Starting phenix.real_space_refine on Fri Sep 27 00:13:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/09_2024/7mjp_23881_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/09_2024/7mjp_23881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/09_2024/7mjp_23881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/09_2024/7mjp_23881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/09_2024/7mjp_23881_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjp_23881/09_2024/7mjp_23881_neut.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 S 1 5.16 5 Cl 1 4.86 5 C 8398 2.51 5 N 2849 2.21 5 O 2899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 1812 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 12, 'TRANS': 353} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1460 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 18, 'GLU:plan': 24, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 582 Chain: "B" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1674 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 327} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1041 Unresolved non-hydrogen angles: 1341 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1677 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 10, 'TRANS': 328} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1348 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1677 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 10, 'TRANS': 328} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1348 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 8, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 536 Chain: "E" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 7107 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1248} Link IDs: {'PTRANS': 47, 'TRANS': 1388} Chain breaks: 4 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 4520 Unresolved non-hydrogen angles: 5845 Unresolved non-hydrogen dihedrals: 3784 Unresolved non-hydrogen chiralities: 497 Planarities with less than four sites: {'GLN:plan1': 48, 'ARG:plan': 61, 'TYR:plan': 44, 'ASN:plan1': 65, 'TRP:plan': 28, 'ASP:plan': 56, 'PHE:plan': 75, 'GLU:plan': 65, 'HIS:plan': 33} Unresolved non-hydrogen planarities: 2295 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.64, per 1000 atoms: 0.68 Number of scatterers: 14163 At special positions: 0 Unit cell: (125.54, 170.734, 156.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 1 16.00 P 15 15.00 O 2899 8.00 N 2849 7.00 C 8398 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG N 1 " - " ASN E 9 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 3.2 seconds 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 21 sheets defined 50.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.263A pdb=" N GLU A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 21' Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.776A pdb=" N ILE A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 removed outlier: 3.853A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.583A pdb=" N ALA A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 removed outlier: 4.577A pdb=" N ILE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 183 removed outlier: 3.623A pdb=" N ILE A 156 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.171A pdb=" N ASP A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 280 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.870A pdb=" N ILE B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.144A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.920A pdb=" N GLY B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 152 through 183 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.122A pdb=" N VAL B 286 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.917A pdb=" N LYS B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.686A pdb=" N PHE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 97 removed outlier: 4.625A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.660A pdb=" N ALA C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 183 removed outlier: 3.901A pdb=" N ILE C 156 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.007A pdb=" N ASP C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 68 through 98 removed outlier: 4.183A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 4.006A pdb=" N ALA D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.542A pdb=" N ALA D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D 119 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 139 removed outlier: 3.793A pdb=" N VAL D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 183 removed outlier: 4.014A pdb=" N ILE D 156 " --> pdb=" O CYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.271A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.579A pdb=" N LEU D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.680A pdb=" N LYS D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 22 through 47 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 69 through 96 Processing helix chain 'E' and resid 101 through 104 removed outlier: 4.291A pdb=" N LEU E 104 " --> pdb=" O HIS E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 101 through 104' Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 130 through 133 Processing helix chain 'E' and resid 134 through 159 removed outlier: 3.636A pdb=" N LEU E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 192 Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.906A pdb=" N VAL E 220 " --> pdb=" O GLN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 removed outlier: 3.963A pdb=" N THR E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 256 through 278 removed outlier: 3.710A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 294 through 312 removed outlier: 3.939A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.714A pdb=" N LEU E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.993A pdb=" N LEU E 345 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 394 removed outlier: 3.642A pdb=" N ALA E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG E 394 " --> pdb=" O ASN E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 416 removed outlier: 3.579A pdb=" N ILE E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 427 removed outlier: 3.545A pdb=" N LEU E 427 " --> pdb=" O TRP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 433 through 450 removed outlier: 4.245A pdb=" N LEU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 removed outlier: 4.051A pdb=" N VAL E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 498 removed outlier: 3.523A pdb=" N ILE E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 506 removed outlier: 4.010A pdb=" N LEU E 502 " --> pdb=" O GLY E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 559 removed outlier: 4.146A pdb=" N VAL E 515 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E 529 " --> pdb=" O SER E 525 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 4.174A pdb=" N HIS E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 557 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 606 removed outlier: 3.699A pdb=" N ALA E 568 " --> pdb=" O LYS E 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 572 " --> pdb=" O ALA E 568 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 573 " --> pdb=" O PHE E 569 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS E 576 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) Proline residue: E 581 - end of helix removed outlier: 3.804A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 716 Processing helix chain 'E' and resid 761 through 768 Processing helix chain 'E' and resid 773 through 784 Processing helix chain 'E' and resid 785 through 793 removed outlier: 4.592A pdb=" N ASP E 789 " --> pdb=" O SER E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 799 Processing helix chain 'E' and resid 809 through 823 removed outlier: 3.509A pdb=" N TYR E 823 " --> pdb=" O ALA E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 855 Processing helix chain 'E' and resid 891 through 897 removed outlier: 3.518A pdb=" N THR E 897 " --> pdb=" O LYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 910 removed outlier: 4.168A pdb=" N GLU E 904 " --> pdb=" O VAL E 900 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET E 910 " --> pdb=" O TRP E 906 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 983 Processing helix chain 'E' and resid 987 through 1018 removed outlier: 4.055A pdb=" N PHE E 991 " --> pdb=" O PHE E 987 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU E 992 " --> pdb=" O PHE E 988 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET E 993 " --> pdb=" O LEU E 989 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E1008 " --> pdb=" O ILE E1004 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E1018 " --> pdb=" O TRP E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1073 removed outlier: 3.804A pdb=" N SER E1050 " --> pdb=" O CYS E1046 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E1051 " --> pdb=" O LEU E1047 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E1073 " --> pdb=" O LEU E1069 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1083 removed outlier: 3.793A pdb=" N PHE E1080 " --> pdb=" O PRO E1076 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E1083 " --> pdb=" O PHE E1079 " (cutoff:3.500A) Processing helix chain 'E' and resid 1086 through 1102 removed outlier: 4.481A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1128 removed outlier: 3.721A pdb=" N THR E1106 " --> pdb=" O HIS E1102 " (cutoff:3.500A) Processing helix chain 'E' and resid 1129 through 1177 removed outlier: 3.736A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E1136 " --> pdb=" O LEU E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix removed outlier: 4.223A pdb=" N ARG E1150 " --> pdb=" O GLN E1146 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP E1155 " --> pdb=" O VAL E1151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER E1162 " --> pdb=" O GLU E1158 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E1165 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.802A pdb=" N PHE E1171 " --> pdb=" O LEU E1167 " (cutoff:3.500A) Processing helix chain 'E' and resid 1177 through 1184 Processing helix chain 'E' and resid 1186 through 1236 removed outlier: 3.804A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E1233 " --> pdb=" O THR E1229 " (cutoff:3.500A) Processing helix chain 'E' and resid 1241 through 1258 removed outlier: 3.598A pdb=" N GLY E1247 " --> pdb=" O LEU E1243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E1255 " --> pdb=" O ALA E1251 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1259 through 1282 removed outlier: 3.733A pdb=" N ARG E1263 " --> pdb=" O ASN E1259 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1294 through 1298 removed outlier: 3.558A pdb=" N VAL E1298 " --> pdb=" O