Starting phenix.real_space_refine (version: 1.19rc7) on Wed Jan 6 02:26:14 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/01_2021/7a5s_11647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/01_2021/7a5s_11647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/01_2021/7a5s_11647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/01_2021/7a5s_11647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/01_2021/7a5s_11647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/01_2021/7a5s_11647.pdb" } resolution = 3.9 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= 0.002 sd= 0.027 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 16608 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1634 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 205, 'PCIS': 2} Chain: "L" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 206, 'PCIS': 3} Chain: "A" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4948 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "M" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 206, 'PCIS': 3} Chain: "B" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4948 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1634 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 205, 'PCIS': 2} Chain: "D" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Time building chain proxies: 9.15, per 1000 atoms: 0.55 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Number of scatterers: 16608 At special positions: 0 Unit cell: (183.703, 190.225, 94.569, 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 68 16.00 O 3212 8.00 N 2748 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.04 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG D 1 " - " ASN A 343 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3932 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 40 sheets defined 5.8% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.689A pdb=" N LEU L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 134' Processing helix chain 'L' and resid 189 through 193 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.690A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 127 through 134' Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.965A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.342A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 144 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 148 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.772A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER L 120 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 143 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 159 through 160 removed outlier: 3.637A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.369A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.838A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.522A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.569A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.761A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.263A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU M 11 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.773A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER M 120 " --> pdb=" O ASN M 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN M 143 " --> pdb=" O SER M 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 159 through 160 removed outlier: 3.637A pdb=" N TYR M 198 " --> pdb=" O PHE M 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 63 through 67 removed outlier: 4.368A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.838A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.522A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.569A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.761A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.264A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL I 108 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.343A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 144 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 184 " --> pdb=" O CYS I 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 148 " --> pdb=" O TYR I 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1344 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: 6.73 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4594 1.33 - 1.46: 3725 1.46 - 1.58: 8629 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 17028 Sorted by residual: bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.24e+01 bond pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" N VAL B 534 " pdb=" CA VAL B 534 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL B 551 " pdb=" CA VAL B 551 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.22e-02 6.72e+03 1.07e+01 ... (remaining 17023 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 554 106.62 - 113.46: 9028 113.46 - 120.30: 6162 120.30 - 127.15: 7240 127.15 - 133.99: 188 Bond angle restraints: 23172 Sorted by residual: angle pdb=" N PRO A 217 " pdb=" CA PRO A 217 " pdb=" C PRO A 217 " ideal model delta sigma weight residual 111.22 116.86 -5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" N PRO B 217 " pdb=" CA PRO B 217 " pdb=" C PRO B 217 " ideal model delta sigma weight residual 111.22 116.86 -5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" N ASN B 536 " pdb=" CA ASN B 536 " pdb=" C ASN B 536 " ideal model delta sigma weight residual 111.74 117.02 -5.28 1.35e+00 5.49e-01 1.53e+01 angle pdb=" N ASN A 536 " pdb=" CA ASN A 536 " pdb=" C ASN A 536 " ideal model delta sigma weight residual 111.74 117.02 -5.28 1.35e+00 5.49e-01 1.53e+01 angle pdb=" CA GLY B 268 " pdb=" C GLY B 268 " pdb=" O GLY B 268 " ideal model delta sigma weight residual 121.76 117.78 3.98 1.03e+00 9.43e-01 1.49e+01 ... (remaining 23167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 9231 18.03 - 36.07: 661 36.07 - 54.10: 154 54.10 - 72.14: 30 72.14 - 90.17: 10 Dihedral angle restraints: 10086 sinusoidal: 3926 harmonic: 6160 