745 " pdb=" N PRO B 746 " pdb=" CA PRO B 746 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 10370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2325 0.065 - 0.129: 330 0.129 - 0.194: 20 0.194 - 0.259: 9 0.259 - 0.323: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CA ILE G 570 " pdb=" N ILE G 570 " pdb=" C ILE G 570 " pdb=" CB ILE G 570 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PRO C 641 " pdb=" N PRO C 641 " pdb=" C PRO C 641 " pdb=" CB PRO C 641 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO F 599 " pdb=" N PRO F 599 " pdb=" C PRO F 599 " pdb=" CB PRO F 599 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2682 not shown) Planarity restraints: 2978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 646 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C LYS C 646 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS C 646 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE C 647 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 640 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C ARG C 640 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG C 640 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO C 641 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 569 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C PRO G 569 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO G 569 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE G 570 " 0.013 2.00e-02 2.50e+03 ... (remaining 2975 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 37 2.21 - 2.88: 7747 2.88 - 3.55: 27650 3.55 - 4.23: 38440 4.23 - 4.90: 60449 Nonbonded interactions: 134323 Sorted by model distance: nonbonded pdb=" O ALA C 643 " pdb=" CG1 ILE C 647 " model vdw 1.532 3.440 nonbonded pdb=" O ALA C 643 " pdb=" CD1 ILE C 647 " model vdw 1.960 3.460 nonbonded pdb=" OD1 ASN I 110 " pdb=" OG SER I 113 " model vdw 2.040 2.440 nonbonded pdb=" O LEU H 78 " pdb=" OG SER H 81 " model vdw 2.080 2.440 nonbonded pdb=" O PRO E 308 " pdb=" OG SER E 311 " model vdw 2.110 2.440 ... (remaining 134318 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 'K' selection = (chain 'N' and resid 5 through 32) } ncs_group { reference = chain 'L' selection = chain 'O' } 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=0.00 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: 2.970 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: 0.020 Extract box with map and model: 12.180 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 43.380 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.100 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 0.086 16906 Z= 0.379 Angle : 0.880 13.441 22919 Z= 0.509 Chirality : 0.046 0.323 2685 Planarity : 0.005 0.054 2978 Dihedral : 15.161 89.304 6079 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 17.68 % Favored : 82.05 % Rotamer: Outliers : 0.48 % Allowed : 10.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.15), residues: 1872 helix: -2.55 (0.12), residues: 1039 sheet: -3.79 (0.63), residues: 28 loop : -4.49 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 313 HIS 0.012 0.002 HIS B 771 PHE 0.021 0.002 PHE G 681 TYR 0.021 0.002 TYR B1092 ARG 0.007 0.001 ARG B 926 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.7385 (mt) cc_final: 0.7017 (mm) REVERT: A 542 GLN cc_start: 0.8719 (pt0) cc_final: 0.8036 (pt0) REVERT: A 590 GLU cc_start: 0.9505 (tt0) cc_final: 0.9058 (tm-30) REVERT: B 755 LEU cc_start: 0.9459 (tp) cc_final: 0.9191 (tt) REVERT: B 772 ARG cc_start: 0.9085 (mpp-170) cc_final: 0.8663 (mtm-85) REVERT: B 938 MET cc_start: 0.8276 (tmm) cc_final: 0.7984 (tmm) REVERT: B 1298 GLN cc_start: 0.9602 (mm110) cc_final: 0.9209 (mm110) REVERT: C 575 PHE cc_start: 0.9072 (m-80) cc_final: 0.8753 (t80) REVERT: C 579 MET cc_start: 0.8978 (mpp) cc_final: 0.8685 (mmt) REVERT: D 412 TYR cc_start: 0.7352 (m-80) cc_final: 0.7128 (m-80) REVERT: D 433 GLN cc_start: 0.9528 (pm20) cc_final: 0.8848 (pp30) REVERT: E 344 MET cc_start: 0.9405 (ttm) cc_final: 0.8821 (tpp) REVERT: E 346 TYR cc_start: 0.9217 (m-80) cc_final: 0.8889 (m-80) REVERT: F 533 GLN cc_start: 0.9355 (tt0) cc_final: 0.9100 (tm-30) REVERT: F 717 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.9119 (mtt90) REVERT: F 726 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8109 (tpp-160) REVERT: G 711 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9125 (mm-30) REVERT: G 712 ARG cc_start: 0.8630 (tpt170) cc_final: 0.8418 (tpp80) REVERT: H 92 ARG cc_start: 0.9092 (mmp-170) cc_final: 0.8888 (mmm160) REVERT: H 105 ARG cc_start: 0.8586 (mmp-170) cc_final: 0.8207 (mmp-170) REVERT: H 541 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8238 (mtt90) REVERT: I 96 ASP cc_start: 0.8798 (m-30) cc_final: 0.8398 (m-30) REVERT: I 109 LYS cc_start: 0.9575 (ttmt) cc_final: 0.9318 (tttt) REVERT: I 123 LEU cc_start: 0.9331 (mt) cc_final: 0.8956 (mp) outliers start: 8 outliers final: 3 residues processed: 272 average time/residue: 0.3491 time to fit residues: 135.0661 Evaluate side-chains 192 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 588 ASN B 718 ASN B 805 ASN B 874 GLN B 915 ASN B 970 ASN B1006 GLN B1026 ASN B1053 ASN B1093 ASN B1104 ASN B1215 ASN B1243 GLN B1284 GLN B1298 GLN B1300 GLN B1304 ASN C 410 ASN C 437 HIS C 466 GLN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 394 GLN D 416 HIS E 352 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN F 552 ASN F 718 GLN F 738 ASN G 533 GLN G 555 ASN G 567 GLN G 684 ASN G 725 GLN G 745 ASN H 118 ASN ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 ASN H 493 ASN H 516 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16906 Z= 0.205 Angle : 0.705 12.937 22919 Z= 0.363 Chirality : 0.042 0.253 2685 Planarity : 0.005 0.054 2978 Dihedral : 6.035 37.053 2305 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.34 % Favored : 87.55 % Rotamer: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1872 helix: -0.32 (0.15), residues: 1059 sheet: -3.23 (0.56), residues: 28 loop : -3.74 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 313 HIS 0.014 0.001 HIS C 605 PHE 0.027 0.002 PHE H 112 TYR 0.025 0.002 TYR F 666 ARG 0.007 0.001 ARG I 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.7189 (mt) cc_final: 0.6846 (mm) REVERT: A 533 TYR cc_start: 0.9347 (t80) cc_final: 0.8608 (t80) REVERT: A 567 PHE cc_start: 0.8482 (m-10) cc_final: 0.6946 (m-10) REVERT: A 590 GLU cc_start: 0.9461 (tt0) cc_final: 0.8987 (tm-30) REVERT: A 595 GLU cc_start: 0.9469 (tt0) cc_final: 0.9195 (mm-30) REVERT: B 721 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 770 TYR cc_start: 0.8675 (m-10) cc_final: 0.8370 (m-10) REVERT: B 772 ARG cc_start: 0.8772 (mpp-170) cc_final: 0.8568 (mtm-85) REVERT: B 890 LYS cc_start: 0.9398 (tttt) cc_final: 0.9189 (tptm) REVERT: C 492 VAL cc_start: 0.9763 (t) cc_final: 0.9484 (p) REVERT: C 603 MET cc_start: 0.9488 (ptp) cc_final: 0.8943 (tpt) REVERT: D 349 PHE cc_start: 0.8778 (t80) cc_final: 0.8288 (t80) REVERT: D 368 ARG cc_start: 0.9185 (mtm110) cc_final: 0.8700 (ptp-110) REVERT: D 374 ASP cc_start: 0.8991 (t0) cc_final: 0.8662 (t0) REVERT: D 380 ARG cc_start: 0.9430 (mtm180) cc_final: 0.8653 (mtm180) REVERT: D 412 TYR cc_start: 0.7059 (m-80) cc_final: 0.4800 (m-80) REVERT: D 433 GLN cc_start: 0.9534 (pm20) cc_final: 0.8866 (pp30) REVERT: E 307 ILE cc_start: 0.9584 (tp) cc_final: 0.9370 (tp) REVERT: E 313 TRP cc_start: 0.9565 (p-90) cc_final: 0.8190 (p-90) REVERT: E 316 LEU cc_start: 0.9146 (pt) cc_final: 0.8742 (pt) REVERT: E 344 MET cc_start: 0.9312 (ttm) cc_final: 0.8719 (tpp) REVERT: E 346 TYR cc_start: 0.9103 (m-80) cc_final: 0.8732 (m-80) REVERT: E 366 THR cc_start: 0.9622 (m) cc_final: 0.9385 (m) REVERT: F 533 GLN cc_start: 0.9327 (tt0) cc_final: 0.9076 (tm-30) REVERT: F 689 LEU cc_start: 0.9785 (mm) cc_final: 0.9289 (tp) REVERT: F 691 MET cc_start: 0.9326 (mmp) cc_final: 0.8930 (mtp) REVERT: F 725 GLN cc_start: 0.8764 (mm110) cc_final: 0.8306 (mm-40) REVERT: F 726 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.7929 (tpp-160) REVERT: G 691 MET cc_start: 0.9470 (mmp) cc_final: 0.9225 (mmp) REVERT: G 711 GLU cc_start: 0.9536 (mt-10) cc_final: 0.9085 (mm-30) REVERT: G 717 ARG cc_start: 0.8610 (ttm170) cc_final: 0.8299 (ttm170) REVERT: H 92 ARG cc_start: 0.9038 (mmp-170) cc_final: 0.8799 (mmp-170) REVERT: H 93 ASN cc_start: 0.8524 (m110) cc_final: 0.8107 (m110) REVERT: H 104 GLU cc_start: 0.9460 (mt-10) cc_final: 0.8981 (mt-10) REVERT: H 535 TYR cc_start: 0.9316 (m-80) cc_final: 0.9107 (m-10) REVERT: H 541 ARG cc_start: 0.8906 (mtt90) cc_final: 0.8573 (mpt-90) REVERT: I 109 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9282 (tttt) REVERT: I 123 LEU cc_start: 0.9196 (mt) cc_final: 0.8974 (mp) outliers start: 3 outliers final: 0 residues processed: 294 average time/residue: 0.3313 time