PRO E1295 " (cutoff:3.500A) Processing helix chain 'E' and resid 1349 through 1356 removed outlier: 3.947A pdb=" N PHE E1356 " --> pdb=" O SER E1352 " (cutoff:3.500A) Processing helix chain 'E' and resid 1367 through 1371 Processing helix chain 'E' and resid 1372 through 1376 removed outlier: 3.505A pdb=" N LYS E1375 " --> pdb=" O ASP E1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 1377 through 1383 Processing helix chain 'E' and resid 1414 through 1420 Processing helix chain 'E' and resid 1442 through 1461 removed outlier: 4.774A pdb=" N GLY E1448 " --> pdb=" O ASN E1444 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN E1451 " --> pdb=" O VAL E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1475 through 1489 Processing helix chain 'E' and resid 1505 through 1509 removed outlier: 4.489A pdb=" N THR E1508 " --> pdb=" O THR E1505 " (cutoff:3.500A) Processing helix chain 'E' and resid 1528 through 1533 removed outlier: 3.994A pdb=" N GLU E1533 " --> pdb=" O LEU E1529 " (cutoff:3.500A) Processing helix chain 'E' and resid 1534 through 1540 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.604A pdb=" N LYS A 48 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 3.819A pdb=" N VAL A 212 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 265 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 248 removed outlier: 5.444A pdb=" N THR A 233 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 223 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 297 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 225 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 295 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 227 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 293 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 229 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU A 291 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 294 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 300 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.175A pdb=" N VAL A 337 " --> pdb=" O LYS D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AA9, first strand: chain 'B' and resid 191 through 193 removed outlier: 6.686A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 220 through 230 removed outlier: 5.428A pdb=" N SER B 222 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL B 299 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 324 Processing sheet with id=AB4, first strand: chain 'C' and resid 47 through 48 removed outlier: 4.095A pdb=" N LYS C 48 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 5.471A pdb=" N ALA C 197 " --> pdb=" O GLN C 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 248 removed outlier: 4.512A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 223 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU C 297 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL C 225 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 295 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 227 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 293 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 229 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU C 291 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 322 through 323 removed outlier: 3.508A pdb=" N ARG C 323 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 346 " --> pdb=" O ARG C 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 191 through 193 Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 193 removed outlier: 4.342A pdb=" N ILE D 199 " --> pdb=" O GLN D 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 244 through 248 removed outlier: 4.440A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 223 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU D 297 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 225 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE D 295 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 227 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 293 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 296 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 309 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 298 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AC3, first strand: chain 'E' and resid 880 through 881 removed outlier: 7.029A pdb=" N ALA E 880 " --> pdb=" O VAL E 886 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 3054 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2829 1.30 - 1.43: 2898 1.43 - 1.56: 8407 1.56 - 1.69: 32 1.69 - 1.81: 3 Bond restraints: 14169 Sorted by residual: bond pdb=" O5 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.448 1.643 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" O4 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.453 1.645 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.38e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP E1601 " pdb=" C5 ATP E1601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 ... (remaining 14164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 19542 4.16 - 8.31: 180 8.31 - 12.47: 28 12.47 - 16.62: 3 16.62 - 20.78: 7 Bond angle restraints: 19760 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 122.73 17.14 1.00e+00 1.00e+00 2.94e+02 ... (remaining 19755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 8282 23.45 - 46.90: 65 46.90 - 70.35: 27 70.35 - 93.80: 5 93.80 - 117.24: 3 Dihedral angle restraints: 8382 sinusoidal: 241 