Starting phenix.real_space_refine (version: dev) on Mon Feb 20 21:29:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyh_20524/02_2023/6pyh_20524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyh_20524/02_2023/6pyh_20524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyh_20524/02_2023/6pyh_20524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyh_20524/02_2023/6pyh_20524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyh_20524/02_2023/6pyh_20524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyh_20524/02_2023/6pyh_20524.pdb" } resolution = 4.3 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A GLU 855": "OE1" <-> "OE2" Residue "A TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "D TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 846": "OD1" <-> "OD2" Residue "D ARG 853": "NH1" <-> "NH2" Residue "D TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13187 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6360 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 46, 'TRANS': 744} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 416 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6411 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 754} Chain breaks: 10 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 7.39, per 1000 atoms: 0.56 Number of scatterers: 13187 At special positions: 0 Unit cell: (120.91, 113.42, 171.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2458 8.00 N 2285 7.00 C 8342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.02 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 459 " distance=2.03 Simple disulfide: pdb=" SG CYS A 671 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 777 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 48 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 22 " distance=2.02 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 175 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 181 " distance=2.04 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 221 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 234 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 273 " distance=2.04 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 324 " distance=2.03 Simple disulfide: pdb=" SG CYS D 777 " - pdb=" SG CYS D 786 " distance=2.04 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: 5.15 Conformation dependent library (CDL) restraints added in 1.9 seconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 13.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 248 through 254 removed outlier: 4.594A pdb=" N CYS A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.767A pdb=" N ALA A 318 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N MET A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 4.526A pdb=" N GLU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 4.489A pdb=" N PHE A 372 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.854A pdb=" N ILE A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 702 removed outlier: 4.013A pdb=" N ALA A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 685 " --> pdb=" O GLN A 681 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 697 " --> pdb=" O PHE A 693 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 702 " --> pdb=" O HIS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.965A pdb=" N VAL B 11 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 248 through 254 removed outlier: 3.613A pdb=" N CYS D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 340 through 350 removed outlier: 4.025A pdb=" N GLU D 344 " --> pdb=" O ASN D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 373 removed outlier: 4.235A pdb=" N PHE D 372 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 428 through 437 Processing helix chain 'D' and resid 625 through 631 removed outlier: 3.966A pdb=" N TYR D 629 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 699 removed outlier: 3.523A pdb=" N LYS D 680 " --> pdb=" O THR D 676 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE D 696 " --> pdb=" O VAL D 692 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 697 " --> pdb=" O PHE D 693 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 860 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.534A pdb=" N THR A 52 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N VAL A 50 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N TRP A 79 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR A 52 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.539A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 114 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N VAL A 140 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 113 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.629A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 209 removed outlier: 7.098A pdb=" N SER A 208 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 284 removed outlier: 4.693A pdb=" N TYR A 290 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 5.668A pdb=" N LEU A 331 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG A 362 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 333 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 359 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 394 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 361 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR A 418 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR A 392 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA A 420 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 394 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 462 through 463 removed