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -176.17 90.17 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -176.14 90.14 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" C ASP A 578 " pdb=" N ASP A 578 " pdb=" CA ASP A 578 " pdb=" CB ASP A 578 " ideal model delta harmonic sigma weight residual -122.60 -133.80 11.20 0 2.50e+00 1.60e-01 2.01e+01 ... (remaining 10083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2023 0.069 - 0.137: 466 0.137 - 0.206: 61 0.206 - 0.275: 20 0.275 - 0.343: 6 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CA ASN B 536 " pdb=" N ASN B 536 " pdb=" C ASN B 536 " pdb=" CB ASN B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ASN A 536 " pdb=" N ASN A 536 " pdb=" C ASN A 536 " pdb=" CB ASN A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP A 578 " pdb=" N ASP A 578 " pdb=" C ASP A 578 " pdb=" CB ASP A 578 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2573 not shown) Planarity restraints: 2976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLY B 548 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 549 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 548 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLY A 548 " -0.061 2.00e-02 2.50e+03 pdb=" O GLY A 548 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 549 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 571 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C ASP A 571 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 571 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 572 " -0.015 2.00e-02 2.50e+03 ... (remaining 2973 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 6 1.93 - 2.67: 277 2.67 - 3.42: 20398 3.42 - 4.16: 36938 4.16 - 4.90: 65913 Nonbonded interactions: 123532 Sorted by model distance: nonbonded pdb=" NH2 ARG B 273 " pdb=" OD2 ASP B 290 " model vdw 1.188 2.520 nonbonded pdb=" NH2 ARG A 273 " pdb=" OD2 ASP A 290 " model vdw 1.189 2.520 nonbonded pdb=" NH2 ARG A 273 " pdb=" CG ASP A 290 " model vdw 1.373 3.350 nonbonded pdb=" NH2 ARG B 273 " pdb=" CG ASP B 290 " model vdw 1.373 3.350 nonbonded pdb=" NH2 ARG A 273 " pdb=" OD1 ASP A 290 " model vdw 1.766 2.520 ... (remaining 123527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 16608 16608 False True 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 68 5.16 5 C 10580 2.51 5 N 2748 2.21 5 O 3212 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.750 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.860 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.070 Process input model: 48.550 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 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:2.320 Internal consistency checks: 0.000 Total: 69.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.052 17028 Angle : 0.942 10.648 23172 Chirality : 0.062 0.343 2576 Planarity : 0.005 0.051 2974 Dihedral : 13.361 89.368 6076 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.94 % Favored : 92.68 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 8.93 % 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: -2.00 (0.17), residues: 2104 helix: -2.03 (0.51), residues: 88 sheet: 0.09 (0.20), residues: 698 loop : -2.23 (0.15), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 200 time to evaluate : 2.096 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 208 average time/residue: 0.3527 time to fit residues: 76.6417 Evaluate side-chains 92 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 90 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1566 time to fit residues: 2.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 39 GLN H 77 ASN ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN L 6 GLN L 35 ASN L 44 GLN L 106 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 115 GLN A 164 ASN A 239 GLN A 245 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 641 ASN A 658 ASN A 675 GLN M 6 GLN M 35 ASN M 44 GLN M 106 GLN B 66 HIS B 115 GLN B 164 ASN B 239 GLN B 245 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 493 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 641 ASN B 658 ASN B 675 GLN I 1 GLN I 39 GLN I 77 ASN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.063 17028 Angle : 0.688 10.188 23172 Chirality : 0.047 0.160 2576 Planarity : 0.005 0.044 2974 Dihedral : 5.164 17.824 2318 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.53 (0.17), residues: 2104 helix: -1.86 (0.57), residues: 76 sheet: 0.41 (0.19), residues: 776 loop : -2.02 (0.16), residues: 1252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 126 time to evaluate : 1.838 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.2963 time to fit residues: 40.3347 Evaluate side-chains 70 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1536 time to fit residues: 2.8227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 0.0070 chunk 65 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 196 GLN L 22 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 474 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN M 22 ASN B 271 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 474 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN I 1 GLN I 196 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.051 17028 Angle : 0.629 9.158 23172 Chirality : 0.046 0.186 2576 Planarity : 0.004 0.043 2974 Dihedral : 4.877 18.064 2318 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.34 (0.18), residues: 2104 helix: -1.79 (0.59), residues: 76 sheet: 0.64 (0.19), residues: 714 loop : -1.85 (0.16), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 112 time to evaluate : 2.135 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 112 average time/residue: 0.2703 time to fit residues: 33.4342 Evaluate side-chains 67 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1597 time to fit residues: 3.0446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.069 17028 Angle : 0.663 9.192 23172 Chirality : 0.047 0.154 2576 Planarity : 0.004 0.042 2974 Dihedral : 5.140 19.121 2318 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.49 (0.17), residues: 2104 helix: -2.09 (0.57), residues: 76 sheet: 0.40 (0.19), residues: 732 loop : -1.87 (0.16), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 101 time to evaluate : 2.132 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.3140 time to fit residues: 34.9467 Evaluate side-chains 52 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 182 optimal weight: 0.0010 chunk 51 optimal weight: 10.