harmonic: 8141 Sorted by residual: dihedral pdb=" CA LEU E1325 " pdb=" C LEU E1325 " pdb=" N LYS E1326 " pdb=" CA LYS E1326 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL E1298 " pdb=" C VAL E1298 " pdb=" N PRO E1299 " pdb=" CA PRO E1299 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL E1496 " pdb=" C VAL E1496 " pdb=" N VAL E1497 " pdb=" CA VAL E1497 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 2695 0.381 - 0.762: 1 0.762 - 1.143: 0 1.143 - 1.524: 0 1.524 - 1.905: 1 Chirality restraints: 2697 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 9 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.49 -1.91 2.00e-01 2.50e+01 9.07e+01 chirality pdb=" CA CYS E 263 " pdb=" N CYS E 263 " pdb=" C CYS E 263 " pdb=" CB CYS E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA VAL A 241 " pdb=" N VAL A 241 " pdb=" C VAL A 241 " pdb=" CB VAL A 241 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2694 not shown) Planarity restraints: 2825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 9 " 0.052 2.00e-02 2.50e+03 7.86e-02 7.72e+01 pdb=" CG ASN E 9 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 9 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 9 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 104 " 0.028 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C TYR C 104 " -0.099 2.00e-02 2.50e+03 pdb=" O TYR C 104 " 0.036 2.00e-02 2.50e+03 pdb=" N MET C 105 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 581 " -0.027 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C PRO E 581 " 0.091 2.00e-02 2.50e+03 pdb=" O PRO E 581 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU E 582 " -0.031 2.00e-02 2.50e+03 ... (remaining 2822 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 4 2.16 - 2.85: 5605 2.85 - 3.53: 19564 3.53 - 4.22: 23383 4.22 - 4.90: 39819 Nonbonded interactions: 88375 Sorted by model distance: nonbonded pdb=" CD PRO E1392 " pdb=" CB ARG E1450 " model vdw 1.477 3.840 nonbonded pdb=" O GLY E1397 " pdb=" O THR E1437 " model vdw 1.985 3.040 nonbonded pdb=" ND2 ASN E 9 " pdb=" N2 NAG N 1 " model vdw 2.004 2.560 nonbonded pdb=" CG PRO E1392 " pdb=" CB ARG E1450 " model vdw 2.150 3.840 nonbonded pdb=" N ARG B 195 " pdb=" O2A ATP B 501 " model vdw 2.228 3.120 ... (remaining 88370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 366) selection = (chain 'B' and ((resid 30 through 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 through 366)) selection = (chain 'C' and resid 30 through 366) selection = (chain 'D' and resid 30 through 366) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.860 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 : 0.008 0.195 14169 Z= 0.558 Angle : 1.114 20.778 19760 Z= 0.812 Chirality : 0.073 1.905 2697 Planarity : 0.005 0.057 2824 Dihedral : 10.540 117.245 3050 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2800 helix: 0.86 (0.15), residues: 1291 sheet: -0.22 (0.35), residues: 210 loop : -2.70 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.576 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1266 time to fit residues: 20.9989 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 chunk 112 optimal weight: 0.4980 chunk 217 optimal weight: 0.0770 chunk 84 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 252 optimal weight: 10.0000 overall best weight: 3.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14169 Z= 0.132 Angle : 0.486 10.346 19760 Z= 0.287 Chirality : 0.046 0.271 2697 Planarity : 0.002 0.023 2824 Dihedral : 9.130 83.748 3039 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2800 helix: 1.79 (0.15), residues: 1319 sheet: -0.23 (0.33), residues: 238 loop : -2.48 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.497 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1234 time to fit residues: 20.2610 Evaluate side-chains 78 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 252 optimal weight: 8.9990 chunk 273 optimal weight: 50.0000 chunk 225 optimal weight: 40.0000 chunk 250 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 overall best weight: 15.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 14169 Z= 0.370 Angle : 0.795 13.629 19760 Z= 0.499 Chirality : 0.054 0.606 2697 Planarity : 0.005 0.032 2824 Dihedral : 10.444 89.249 3039 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.07 % Favored : 87.86 % Rotamer: Outliers : 25.00 % Allowed : 0.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 2800 helix: 0.00 (0.14), residues: 1277 sheet: -0.77 (0.36), residues: 195 loop : -2.84 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.485 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.1272 time to fit residues: 21.1195 Evaluate side-chains 80 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 131 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 chunk 253 optimal weight: 0.3980 chunk 268 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 240 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 overall best weight: 7.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14169 Z= 0.191 Angle : 0.557 13.253 19760 Z= 0.337 Chirality : 0.048 0.376 2697 Planarity : 0.003 0.028 2824 Dihedral : 9.750 88.431 3039 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2800 helix: 0.81 (0.14), residues: 1290 sheet: -0.92 (0.36), residues: 191 loop : -2.82 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.458 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1264 time to fit residues: 21.1128 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 200 optimal weight: 50.0000 chunk 110 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 137 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 67 optimal weight: 50.