Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 10:39:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/10_2023/6uxv_20933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/10_2023/6uxv_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_20933/10_2023/6uxv_20933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/10_2023/6uxv_20933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/10_2023/6uxv_20933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxv_20933/10_2023/6uxv_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 9.32, per 1000 atoms: 0.56 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: 7.77 Conformation dependent library (CDL) restraints added in 2.2 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: 1.21 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: 4.40 Time building geometry restraints manager: 8.21 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: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.200 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.640 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.720 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 272 average time/residue: 0.3406 time to fit residues: 131.8687 Evaluate side-chains 181 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1544 time to fit residues: 3.3358 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B1300 GLN B1304 ASN C 410 ASN ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 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** 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 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 H 556 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16906 Z= 0.207 Angle : 0.718 12.889 22919 Z= 0.370 Chirality : 0.042 0.284 2685 Planarity : 0.005 0.072 2978 Dihedral : 6.092 37.733 2305 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.13 % Favored : 87.77 % Rotamer: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.56 % 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: -2.65 (0.19), residues: 1872 helix: -0.41 (0.15), residues: 1063 sheet: -3.24 (0.58), residues: 28 loop : -3.75 (0.21), residues: 781 *********************** 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 288 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 1.905 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 outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.3257 time to fit residues: 134.6771 Evaluate side-chains 193 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5531 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN B 804 ASN B 915 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1216 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 567 GLN F 684 ASN F 690 GLN F 718 GLN F 721 ASN F 738 ASN 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 H 326 HIS H 556 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 16906 Z= 0.465 Angle : 0.918 15.302 22919 Z= 0.481 Chirality : 0.046 0.209 2685 Planarity : 0.006 0.062 2978 Dihedral : 6.615 41.075 2305 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 29.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 16.03 % Favored : 83.87 % Rotamer: Outliers : 0.42 % Allowed : 7.11 % Favored : 92.47 % 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: -2.78 (0.18), residues: 1872 helix: -0.52 (0.15), residues: 1066 sheet: -2.78 (0.64), residues: 35 loop : -3.82 (0.21), residues: 771 *********************** 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 237 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 1.980 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 outliers start: 7 outliers final: 3 residues processed: 236 average time/residue: 0.3204 time to fit residues: 111.1666 Evaluate side-chains 169 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1669 time to fit residues: 3.5058 ------------------------------------------------------------------------------- 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: 0.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 762 ASN B 792 HIS B 806 ASN B1006 GLN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 556 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16906 Z= 0.279 Angle : 0.750 12.464 22919 Z= 0.391 Chirality : 0.043 0.221 2685 Planarity : 0.005 0.065 2978 Dihedral : 6.200 38.044 2305 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.35 % Favored : 86.54 % Rotamer: Outliers : 0.18 % Allowed : 5.02 % Favored : 94.80 % 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: -2.08 (0.19), residues: 1872 helix: 0.09 (0.15), residues: 1074 sheet: -2.59 (0.68), residues: 35 loop : -3.63 (0.22), residues: 763 *********************** 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 243 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 1.773 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 outliers start: 3 outliers final: 2 residues processed: 242 average time/residue: 0.2867 time to fit residues: 103.8904 Evaluate side-chains 175 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1965 time to fit residues: 3.4181 ------------------------------------------------------------------------------- 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: 0.0030 chunk 110 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- 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 804 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16906 Z= 0.183 Angle : 0.690 15.906 22919 Z= 0.351 Chirality : 0.041 0.208 2685 Planarity : 0.005 0.056 2978 Dihedral : 5.606 35.936 2305 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.38 % Favored : 88.51 % Rotamer: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % 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: -1.14 (0.20), residues: 1872 helix: 0.98 (0.16), residues: 1066 sheet: -2.88 (0.61), residues: 28 loop : -3.35 (0.22), residues: 778 *********************** 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: 1 poor density : 283 time to evaluate : 1.979 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 outliers start: 1 outliers final: 1 residues processed: 283 average time/residue: 0.3094 time to fit residues: 128.7756 Evaluate side-chains 195 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1926 time to fit residues: 2.7428 ------------------------------------------------------------------------------- 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: 2.9990 chunk 174 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** A 589 HIS ** 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** ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN G 730 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16906 Z= 0.194 Angle : 0.691 15.123 22919 Z= 0.356 Chirality : 0.041 0.167 2685 Planarity : 0.005 0.057 2978 Dihedral : 5.539 34.478 