Starting phenix.real_space_refine (version: dev) on Tue Apr 5 17:47:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2022/6lba_0868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2022/6lba_0868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2022/6lba_0868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2022/6lba_0868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2022/6lba_0868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lba_0868/04_2022/6lba_0868.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 14992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3748 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 12 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 8.95, per 1000 atoms: 0.60 Number of scatterers: 14992 At special positions: 0 Unit cell: (108.443, 126.734, 103.217, 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 100 16.00 O 2612 8.00 N 2624 7.00 C 9656 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: 6.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 64.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid -1 through 19 Processing helix chain 'A' and resid 30 through 53 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 88 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA A 126 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 171 No H-bonds generated for 'chain 'A' and resid 170 through 171' Processing helix chain 'A' and resid 173 through 174 No H-bonds generated for 'chain 'A' and resid 173 through 174' Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.688A pdb=" N HIS A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.609A pdb=" N SER A 280 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.520A pdb=" N TYR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.656A pdb=" N VAL A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 484 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 0 through 19 Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 88 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 171 No H-bonds generated for 'chain 'C' and resid 170 through 171' Processing helix chain 'C' and resid 173 through 174 No H-bonds generated for 'chain 'C' and resid 173 through 174' Processing helix chain 'C' and resid 175 through 198 removed outlier: 3.687A pdb=" N HIS C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG C 185 " --> pdb=" O TRP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.610A pdb=" N SER C 280 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 281 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.519A pdb=" N TYR C 318 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS C 351 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 478 through 490 removed outlier: 3.657A pdb=" N VAL C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 484 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.193A pdb=" N LEU C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 0 through 19 Processing helix chain 'B' and resid 30 through 53 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.690A pdb=" N SER B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.911A pdb=" N ALA B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 171 No H-bonds generated for 'chain 'B' and resid 170 through 171' Processing helix chain 'B' and resid 173 through 174 No H-bonds generated for 'chain 'B' and resid 173 through 174' Processing helix chain 'B' and resid 175 through 198 removed outlier: 3.688A pdb=" N HIS B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 185 " --> pdb=" O TRP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.609A pdb=" N SER B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 removed outlier: 3.519A pdb=" N TYR B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 351 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.698A pdb=" N TRP B 406 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 432 through 447 removed outlier: 4.063A pdb=" N SER B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.657A pdb=" N VAL B 482 " --> pdb=" O PRO B 478 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.609A pdb=" N TYR B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 0 through 19 Processing helix chain 'D' and resid 30 through 53 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 88 Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.689A pdb=" N SER D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.912A pdb=" N ALA D 126 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.916A pdb=" N MET D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 171 No H-bonds generated for 'chain 'D' and resid 170 through 171' Processing helix chain 'D' and resid 173 through 174 No H-bonds generated for 'chain 'D' and resid 173 through 174' Processing helix chain 'D' and resid 175 through 198 removed outlier: 3.687A pdb=" N HIS D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG D 185 " --> pdb=" O TRP D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.610A pdb=" N SER D 280 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 removed outlier: 3.521A pdb=" N TYR D 318 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 320 " --> pdb=" O GLN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 4.290A pdb=" N ASP D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS D 351 " --> pdb=" O MET D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.697A pdb=" N TRP D 406 " --> pdb=" O PRO D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.064A pdb=" N SER D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 478 through 490 removed outlier: 3.656A pdb=" N VAL D 482 " --> pdb=" O PRO D 478 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 484 " --> pdb=" O THR D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.906A pdb=" N ARG D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 4.192A pdb=" N LEU D 534 " --> pdb=" O ASP D 530 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 554 No H-bonds generated for 'chain 'D' and resid 552 through 554' Processing helix chain 'D' and resid 555 through 570 removed outlier: 3.608A pdb=" N TYR D 563 " --> pdb=" O GLN D 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA2, first strand: chain 'C' and resid 365 through 366 Processing sheet with id=AA3, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'D' and resid 365 through 366 737 hydrogen bonds defined for protein. 