to fit residues: 138.9971 Evaluate side-chains 220 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN B 762 ASN B 791 GLN B 792 HIS B 915 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1216 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 690 GLN F 718 GLN F 721 ASN ** F 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 ASN G 699 ASN G 730 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 16906 Z= 0.407 Angle : 0.850 15.177 22919 Z= 0.446 Chirality : 0.044 0.196 2685 Planarity : 0.006 0.060 2978 Dihedral : 6.346 39.951 2305 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.17 % Favored : 84.72 % Rotamer: Outliers : 0.42 % Allowed : 6.69 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.49 (0.19), residues: 1872 helix: -0.24 (0.15), residues: 1064 sheet: -2.74 (0.63), residues: 35 loop : -3.77 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 388 HIS 0.014 0.002 HIS B 771 PHE 0.026 0.003 PHE D 349 TYR 0.031 0.003 TYR E 310 ARG 0.010 0.001 ARG C 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 243 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.9361 (t80) cc_final: 0.8623 (t80) REVERT: A 534 TYR cc_start: 0.8841 (m-80) cc_final: 0.8628 (m-80) REVERT: A 542 GLN cc_start: 0.9153 (pt0) cc_final: 0.8837 (pt0) REVERT: A 590 GLU cc_start: 0.9482 (tt0) cc_final: 0.9020 (tm-30) REVERT: A 595 GLU cc_start: 0.9497 (tt0) cc_final: 0.9105 (mm-30) REVERT: B 795 MET cc_start: 0.8641 (mmt) cc_final: 0.8380 (mmm) REVERT: B 1142 GLN cc_start: 0.9205 (tp-100) cc_final: 0.8848 (tp-100) REVERT: C 543 ARG cc_start: 0.8673 (mpp-170) cc_final: 0.7765 (mtm-85) REVERT: D 349 PHE cc_start: 0.8772 (t80) cc_final: 0.8347 (t80) REVERT: D 433 GLN cc_start: 0.9507 (pm20) cc_final: 0.8894 (pp30) REVERT: E 344 MET cc_start: 0.9389 (ttm) cc_final: 0.9003 (tpp) REVERT: E 346 TYR cc_start: 0.9171 (m-80) cc_final: 0.8764 (m-80) REVERT: E 366 THR cc_start: 0.9608 (m) cc_final: 0.9399 (m) REVERT: E 370 ASN cc_start: 0.9325 (m110) cc_final: 0.9025 (m110) REVERT: F 533 GLN cc_start: 0.9339 (tt0) cc_final: 0.9076 (tm-30) REVERT: F 681 PHE cc_start: 0.9229 (m-80) cc_final: 0.8836 (m-80) REVERT: F 691 MET cc_start: 0.9384 (mmp) cc_final: 0.8871 (mtp) REVERT: F 707 PHE cc_start: 0.9012 (m-80) cc_final: 0.8541 (m-80) REVERT: F 708 MET cc_start: 0.8961 (mmp) cc_final: 0.8756 (mmp) REVERT: F 712 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8162 (mtm-85) REVERT: F 717 ARG cc_start: 0.9363 (mmm-85) cc_final: 0.9073 (ttm-80) REVERT: F 718 GLN cc_start: 0.9543 (mm-40) cc_final: 0.9300 (mm-40) REVERT: G 691 MET cc_start: 0.9514 (mmp) cc_final: 0.9221 (mmm) REVERT: G 711 GLU cc_start: 0.9576 (mt-10) cc_final: 0.9134 (mm-30) REVERT: G 717 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8526 (ttm170) REVERT: H 93 ASN cc_start: 0.8586 (m110) cc_final: 0.8223 (m110) REVERT: H 97 LYS cc_start: 0.9565 (mmtt) cc_final: 0.9252 (mmmm) REVERT: H 535 TYR cc_start: 0.9125 (m-80) cc_final: 0.8800 (m-10) REVERT: H 552 MET cc_start: 0.9219 (ptm) cc_final: 0.8940 (ptm) REVERT: I 109 LYS cc_start: 0.9594 (ttmt) cc_final: 0.9356 (tttt) REVERT: I 123 LEU cc_start: 0.9344 (mt) cc_final: 0.9069 (mp) outliers start: 7 outliers final: 3 residues processed: 250 average time/residue: 0.3151 time to fit residues: 114.0893 Evaluate side-chains 199 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 6.9990 chunk 137 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 95 optimal weight: 0.0270 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B1006 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16906 Z= 0.231 Angle : 0.711 14.651 22919 Z= 0.368 Chirality : 0.042 0.199 2685 Planarity : 0.005 0.070 2978 Dihedral : 5.939 35.796 2305 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.23 % Favored : 87.66 % Rotamer: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1872 helix: 0.39 (0.16), residues: 1079 sheet: -3.05 (0.62), residues: 28 loop : -3.63 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 313 HIS 0.008 0.001 HIS B 771 PHE 0.037 0.002 PHE A 552 TYR 0.044 0.002 TYR D 412 ARG 0.013 0.001 ARG H 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.7371 (mt) cc_final: 0.6988 (mm) REVERT: A 532 ASP cc_start: 0.9216 (m-30) cc_final: 0.9004 (m-30) REVERT: A 533 TYR cc_start: 0.9392 (t80) cc_final: 0.8608 (t80) REVERT: A 560 LEU cc_start: 0.9418 (mt) cc_final: 0.9214 (mt) REVERT: A 586 TYR cc_start: 0.8994 (m-80) cc_final: 0.8651 (m-80) REVERT: A 590 GLU cc_start: 0.9423 (tt0) cc_final: 0.8977 (tm-30) REVERT: A 595 GLU cc_start: 0.9458 (tt0) cc_final: 0.9116 (mm-30) REVERT: B 747 GLU cc_start: 0.9203 (pt0) cc_final: 0.8914 (pt0) REVERT: B 795 MET cc_start: 0.8606 (mmt) cc_final: 0.8361 (mmm) REVERT: B 938 MET cc_start: 0.7522 (tmm) cc_final: 0.5380 (tmm) REVERT: B 1142 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8672 (tp-100) REVERT: D 368 ARG cc_start: 0.9040 (ptp90) cc_final: 0.8738 (ptp90) REVERT: D 433 GLN cc_start: 0.9461 (pm20) cc_final: 0.8897 (pp30) REVERT: E 316 LEU cc_start: 0.9225 (pt) cc_final: 0.8962 (pt) REVERT: E 346 TYR cc_start: 0.9156 (m-80) cc_final: 0.8660 (m-80) REVERT: E 366 THR cc_start: 0.9622 (m) cc_final: 0.9402 (m) REVERT: E 370 ASN cc_start: 0.9314 (m110) cc_final: 0.9038 (m110) REVERT: E 420 ARG cc_start: 0.8320 (pmt-80) cc_final: 0.7927 (tpt170) REVERT: F 533 GLN cc_start: 0.9317 (tt0) cc_final: 0.9056 (tm-30) REVERT: F 681 PHE cc_start: 0.9204 (m-80) cc_final: 0.8814 (m-80) REVERT: F 691 MET cc_start: 0.9350 (mmp) cc_final: 0.8803 (mtp) REVERT: F 717 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.9021 (mtp180) REVERT: F 718 GLN cc_start: 0.9512 (mm-40) cc_final: 0.9261 (mm-40) REVERT: F 725 GLN cc_start: 0.8887 (mm110) cc_final: 0.8447 (mm-40) REVERT: F 726 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.7985 (tpp-160) REVERT: G 560 GLN cc_start: 0.9399 (mt0) cc_final: 0.9112 (mt0) REVERT: G 691 MET cc_start: 0.9484 (mmp) cc_final: 0.9249 (mmp) REVERT: G 711 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9169 (mm-30) REVERT: G 712 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8205 (mmm-85) REVERT: G 717 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8355 (ttm170) REVERT: H 88 PHE cc_start: 0.9026 (m-80) cc_final: 0.8511 (m-10) REVERT: H 93 ASN cc_start: 0.8562 (m110) cc_final: 0.8078 (m110) REVERT: H 97 LYS cc_start: 0.9507 (mmtt) cc_final: 0.9204 (mmmm) REVERT: H 104 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9156 (mt-10) REVERT: H 535 TYR cc_start: 0.9022 (m-80) cc_final: 0.8675 (m-80) REVERT: H 541 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8491 (mtt90) REVERT: H 552 MET cc_start: 0.9242 (ptm) cc_final: 0.8973 (ptm) REVERT: I 109 LYS cc_start: 0.9533 (ttmt) cc_final: 0.9221 (tttt) REVERT: I 123 LEU cc_start: 0.9291 (mt) cc_final: 0.9073 (mp) outliers start: 1 outliers final: 1 residues processed: 267 average time/residue: 0.3236 time to fit residues: 127.1110 Evaluate side-chains 198 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 144 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.0170 chunk 174 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16906 Z= 0.186 Angle : 0.667 13.911 22919 Z= 0.341 Chirality : 0.041 0.208 2685 Planarity : 0.004 0.054 2978 Dihedral : 5.575 35.477 2305 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.75 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1872 helix: 0.88 (0.16), residues: 1072 sheet: -2.79 (0.63), residues: 28 loop : -3.44 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1032 HIS 0.008 0.001 HIS C 605 PHE 0.027 0.002 PHE F 729 TYR 0.036 0.002 TYR A 534 ARG 0.008 0.001 ARG H 554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.7043 (mt) cc_final: 0.6663 (mm) REVERT: A 533 TYR cc_start: 0.9330 (t80) cc_final: 0.8624 (t80) REVERT: A 542 GLN cc_start: 0.9264 (pt0) cc_final: 0.9058 (pt0) REVERT: A 567 PHE cc_start: 0.8477 (m-10) cc_final: 0.8127 (m-10) REVERT: A 586 TYR cc_start: 0.8949 (m-80) cc_final: 0.8503 (m-80) REVERT: A 590 GLU cc_start: 0.9384 (tt0) cc_final: 0.8937 (tm-30) REVERT: A 595 GLU cc_start: 0.9440 (tt0) cc_final: 0.9114 (mm-30) REVERT: B 760 LEU cc_start: 0.9385 (tt) cc_final: 0.9152 (tt) REVERT: B 795 MET cc_start: 0.8590 (mmt) cc_final: 0.8329 (mmm) REVERT: B 1142 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8580 (tp-100) REVERT: B 1239 ILE cc_start: 0.9451 (tp) cc_final: 0.8997 (tt) REVERT: C 561 PHE cc_start: 0.8858 (p90) cc_final: 0.8555 (p90) REVERT: C 575 PHE cc_start: 0.8746 (t80) cc_final: 0.8459 (t80) REVERT: C 579 MET cc_start: 0.9098 (mmm) cc_final: 0.8733 (mmp) REVERT: D 355 ARG cc_start: 0.4014 (ptt180) cc_final: 0.3660 (ptm160) REVERT: D 368 ARG cc_start: 0.9186 (ptp90) cc_final: 0.8619 (ptt-90) REVERT: D 391 ILE cc_start: 0.9529 (pt) cc_final: 0.9241 (mp) REVERT: D 404 ILE cc_start: 0.9064 (pt) cc_final: 0.7836 (pt) REVERT: D 412 TYR cc_start: 0.7323 (m-80) cc_final: 0.6991 (m-80) REVERT: D 433 GLN cc_start: 0.9425 (pm20) cc_final: 0.8920 (pp30) REVERT: E 313 TRP cc_start: 0.8639 (p-90) cc_final: 0.8173 (p-90) REVERT: E 370 ASN cc_start: 0.9348 (m110) cc_final: 0.9098 (m110) REVERT: F 533 GLN cc_start: 0.9333 (tt0) cc_final: 0.9071 (tm-30) REVERT: F 681 PHE cc_start: 0.9099 (m-80) cc_final: 0.8764 (m-80) REVERT: F 691 MET cc_start: 0.9300 (mmp) cc_final: 0.8895 (mtp) REVERT: G 560 GLN cc_start: 0.9370 (mt0) cc_final: 0.9129 (mt0) REVERT: G 561 CYS cc_start: 0.9424 (m) cc_final: 0.9152 (m) REVERT: G 691 MET cc_start: 0.9448 (mmp) cc_final: 0.9230 (mmp) REVERT: G 711 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9045 (mm-30) REVERT: G 717 ARG cc_start: 0.8736 (ttm170) cc_final: 0.8401 (ttm170) REVERT: G 726 ARG cc_start: 0.8835 (ttm110) cc_final: 0.7987 (ttt180) REVERT: H 88 PHE cc_start: 0.9035 (m-80) cc_final: 0.8551 (m-10) REVERT: H 92 ARG cc_start: 0.8978 (mmp-170) cc_final: 0.8724 (mmp-170) REVERT: H 93 ASN cc_start: 0.8593 (m110) cc_final: 0.8132 (m110) REVERT: H 97 LYS cc_start: 0.9530 (mmtt) cc_final: 0.9204 (mmmm) REVERT: H 104 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9057 (mt-10) REVERT: H 305 GLU cc_start: 0.6013 (mt-10) cc_final: 0.5588 (pm20) REVERT: H 541 ARG cc_start: 0.8955 (mtt90) cc_final: 0.8570 (mpt-90) REVERT: I 109 LYS cc_start: 0.9439 (ttmt) cc_final: 0.9166 (tttt) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3275 time to fit residues: 134.1013 Evaluate side-chains 205 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN F 718 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16906 Z= 0.191 Angle : 0.672 17.762 22919 Z= 0.342 Chirality : 0.041 0.173 2685 Planarity : 0.005 0.058 2978 Dihedral : 5.476 34.784 2305 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.70 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1872 helix: 1.13 (0.16), residues: 1066 sheet: -2.62 (0.65), residues: 28 loop : -3.29 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1032 HIS 0.010 0.001 HIS B 771 PHE 0.026 0.002 PHE A 567 TYR 0.048 0.002 TYR F 666 ARG 0.010 0.001 ARG B 966 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.6876 (mt) cc_final: 0.6499 (mm) REVERT: A 532 ASP cc_start: 0.9242 (m-30) cc_final: 0.9036 (m-30) REVERT: A 533 TYR cc_start: 0.9366 (t80) cc_final: 0.8643 (t80) REVERT: A 586 TYR cc_start: 0.8952 (m-80) cc_final: 0.8509 (m-80) REVERT: A 590 GLU cc_start: 0.9357 (tt0) cc_final: 0.8941 (tm-30) REVERT: A 595 GLU cc_start: 0.9479 (tt0) cc_final: 0.9103 (mm-30) REVERT: B 721 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8568 (mm-30) REVERT: B 795 MET cc_start: 0.8572 (mmt) cc_final: 0.8324 (mmm) REVERT: B 987 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 1142 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8571 (tp-100) REVERT: B 1239 ILE cc_start: 0.9430 (tp) cc_final: 0.8978 (tt) REVERT: C 561 PHE cc_start: 0.8760 (p90) cc_final: 0.8523 (p90) REVERT: C 575 PHE cc_start: 0.8866 (t80) cc_final: 0.8418 (t80) REVERT: C 579 MET cc_start: 0.9094 (mmm) cc_final: 0.8709 (mmm) REVERT: D 355 ARG cc_start: 0.4016 (ptt180) cc_final: 0.3673 (ptm160) REVERT: D 433 GLN cc_start: 0.9423 (pm20) cc_final: 0.8915 (pp30) REVERT: E 313 TRP cc_start: 0.8772 (p-90) cc_final: 0.7621 (p-90) REVERT: E 370 ASN cc_start: 0.9307 (m110) cc_final: 0.9080 (m110) REVERT: F 681 PHE cc_start: 0.9100 (m-80) cc_final: 0.8793 (m-80) REVERT: F 691 MET cc_start: 0.9315 (mmp) cc_final: 0.8892 (mtp) REVERT: G 560 GLN cc_start: 0.9332 (mt0) cc_final: 0.9125 (mt0) REVERT: G 561 CYS cc_start: 0.9419 (m) cc_final: 0.9149 (m) REVERT: G 691 MET cc_start: 0.9429 (mmp) cc_final: 0.8929 (mmm) REVERT: G 692 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8751 (mm-30) REVERT: G 693 LYS cc_start: 0.9640 (mtmm) cc_final: 0.9368 (mttt) REVERT: G 711 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9055 (mm-30) REVERT: G 712 ARG cc_start: 0.8351 (tpp80) cc_final: 0.8122 (tpp80) REVERT: G 717 ARG cc_start: 0.8510 (ttm170) cc_final: 0.8217 (ttm170) REVERT: G 726 ARG cc_start: 0.8899 (ttm110) cc_final: 0.8009 (ttt180) REVERT: H 85 LEU cc_start: 0.9251 (mp) cc_final: 0.9030 (mp) REVERT: H 88 PHE cc_start: 0.9061 (m-80) cc_final: 0.8606 (m-10) REVERT: H 92 ARG cc_start: 0.8964 (mmp-170) cc_final: 0.8729 (mmp-170) REVERT: H 93 ASN cc_start: 0.8640 (m110) cc_final: 0.8138 (m110) REVERT: H 97 LYS cc_start: 0.9530 (mmtt) cc_final: 0.9204 (mmmm) REVERT: H 104 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9048 (mt-10) REVERT: H 305 GLU cc_start: 0.5931 (mt-10) cc_final: 0.5639 (pm20) REVERT: H 539 MET cc_start: 0.8829 (ttp) cc_final: 0.8552 (ttp) REVERT: H 541 ARG cc_start: 0.8985 (mtt90) cc_final: 0.8344 (mpt-90) REVERT: I 108 LEU cc_start: 0.9698 (tp) cc_final: 0.9495 (tp) REVERT: I 109 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9172 (tttt) REVERT: I 120 MET cc_start: 0.9121 (ppp) cc_final: 0.8911 (ppp) REVERT: I 146 MET cc_start: 0.8687 (ptp) cc_final: 0.8483 (tmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3322 time to fit residues: 135.8586 Evaluate side-chains 205 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1260 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 HIS E 348 ASN ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN F 718 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 16906 Z= 0.327 Angle : 0.766 9.853 22919 Z= 0.400 Chirality : 0.044 0.187 2685 Planarity : 0.006 0.177 2978 Dihedral : 5.909 35.399 2305 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.84 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1872 helix: 0.74 (0.16), residues: 1073 sheet: -2.64 (0.59), residues: 35 loop : -3.39 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B1032 HIS 0.017 0.002 HIS B 771 PHE 0.027 0.002 PHE A 567 TYR 0.046 0.003 TYR D 412 ARG 0.015 0.001 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.6855 (mt) cc_final: 0.6480 (mm) REVERT: A 567 PHE cc_start: 0.8550 (m-10) cc_final: 0.7513 (m-10) REVERT: A 590 GLU cc_start: 0.9411 (tt0) cc_final: 0.8975 (tm-30) REVERT: A 595 GLU cc_start: 0.9483 (tt0) cc_final: 0.9081 (mm-30) REVERT: B 721 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 795 MET cc_start: 0.8586 (mmt) cc_final: 0.8330 (mmm) REVERT: B 987 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8298 (mm-30) REVERT: B 1142 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8866 (tp-100) REVERT: C 575 PHE cc_start: 0.9238 (t80) cc_final: 0.8538 (t80) REVERT: C 579 MET cc_start: 0.9345 (mmm) cc_final: 0.8712 (mmp) REVERT: D 404 ILE cc_start: 0.8859 (pt) cc_final: 0.8621 (pt) REVERT: D 433 GLN cc_start: 0.9501 (pm20) cc_final: 0.8914 (pp30) REVERT: E 313 TRP cc_start: 0.9056 (p-90) cc_final: 0.8624 (p-90) REVERT: E 400 LEU cc_start: 0.8510 (tp) cc_final: 0.8291 (tp) REVERT: F 681 PHE cc_start: 0.9156 (m-80) cc_final: 0.8786 (m-80) REVERT: F 691 MET cc_start: 0.9321 (mmp) cc_final: 0.8834 (mtp) REVERT: F 726 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.7941 (tpp-160) REVERT: G 561 CYS cc_start: 0.9473 (m) cc_final: 0.9179 (m) REVERT: G 691 MET cc_start: 0.9466 (mmp) cc_final: 0.9148 (mmm) REVERT: G 693 LYS cc_start: 0.9647 (mtmm) cc_final: 0.9433 (mttt) REVERT: G 717 ARG cc_start: 0.8647 (ttm170) cc_final: 0.8267 (ttm170) REVERT: G 726 ARG cc_start: 0.8808 (ttm110) cc_final: 0.8031 (ttt180) REVERT: H 88 PHE cc_start: 0.9051 (m-80) cc_final: 0.8653 (m-10) REVERT: H 93 ASN cc_start: 0.8603 (m110) cc_final: 0.8064 (m110) REVERT: H 97 LYS cc_start: 0.9580 (mmtt) cc_final: 0.9224 (mmmm) REVERT: H 104 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9094 (mt-10) REVERT: H 305 GLU cc_start: 0.6075 (mt-10) cc_final: 0.5815 (pm20) REVERT: H 539 MET cc_start: 0.8830 (ttp) cc_final: 0.8584 (ttp) REVERT: I 96 ASP cc_start: 0.8682 (m-30) cc_final: 0.8422 (m-30) REVERT: I 108 LEU cc_start: 0.9728 (tp) cc_final: 0.9524 (tp) REVERT: I 109 LYS cc_start: 0.9489 (ttmt) cc_final: 0.9230 (tttt) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3033 time to fit residues: 111.5696 Evaluate side-chains 184 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 123 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16906 Z= 0.190 Angle : 0.684 9.935 22919 Z= 0.348 Chirality : 0.041 0.192 2685 Planarity : 0.005 0.107 2978 Dihedral : 5.485 36.629 2305 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.47 % Favored : 89.42 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1872 helix: 1.07 (0.16), residues: 1072 sheet: -2.38 (0.62), residues: 35 loop : -3.23 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1032 HIS 0.008 0.001 HIS B 880 PHE 0.028 0.002 PHE G 729 TYR 0.044 0.002 TYR F 666 ARG 0.010 0.001 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.6783 (mt) cc_final: 0.6394 (mm) REVERT: A 590 GLU cc_start: 0.9366 (tt0) cc_final: 0.8923 (tm-30) REVERT: A 595 GLU cc_start: 0.9506 (tt0) cc_final: 0.9112 (mm-30) REVERT: B 721 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8434 (mm-30) REVERT: B 795 MET cc_start: 0.8524 (mmt) cc_final: 0.8242 (mmm) REVERT: B 987 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8048 (mm-30) REVERT: C 575 PHE cc_start: 0.9072 (t80) cc_final: 0.8331 (t80) REVERT: C 579 MET cc_start: 0.9102 (mmm) cc_final: 0.8409 (mmm) REVERT: D 323 GLU cc_start: 0.9632 (pt0) cc_final: 0.9306 (pt0) REVERT: D 355 ARG cc_start: 0.3941 (ptt180) cc_final: 0.3564 (ptm160) REVERT: D 391 ILE cc_start: 0.9497 (pt) cc_final: 0.9159 (mp) REVERT: D 433 GLN cc_start: 0.9438 (pm20) cc_final: 0.8893 (pp30) REVERT: E 313 TRP cc_start: 0.8890 (p-90) cc_final: 0.8420 (p-90) REVERT: E 320 HIS cc_start: 0.8858 (t-90) cc_final: 0.7818 (t-90) REVERT: E 380 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8126 (ttp-110) REVERT: F 681 PHE cc_start: 0.9101 (m-80) cc_final: 0.8731 (m-80) REVERT: F 689 LEU cc_start: 0.9755 (mm) cc_final: 0.9547 (pp) REVERT: F 691 MET cc_start: 0.9281 (mmp) cc_final: 0.8745 (mtp) REVERT: G 691 MET cc_start: 0.9386 (mmp) cc_final: 0.9084 (mmm) REVERT: G 693 LYS cc_start: 0.9675 (mtmm) cc_final: 0.9423 (mttt) REVERT: G 717 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8160 (ttm170) REVERT: G 725 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8594 (mm110) REVERT: G 726 ARG cc_start: 0.8683 (ttm110) cc_final: 0.7774 (ttt180) REVERT: G 739 VAL cc_start: 0.8814 (t) cc_final: 0.8604 (p) REVERT: H 85 LEU cc_start: 0.9240 (mp) cc_final: 0.9038 (mp) REVERT: H 88 PHE cc_start: 0.9030 (m-80) cc_final: 0.8520 (m-10) REVERT: H 93 ASN cc_start: 0.8574 (m110) cc_final: 0.7966 (m110) REVERT: H 97 LYS cc_start: 0.9549 (mmtt) cc_final: 0.9192 (mmmm) REVERT: H 104 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9055 (mt-10) REVERT: H 539 MET cc_start: 0.8816 (ttp) cc_final: 0.8537 (ttp) REVERT: I 109 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9165 (tttt) REVERT: I 120 MET cc_start: 0.9045 (ppp) cc_final: 0.8716 (ppp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3092 time to fit residues: 120.5146 Evaluate side-chains 199 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 HIS ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 684 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16906 Z= 0.188 Angle : 0.685 9.686 22919 Z= 0.350 Chirality : 0.041 0.174 2685 Planarity : 0.006 0.202 2978 Dihedral : 5.378 36.364 2305 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.95 % Favored : 88.94 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1872 helix: 1.15 (0.16), residues: 1070 sheet: -2.15 (0.66), residues: 35 loop : -3.22 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1032 HIS 0.009 0.001 HIS B 880 PHE 0.021 0.002 PHE H 503 TYR 0.028 0.002 TYR E 310 ARG 0.012 0.001 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.6577 (mt) cc_final: 0.6133 (mm) REVERT: A 546 ARG cc_start: 0.8622 (ttm110) cc_final: 0.7825 (ttm170) REVERT: A 560 LEU cc_start: 0.9394 (mt) cc_final: 0.9159 (mt) REVERT: A 567 PHE cc_start: 0.8540 (m-80) cc_final: 0.7602 (m-80) REVERT: A 590 GLU cc_start: 0.9362 (tt0) cc_final: 0.8921 (tm-30) REVERT: A 595 GLU cc_start: 0.9463 (tt0) cc_final: 0.9103 (mm-30) REVERT: B 795 MET cc_start: 0.8521 (mmt) cc_final: 0.8232 (mmm) REVERT: C 582 GLU cc_start: 0.8582 (mp0) cc_final: 0.8070 (mp0) REVERT: D 323 GLU cc_start: 0.9626 (pt0) cc_final: 0.9333 (pt0) REVERT: D 355 ARG cc_start: 0.4175 (ptt180) cc_final: 0.3814 (ptm160) REVERT: D 391 ILE cc_start: 0.9524 (pt) cc_final: 0.9173 (mp) REVERT: D 433 GLN cc_start: 0.9408 (pm20) cc_final: 0.8831 (pp30) REVERT: E 313 TRP cc_start: 0.9069 (p-90) cc_final: 0.8435 (p-90) REVERT: E 320 HIS cc_start: 0.8889 (t-90) cc_final: 0.7993 (t-90) REVERT: E 380 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8183 (ttp-110) REVERT: E 426 GLU cc_start: 0.8149 (mp0) cc_final: 0.7771 (mp0) REVERT: F 681 PHE cc_start: 0.9066 (m-80) cc_final: 0.8750 (m-80) REVERT: F 691 MET cc_start: 0.9273 (mmp) cc_final: 0.8734 (mtp) REVERT: F 718 GLN cc_start: 0.9136 (mt0) cc_final: 0.8822 (mt0) REVERT: G 561 CYS cc_start: 0.9350 (m) cc_final: 0.9001 (m) REVERT: G 691 MET cc_start: 0.9404 (mmp) cc_final: 0.9076 (mmm) REVERT: G 717 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8195 (ttm170) REVERT: G 725 