2305 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.49 % Favored : 88.41 % Rotamer: Outliers : 0.06 % Allowed : 2.09 % 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: -0.98 (0.20), residues: 1872 helix: 1.10 (0.16), residues: 1063 sheet: -2.75 (0.60), residues: 28 loop : -3.25 (0.22), residues: 781 *********************** 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 267 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 1.987 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 outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.3073 time to fit residues: 121.7654 Evaluate side-chains 189 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1978 time to fit residues: 2.9059 ------------------------------------------------------------------------------- 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: 1.9990 chunk 110 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B1260 ASN ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 HIS ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN G 730 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS 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: 0.8175 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 16906 Z= 0.427 Angle : 0.879 15.398 22919 Z= 0.460 Chirality : 0.046 0.176 2685 Planarity : 0.006 0.060 2978 Dihedral : 6.249 37.211 2305 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.42 % Favored : 85.47 % Rotamer: Outliers : 0.12 % Allowed : 2.81 % Favored : 97.07 % 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: -1.76 (0.19), residues: 1872 helix: 0.40 (0.16), residues: 1072 sheet: -2.78 (0.60), residues: 35 loop : -3.55 (0.21), residues: 765 *********************** 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 232 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.857 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 outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.2832 time to fit residues: 99.4647 Evaluate side-chains 155 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5270 ------------------------------------------------------------------------------- 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: 3.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN A 584 GLN ** 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 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 HIS F 725 GLN G 730 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16906 Z= 0.199 Angle : 0.718 13.280 22919 Z= 0.364 Chirality : 0.042 0.190 2685 Planarity : 0.005 0.067 2978 Dihedral : 5.672 35.534 2305 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.22 % Favored : 88.68 % Rotamer: Outliers : 0.12 % Allowed : 1.20 % Favored : 98.68 % 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: -1.09 (0.20), residues: 1872 helix: 0.96 (0.16), residues: 1064 sheet: -2.78 (0.63), residues: 28 loop : -3.23 (0.22), residues: 780 *********************** 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 260 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 258 time to evaluate : 1.971 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 outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.3009 time to fit residues: 117.1872 Evaluate side-chains 182 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4259 ------------------------------------------------------------------------------- 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: 10.0000 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 170 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 118 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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** ** 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** D 416 HIS ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16906 Z= 0.195 Angle : 0.699 13.409 22919 Z= 0.356 Chirality : 0.042 0.253 2685 Planarity : 0.005 0.067 2978 Dihedral : 5.455 34.944 2305 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.70 % Favored : 88.19 % Rotamer: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.04 % 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: -0.91 (0.20), residues: 1872 helix: 1.11 (0.16), residues: 1065 sheet: -2.65 (0.61), residues: 28 loop : -3.16 (0.22), residues: 779 *********************** 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 259 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.036 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 outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.3007 time to fit residues: 115.8649 Evaluate side-chains 185 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5049 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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** ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 725 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** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16906 Z= 0.351 Angle : 0.829 14.212 22919 Z= 0.432 Chirality : 0.045 0.287 2685 Planarity : 0.006 0.081 2978 Dihedral : 5.977 35.347 2305 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.37 % Favored : 85.52 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.43 (0.20), residues: 1872 helix: 0.66 (0.16), residues: 1067 sheet: -2.63 (0.67), residues: 28 loop : -3.36 (0.21), residues: 777 ********************** 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 233 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.882 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 outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2853 time to fit residues: 101.3340 Evaluate side-chains 164 residues out of total 1802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6306 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 163 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN G 684 ASN G 719 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 556 ASN ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.045460 restraints weight = 135815.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046587 restraints weight = 89158.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.047382 restraints weight = 64100.596| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16906 Z= 0.194 Angle : 0.722 12.814 22919 Z= 0.367 Chirality : 0.043 0.255 2685 Planarity : 0.005 0.065 2978 Dihedral : 5.546 37.362 2305 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.65 % Favored : 88.25 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.46 % 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: -1.00 (0.20), residues: 1872 helix: 1.02 (0.16), residues: 1063 sheet: -2.72 (0.60), residues: 28 loop : -3.16 (0.22), residues: 781 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3076.88 seconds wall clock time: 57 minutes 22.66 seconds (3442.66 seconds total)