2091 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: 4.37 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4816 1.34 - 1.46: 3305 1.46 - 1.58: 7047 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 15320 Sorted by residual: bond pdb=" N PRO A 403 " pdb=" CD PRO A 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO B 403 " pdb=" CD PRO B 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" N PRO C 403 " pdb=" CD PRO C 403 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.46e+01 bond pdb=" N PHE C 331 " pdb=" CA PHE C 331 " ideal model delta sigma weight residual 1.458 1.425 0.032 1.22e-02 6.72e+03 7.02e+00 ... (remaining 15315 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 376 105.97 - 112.99: 8249 112.99 - 120.00: 5276 120.00 - 127.01: 6515 127.01 - 134.02: 224 Bond angle restraints: 20640 Sorted by residual: angle pdb=" CA PRO B 403 " pdb=" N PRO B 403 " pdb=" CD PRO B 403 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA PRO C 403 " pdb=" N PRO C 403 " pdb=" CD PRO C 403 " ideal model delta sigma weight residual 112.00 98.97 13.03 1.40e+00 5.10e-01 8.67e+01 angle pdb=" CA PRO A 403 " pdb=" N PRO A 403 " pdb=" CD PRO A 403 " ideal model delta sigma weight residual 112.00 98.98 13.02 1.40e+00 5.10e-01 8.64e+01 angle pdb=" N ARG B 540 " pdb=" CA ARG B 540 " pdb=" C ARG B 540 " ideal model delta sigma weight residual 111.07 121.01 -9.94 1.07e+00 8.73e-01 8.64e+01 angle pdb=" CA PRO D 403 " pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 112.00 99.00 13.00 1.40e+00 5.10e-01 8.62e+01 ... (remaining 20635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 8056 16.04 - 32.08: 884 32.08 - 48.12: 228 48.12 - 64.16: 32 64.16 - 80.20: 12 Dihedral angle restraints: 9212 sinusoidal: 3760 harmonic: 5452 Sorted by residual: dihedral pdb=" CA HIS C 100 " pdb=" C HIS C 100 " pdb=" N GLN C 101 " pdb=" CA GLN C 101 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CA HIS D 100 " pdb=" C HIS D 100 " pdb=" N GLN D 101 " pdb=" CA GLN D 101 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA HIS A 100 " pdb=" C HIS A 100 " pdb=" N GLN A 101 " pdb=" CA GLN A 101 " ideal model delta harmonic sigma weight residual 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 9209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1944 0.077 - 0.154: 254 0.154 - 0.230: 51 0.230 - 0.307: 11 0.307 - 0.384: 8 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA THR D 206 " pdb=" N THR D 206 " pdb=" C THR D 206 " pdb=" CB THR D 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA THR A 206 " pdb=" N THR A 206 " pdb=" C THR A 206 " pdb=" CB THR A 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA THR B 206 " pdb=" N THR B 206 " pdb=" C THR B 206 " pdb=" CB THR B 206 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 2265 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 333 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO D 334 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO D 334 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 334 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 333 " -0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO A 334 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 333 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO C 334 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " 0.073 5.00e-02 4.00e+02 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 93 2.26 - 2.92: 7786 2.92 - 3.58: 22983 3.58 - 4.24: 33090 4.24 - 4.90: 53716 Nonbonded interactions: 117668 Sorted by model distance: nonbonded pdb=" O LEU C 539 " pdb=" CG PRO C 543 " model vdw 1.605 3.440 nonbonded pdb=" O LEU D 539 " pdb=" CG PRO D 543 " model vdw 1.605 3.440 nonbonded pdb=" O LEU A 539 " pdb=" CG PRO A 543 " model vdw 1.606 3.440 nonbonded pdb=" O LEU B 539 " pdb=" CG PRO B 543 " model vdw 1.606 3.440 nonbonded pdb=" O LEU D 360 " pdb=" OD1 ASN D 361 " model vdw 1.858 3.040 ... (remaining 117663 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9656 2.51 5 N 2624 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.040 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.130 Process input model: 41.810 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.005 0.054 15320 Z= 0.350 Angle : 1.039 13.037 20640 Z= 0.716 Chirality : 0.062 0.384 2268 Planarity : 0.007 0.125 2596 Dihedral : 14.227 80.205 5620 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 70.19 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.91 % Favored : 88.64 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.46 (0.19), residues: 1760 helix: -1.28 (0.15), residues: 1060 sheet: -1.66 (0.75), residues: 56 loop : -2.03 (0.24), residues: 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 455 time to evaluate : 1.927 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: 56 outliers final: 25 residues processed: 479 average time/residue: 0.3065 time to fit residues: 204.0587 Evaluate side-chains 359 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 334 time to evaluate : 1.976 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 25 average time/residue: 0.2362 time to fit residues: 11.5396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 167 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 ASN A 43 ASN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 43 ASN D 51 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 15320 Z= 0.262 Angle : 0.711 7.534 20640 Z= 0.371 Chirality : 0.043 0.192 2268 Planarity : 0.005 0.057 2596 Dihedral : 5.923 41.373 1976 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 1760 helix: 0.14 (0.15), residues: 1092 sheet: -1.03 (0.80), residues: 56 loop : -2.04 (0.25), residues: 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.2807 time to fit residues: 194.2003 Evaluate side-chains 345 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 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 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 51 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 15320 Z= 0.334 Angle : 0.718 8.740 20640 Z= 0.378 Chirality : 0.044 0.153 2268 Planarity : 0.004 0.030 2596 Dihedral : 6.016 41.265 1976 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.48 (0.21), residues: 1760 helix: 0.61 (0.16), residues: 1076 sheet: -0.90 (0.80), residues: 56 loop : -1.89 (0.25), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 2.088 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 outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2478 time to fit residues: 160.8314 Evaluate side-chains 316 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 ASN A 30 GLN A 59 HIS A 102 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 430 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 59 HIS C 102 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN C 312 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 59 HIS B 102 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 59 HIS D 102 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN D 312 HIS D 430 HIS ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 15320 Z= 0.245 Angle : 0.656 10.294 20640 Z= 0.342 Chirality : 0.042 0.173 2268 Planarity : 0.004 0.031 2596 Dihedral : 5.873 40.446 1976 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.03 (0.21), residues: 1760 helix: 0.99 (0.16), residues: 1072 sheet: -0.54 (0.84), residues: 56 loop : -1.62 (0.26), residues: 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.933 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 outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2342 time to fit residues: 137.5236 Evaluate side-chains 309 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 132 optimal weight: 0.0010 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15320 Z= 0.221 Angle : 0.652 8.768 20640 Z= 0.335 Chirality : 0.042 0.212 2268 Planarity : 0.004 0.036 2596 Dihedral : 5.758 38.893 1976 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.04 (0.21), residues: 1760 helix: 0.79 (0.16), residues: 1120 sheet: -0.54 (0.81), residues: 56 loop : -1.53 (0.26), residues: 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2349 time to fit residues: 138.6841 Evaluate side-chains 308 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 0.0370 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN B 366 HIS B 490 HIS ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 15320 Z= 0.236 Angle : 0.668 8.720 20640 Z= 0.343 Chirality : 0.042 0.166 2268 Planarity : 0.004 0.047 2596 Dihedral : 5.702 38.971 1976 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.09 (0.21), residues: 1760 helix: 0.88 (0.16), residues: 1116 sheet: -0.62 (0.77), residues: 56 loop : -1.40 (0.27), residues: 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.989 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 outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2372 time to fit residues: 138.0375 Evaluate side-chains 312 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 312 HIS A 430 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 HIS C 490 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 15320 Z= 0.216 Angle : 0.667 8.390 20640 Z= 0.341 Chirality : 0.042 0.227 2268 Planarity : 0.004 0.049 2596 Dihedral : 5.595 37.726 1976 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.11 (0.21), residues: 1760 helix: 0.89 (0.17), residues: 1112 sheet: -0.70 (0.75), residues: 56 loop : -1.37 (0.27), residues: 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.026 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 outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.2271 time to fit residues: 132.4941 Evaluate side-chains 313 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 HIS ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15320 Z= 0.227 Angle : 0.663 9.708 20640 Z= 0.341 Chirality : 0.041 0.213 2268 Planarity : 0.004 0.048 2596 Dihedral : 5.481 35.668 1976 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.13 (0.21), residues: 1760 helix: 0.85 (0.16), residues: 1116 sheet: -0.74 (0.74), residues: 56 loop : -1.24 (0.27), residues: 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.968 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 outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2295 time to fit residues: 131.9622 Evaluate side-chains 318 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 0.0050 chunk 50 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15320 Z= 0.192 Angle : 0.664 9.592 20640 Z= 0.340 Chirality : 0.041 0.220 2268 Planarity : 0.004 0.049 2596 Dihedral : 5.406 35.586 1976 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.12 (0.21), residues: 1760 helix: 0.84 (0.16), residues: 1108 sheet: -0.67 (0.74), residues: 56 loop : -1.24 (0.27), residues: 596 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.915 Fit side-chains 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: 384 average time/residue: 0.2506 time to fit residues: 148.2622 Evaluate side-chains 320 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.0020 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 0.0170 chunk 115 optimal weight: 6.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 187 ASN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15320 Z= 0.185 Angle : 0.667 9.236 20640 Z= 0.341 Chirality : 0.040 0.243 2268 Planarity : 0.004 0.049 2596 Dihedral : 5.307 33.955 1976 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.13 (0.21), residues: 1760 helix: 0.83 (0.16), residues: 1108 sheet: -0.64 (0.75), residues: 56 loop : -1.16 (0.27), residues: 596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2441 time to fit residues: 142.7752 Evaluate side-chains 325 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110062 restraints weight = 33625.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112384 restraints weight = 22735.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113953 restraints weight = 17241.761| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15320 Z= 0.201 Angle : 0.681 10.224 20640 Z= 0.351 Chirality : 0.041 0.244 2268 Planarity : 0.004 0.049 2596 Dihedral : 5.314 35.014 1976 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.16 (0.21), residues: 1760 helix: 0.82 (0.16), residues: 1108 sheet: -0.80 (0.75), residues: 56 loop : -1.07 (0.27), residues: 596 =============================================================================== Job complete usr+sys time: 3233.70 seconds wall clock time: 59 minutes 45.18 seconds (3585.18 seconds total)