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 196 GLN L 22 ASN A 271 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN M 22 ASN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN I 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.039 17028 Angle : 0.569 7.435 23172 Chirality : 0.045 0.153 2576 Planarity : 0.004 0.040 2974 Dihedral : 4.702 20.232 2318 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.37 (0.18), residues: 2104 helix: -2.45 (0.49), residues: 100 sheet: 0.45 (0.18), residues: 764 loop : -1.75 (0.16), residues: 1240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2848 time to fit residues: 30.2558 Evaluate side-chains 54 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 54 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 203 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN L 22 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.063 17028 Angle : 0.611 7.048 23172 Chirality : 0.046 0.151 2576 Planarity : 0.004 0.041 2974 Dihedral : 4.908 20.044 2318 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.47 (0.17), residues: 2104 helix: -2.22 (0.54), residues: 88 sheet: 0.46 (0.19), residues: 716 loop : -1.84 (0.16), residues: 1300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 83 time to evaluate : 2.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2789 time to fit residues: 26.5349 Evaluate side-chains 49 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 49 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN M 22 ASN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.044 17028 Angle : 0.568 7.311 23172 Chirality : 0.045 0.151 2576 Planarity : 0.004 0.040 2974 Dihedral : 4.718 21.954 2318 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.37 (0.18), residues: 2104 helix: -2.35 (0.50), residues: 100 sheet: 0.49 (0.19), residues: 726 loop : -1.73 (0.16), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 84 time to evaluate : 2.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2855 time to fit residues: 27.1321 Evaluate side-chains 51 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.1980 chunk 80 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.032 17028 Angle : 0.523 7.897 23172 Chirality : 0.044 0.153 2576 Planarity : 0.003 0.038 2974 Dihedral : 4.337 18.122 2318 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.24 (0.18), residues: 2104 helix: -2.00 (0.55), residues: 88 sheet: 0.58 (0.20), residues: 718 loop : -1.65 (0.16), residues: 1298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.956 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2753 time to fit residues: 29.0071 Evaluate side-chains 48 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 48 time to evaluate : 2.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.0970 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN M 22 ASN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.036 17028 Angle : 0.534 7.717 23172 Chirality : 0.044 0.152 2576 Planarity : 0.004 0.038 2974 Dihedral : 4.306 18.213 2318 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.19 (0.18), residues: 2104 helix: -2.01 (0.54), residues: 88 sheet: 0.61 (0.20), residues: 718 loop : -1.62 (0.16), residues: 1298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.985 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2812 time to fit residues: 27.1894 Evaluate side-chains 52 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.080 17028 Angle : 0.683 9.217 23172 Chirality : 0.048 0.151 2576 Planarity : 0.004 0.040 2974 Dihedral : 5.169 26.632 2318 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.59 (0.17), residues: 2104 helix: -2.75 (0.50), residues: 88 sheet: 0.17 (0.19), residues: 740 loop : -1.77 (0.16), residues: 1276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield and 0 Emsley and 2104 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2918 time to fit residues: 25.0577 Evaluate side-chains 44 residues out of total 1856 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 44 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0470 chunk 51 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.110391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073420 restraints weight = 53258.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073594 restraints weight = 35828.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074264 restraints weight = 26024.872| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.006 0.068 17028 ANGLE : 0.662 9.211 23172 CHIRALITY : 0.047 0.152 2576 PLANARITY : 0.004 0.042 2974 DIHEDRAL : 5.154 22.221 2318 MIN NONBONDED DISTANCE : 2.178 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 10.79 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 7.08 % FAVORED : 92.92 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 8.93 % 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: -1.73 (0.17), RESIDUES: 2104 HELIX: -2.79 (0.50), RESIDUES: 88 SHEET: 0.14 (0.19), RESIDUES: 728 LOOP : -1.90 (0.16), RESIDUES: 1288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.068 17028 Angle : 0.662 9.211 23172 Chirality : 0.047 0.152 2576 Planarity : 0.004 0.042 2974 Dihedral : 5.154 22.221 2318 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.73 (0.17), residues: 2104 helix: -2.79 (0.50), residues: 88 sheet: 0.14 (0.19), residues: 728 loop : -1.90 (0.16), residues: 1288 =============================================================================== Job complete usr+sys time: 2527.78 seconds wall clock time: 48 minutes 8.77 seconds (2888.77 seconds total)