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14169 Z= 0.281 Angle : 0.665 14.604 19760 Z= 0.414 Chirality : 0.050 0.269 2697 Planarity : 0.004 0.032 2824 Dihedral : 10.180 89.151 3039 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.15), residues: 2800 helix: 0.17 (0.14), residues: 1305 sheet: -1.29 (0.37), residues: 190 loop : -3.04 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.490 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1290 time to fit residues: 21.3016 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 223 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14169 Z= 0.203 Angle : 0.557 13.493 19760 Z= 0.338 Chirality : 0.048 0.472 2697 Planarity : 0.003 0.029 2824 Dihedral : 9.586 88.071 3039 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2800 helix: 0.74 (0.15), residues: 1289 sheet: -1.30 (0.38), residues: 180 loop : -2.98 (0.15), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.505 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1283 time to fit residues: 21.2019 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 7.9990 chunk 30 optimal weight: 40.0000 chunk 153 optimal weight: 30.0000 chunk 196 optimal weight: 50.0000 chunk 152 optimal weight: 9.9990 chunk 226 optimal weight: 0.0040 chunk 150 optimal weight: 4.9990 chunk 267 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14169 Z= 0.145 Angle : 0.477 10.484 19760 Z= 0.286 Chirality : 0.047 0.337 2697 Planarity : 0.002 0.025 2824 Dihedral : 9.040 86.142 3039 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2800 helix: 1.37 (0.15), residues: 1301 sheet: -1.25 (0.38), residues: 180 loop : -2.84 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.456 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1329 time to fit residues: 21.6740 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 51 optimal weight: 0.0050 chunk 170 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 24 optimal weight: 40.0000 chunk 210 optimal weight: 9.9990 overall best weight: 7.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14169 Z= 0.188 Angle : 0.523 9.469 19760 Z= 0.320 Chirality : 0.047 0.261 2697 Planarity : 0.002 0.025 2824 Dihedral : 9.219 88.060 3039 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2800 helix: 1.16 (0.15), residues: 1292 sheet: -1.51 (0.38), residues: 180 loop : -2.87 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.495 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1353 time to fit residues: 22.4900 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 20.0000 chunk 256 optimal weight: 50.0000 chunk 234 optimal weight: 20.0000 chunk 249 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 196 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 14169 Z= 0.422 Angle : 0.823 10.664 19760 Z= 0.528 Chirality : 0.053 0.282 2697 Planarity : 0.005 0.032 2824 Dihedral : 10.453 87.730 3039 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.15), residues: 2800 helix: -0.44 (0.13), residues: 1268 sheet: -1.54 (0.40), residues: 158 loop : -3.40 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.367 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1232 time to fit residues: 20.3431 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.0270 chunk 264 optimal weight: 30.0000 chunk 161 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 183 optimal weight: 50.0000 chunk 276 optimal weight: 50.0000 chunk 254 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 overall best weight: 4.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14169 Z= 0.132 Angle : 0.478 9.525 19760 Z= 0.288 Chirality : 0.046 0.230 2697 Planarity : 0.002 0.027 2824 Dihedral : 9.180 88.073 3039 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2800 helix: 1.22 (0.15), residues: 1278 sheet: -1.84 (0.38), residues: 176 loop : -3.06 (0.15), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.395 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1275 time to fit residues: 21.0986 Evaluate side-chains 79 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 0.7980 chunk 234 optimal weight: 20.0000 chunk 67 optimal weight: 40.0000 chunk 203 optimal weight: 0.0010 chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 220 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 226 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.237761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.222216 restraints weight = 23349.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.217955 restraints weight = 34907.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.218943 restraints weight = 39425.912| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.024 14169 Z= 0.086 Angle : 0.398 9.545 19760 Z= 0.235 Chirality : 0.045 0.246 2697 Planarity : 0.002 0.026 2824 Dihedral : 8.319 88.330 3039 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2800 helix: 2.16 (0.15), residues: 1292 sheet: -1.51 (0.36), residues: 194 loop : -2.77 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 69 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 12 =============================================================================== Job complete usr+sys time: 1823.97 seconds wall clock time: 32 minutes 58.38 seconds (1978.38 seconds total)