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8713 (mm-40) REVERT: G 726 ARG cc_start: 0.8806 (ttm110) cc_final: 0.7848 (ttt180) REVERT: G 731 GLN cc_start: 0.8902 (tp40) cc_final: 0.8698 (tp40) REVERT: G 739 VAL cc_start: 0.8743 (t) cc_final: 0.8527 (p) REVERT: H 88 PHE cc_start: 0.9015 (m-80) cc_final: 0.8669 (m-10) REVERT: H 93 ASN cc_start: 0.8624 (m110) cc_final: 0.8022 (m110) REVERT: H 104 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9009 (mt-10) REVERT: I 108 LEU cc_start: 0.9690 (tp) cc_final: 0.9480 (tp) REVERT: I 109 LYS cc_start: 0.9447 (ttmt) cc_final: 0.9180 (tttt) REVERT: I 120 MET cc_start: 0.9042 (ppp) cc_final: 0.8736 (ppp) REVERT: I 146 MET cc_start: 0.8540 (tmm) cc_final: 0.8199 (tpp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3071 time to fit residues: 119.1942 Evaluate side-chains 208 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 684 ASN G 560 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 16906 Z= 0.331 Angle : 0.805 10.578 22919 Z= 0.418 Chirality : 0.044 0.250 2685 Planarity : 0.006 0.135 2978 Dihedral : 5.903 36.482 2305 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.00 % Favored : 85.90 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1872 helix: 0.75 (0.16), residues: 1061 sheet: -2.79 (0.60), residues: 28 loop : -3.32 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 103 HIS 0.017 0.002 HIS B 771 PHE 0.026 0.003 PHE H 112 TYR 0.025 0.002 TYR D 412 ARG 0.008 0.001 ARG G 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ILE cc_start: 0.6815 (mt) cc_final: 0.6401 (mm) REVERT: A 560 LEU cc_start: 0.9471 (mt) cc_final: 0.9252 (mt) REVERT: A 567 PHE cc_start: 0.8313 (m-80) cc_final: 0.8111 (m-80) REVERT: A 586 TYR cc_start: 0.9138 (m-10) cc_final: 0.8883 (m-10) REVERT: A 590 GLU cc_start: 0.9437 (tt0) cc_final: 0.9019 (tm-30) REVERT: A 595 GLU cc_start: 0.9509 (tt0) cc_final: 0.9172 (mm-30) REVERT: B 795 MET cc_start: 0.8557 (mmt) cc_final: 0.8282 (mmm) REVERT: D 433 GLN cc_start: 0.9469 (pm20) cc_final: 0.8882 (pp30) REVERT: E 313 TRP cc_start: 0.9402 (p-90) cc_final: 0.8891 (p-90) REVERT: E 320 HIS cc_start: 0.8910 (t-90) cc_final: 0.7966 (t-90) REVERT: E 400 LEU cc_start: 0.8504 (tp) cc_final: 0.8288 (tp) REVERT: F 681 PHE cc_start: 0.9121 (m-80) cc_final: 0.8765 (m-80) REVERT: F 691 MET cc_start: 0.9313 (mmp) cc_final: 0.8756 (mtp) REVERT: G 691 MET cc_start: 0.9439 (mmp) cc_final: 0.9016 (mmm) REVERT: G 717 ARG cc_start: 0.8558 (ttm170) cc_final: 0.8209 (ttm170) REVERT: G 725 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8630 (mm110) REVERT: G 726 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8406 (ttt180) REVERT: H 88 PHE cc_start: 0.9074 (m-80) cc_final: 0.8666 (m-10) REVERT: H 93 ASN cc_start: 0.8592 (m110) cc_final: 0.8018 (m110) REVERT: H 97 LYS cc_start: 0.9581 (mmtt) cc_final: 0.9240 (mmmm) REVERT: H 104 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9090 (mt-10) REVERT: H 535 TYR cc_start: 0.8916 (m-80) cc_final: 0.8566 (m-80) REVERT: H 539 MET cc_start: 0.8838 (ttp) cc_final: 0.8621 (ttp) REVERT: I 109 LYS cc_start: 0.9515 (ttmt) cc_final: 0.9258 (tttt) REVERT: I 120 MET cc_start: 0.9147 (ppp) cc_final: 0.8840 (ppp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2777 time to fit residues: 99.8616 Evaluate side-chains 184 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN F 738 ASN G 560 GLN G 700 HIS ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 495 HIS H 544 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045664 restraints weight = 133265.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.046798 restraints weight = 87035.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.047656 restraints weight = 63089.324| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16906 Z= 0.189 Angle : 0.713 10.386 22919 Z= 0.361 Chirality : 0.042 0.181 2685 Planarity : 0.005 0.065 2978 Dihedral : 5.435 36.660 2305 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.84 % Favored : 89.10 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1872 helix: 1.15 (0.16), residues: 1065 sheet: -2.48 (0.63), residues: 28 loop : -3.11 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1032 HIS 0.008 0.001 HIS B 771 PHE 0.021 0.002 PHE H 503 TYR 0.038 0.002 TYR A 534 ARG 0.007 0.001 ARG A 546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.94 seconds wall clock time: 61 minutes 16.61 seconds (3676.61 seconds total)