outlier: 6.425A pdb=" N ASP A 462 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 568 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 555 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 493 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463 removed outlier: 6.425A pdb=" N ASP A 462 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 568 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 472 Processing sheet with id=AB4, first strand: chain 'A' and resid 586 through 594 removed outlier: 4.550A pdb=" N VAL A 588 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A 601 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER A 590 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 599 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER A 592 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 597 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 759 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 753 removed outlier: 3.534A pdb=" N VAL A 617 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 620 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 818 through 820 Processing sheet with id=AB7, first strand: chain 'A' and resid 847 through 852 Processing sheet with id=AB8, first strand: chain 'A' and resid 847 through 852 removed outlier: 7.136A pdb=" N THR A 879 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 2 through 3 removed outlier: 3.848A pdb=" N ILE D 76 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10 removed outlier: 5.931A pdb=" N ILE D 7 " --> pdb=" O HIS D 30 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU D 32 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE D 9 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 34 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 60 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE D 90 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 57 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 112 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 89 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 114 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 269 Processing sheet with id=AC4, first strand: chain 'D' and resid 281 through 284 removed outlier: 5.949A pdb=" N TYR D 290 " --> pdb=" O ASN D 284 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 312 removed outlier: 6.269A pdb=" N LEU D 331 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG D 362 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 333 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL D 359 " --> pdb=" O TYR D 392 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU D 394 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 361 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 354 through 355 removed outlier: 3.530A pdb=" N VAL D 355 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 379 " --> pdb=" O THR D 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 466 through 468 Processing sheet with id=AC8, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AC9, first strand: chain 'D' and resid 586 through 594 removed outlier: 5.630A pdb=" N ASP D 587 " --> pdb=" O ASN D 603 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN D 603 " --> pdb=" O ASP D 587 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN D 593 " --> pdb=" O GLN D 597 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLN D 597 " --> pdb=" O ASN D 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 612 through 621 Processing sheet with id=AD2, first strand: chain 'D' and resid 810 through 812 removed outlier: 3.767A pdb=" N LEU D 864 " --> pdb=" O ILE D 819 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 847 through 851 removed outlier: 3.733A pdb=" N MET D 835 " --> pdb=" O THR D 879 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 895 " --> pdb=" O GLY D 870 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 642 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: 4.49 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 13366 1.56 - 1.91: 126 1.91 - 2.25: 0 2.25 - 2.59: 0 2.59 - 2.94: 1 Bond restraints: 13493 Sorted by residual: bond pdb=" C PRO A 798 " pdb=" N ALA A 799 " ideal model delta sigma weight residual 1.329 2.936 -1.607 1.40e-02 5.10e+03 1.32e+04 bond pdb=" C ALA A 501 " pdb=" N PRO A 502 " ideal model delta sigma weight residual 1.334 1.308 0.025 8.40e-03 1.42e+04 9.18e+00 bond pdb=" CB TRP A 405 " pdb=" CG TRP A 405 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 bond pdb=" C ALA D 117 " pdb=" N ASP D 118 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.40e-02 5.10e+03 3.00e+00 bond pdb=" CA PRO A 144 " pdb=" C PRO A 144 " ideal model delta sigma weight residual 1.517 1.501 0.016 9.30e-03 1.16e+04 2.88e+00 ... (remaining 13488 not shown) Histogram of bond angle deviations from ideal: 48.76 - 65.81: 1 65.81 - 82.86: 0 82.86 - 99.91: 3 99.91 - 116.96: 9653 116.96 - 134.01: 8639 Bond angle restraints: 18296 Sorted by residual: angle pdb=" O PRO A 798 " pdb=" C PRO A 798 " pdb=" N ALA A 799 " ideal model delta sigma weight residual 122.89 48.76 74.13 1.25e+00 6.40e-01 3.52e+03 angle pdb=" CA PRO A 798 " pdb=" C PRO A 798 " pdb=" N ALA A 799 " ideal model delta sigma weight residual 115.12 126.49 -11.37 1.25e+00 6.40e-01 8.28e+01 angle pdb=" N GLN A 843 " pdb=" CA GLN A 843 " pdb=" C GLN A 843 " ideal model delta sigma weight residual 114.75 108.87 5.88 1.26e+00 6.30e-01 2.18e+01 angle pdb=" C PRO A 798 " pdb=" N ALA A 799 " pdb=" CA ALA A 799 " ideal model delta sigma weight residual 123.00 109.37 13.63 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C MET A 184 " pdb=" N CYS A 185 " pdb=" CA CYS A 185 " ideal model delta sigma weight residual 120.94 113.03 7.91 1.90e+00 2.77e-01 1.73e+01 ... (remaining 18291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7198 17.90 - 35.79: 806 35.79 - 53.69: 150 53.69 - 71.58: 26 71.58 - 89.48: 9 Dihedral angle restraints: 8189 sinusoidal: 3379 harmonic: 4810 Sorted by residual: dihedral pdb=" CA GLU D 816 " pdb=" C GLU D 816 " pdb=" N ASN D 817 " pdb=" CA ASN D 817 " ideal model delta harmonic sigma weight residual -180.00 -130.16 -49.84 0 5.00e+00 4.00e-02 9.94e+01 dihedral pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " pdb=" SG CYS D 200 " pdb=" CB CYS D 200 " ideal model delta sinusoidal sigma weight residual 93.00 3.52 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS D 777 " pdb=" SG CYS D 777 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual -86.00 -167.98 81.98 1 1.00e+01 1.00e-02 8.26e+01 ... (remaining 8186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1125 0.036 - 0.072: 538 0.072 - 0.108: 239 0.108 - 0.143: 67 0.143 - 0.179: 9 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA ILE A 575 " pdb=" N ILE A 575 " pdb=" C ILE A 575 " pdb=" CB ILE A 575 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CB ILE D 448 " pdb=" CA ILE D 448 " pdb=" CG1 ILE D 448 " pdb=" CG2 ILE D 448 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO A 153 " pdb=" N PRO A 153 " pdb=" C PRO A 153 " pdb=" CB PRO A 153 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1975 not shown) Planarity restraints: 2373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 798 " 0.198 2.00e-02 2.50e+03 2.81e-01 7.87e+02 pdb=" C PRO A 798 " -0.460 2.00e-02 2.50e+03 pdb=" O PRO A 798 " 0.254 2.00e-02 2.50e+03 pdb=" N ALA A 799 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 4 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO D 5 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 5 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 5 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 814 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO D 815 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 815 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 815 " 0.026 5.00e-02 4.00e+02 ... (remaining 2370 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 416 2.64 - 3.21: 13832 3.21 - 3.77: 20389 3.77 - 4.34: 27182 4.34 - 4.90: 41536 Nonbonded interactions: 103355 Sorted by model distance: nonbonded pdb=" O SER D 776 " pdb=" OG SER D 787 " model vdw 2.079 2.440 nonbonded pdb=" O LEU A 607 " pdb=" ND2 ASN A 609 " model vdw 2.121 2.520 nonbonded pdb=" OD1 ASN D 84 " pdb=" OG SER D 314 " model vdw 2.125 2.440 nonbonded pdb=" ND2 ASN D 339 " pdb=" OD1 ASN D 340 " model vdw 2.133 2.520 nonbonded pdb=" OG SER D 461 " pdb=" O GLY D 567 " model vdw 2.144 2.440 ... (remaining 103350 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' and (resid 1 through 153 or resid 162 through 186 or (resid 187 and ( \ name N or name CA or name C or name O or name CB )) or resid 188 through 189 or \ resid 193 through 256 or resid 265 through 294 or resid 298 or resid 306 through \ 510 or resid 515 through 526 or resid 532 through 558 or resid 562 through 704 \ or resid 746 through 897)) selection = (chain 'D' and (resid 1 through 35 or resid 41 through 210 or resid 212 through \ 256 or resid 265 through 294 or resid 302 or resid 306 through 625 or resid 671 \ through 897)) } 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 102 5.16 5 C 8342 2.51 5 N 2285 2.21 5 O 2458 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: 1.110 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: 5.680 Check model and map are aligned: 0.210 Process input model: 35.620 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.016 1.607 13493 Z= 0.674 Angle : 1.052 74.130 18296 Z= 0.675 Chirality : 0.050 0.179 1978 Planarity : 0.008 0.281 2373 Dihedral : 14.643 87.364 4995 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 28.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 18.16 % Favored : 81.65 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.17), residues: 1602 helix: -4.27 (0.21), residues: 162 sheet: -3.01 (0.24), residues: 346 loop : -3.74 (0.16), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 96 average time/residue: 0.2686 time to fit residues: 38.3505 Evaluate side-chains 61 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1158 time to fit residues: 3.6451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 14 GLN A 72 ASN A 169 ASN A 284 ASN A 287 GLN A 334 ASN A 363 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN D 275 GLN ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN D 624 GLN ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 ASN D 830 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 13493 Z= 0.218 Angle : 0.677 24.002 18296 Z= 0.355 Chirality : 0.047 0.219 1978 Planarity : 0.005 0.049 2373 Dihedral : 6.533 48.798 1814 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.60 % Favored : 89.34 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.16 (0.18), residues: 1604 helix: -3.04 (0.29), residues: 170 sheet: -2.54 (0.23), residues: 374 loop : -2.97 (0.17), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.676 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.2436 time to fit residues: 35.3109 Evaluate side-chains 58 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1119 time to fit residues: 2.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 HIS ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN D 384 GLN ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 ASN D 830 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13493 Z= 0.268 Angle : 0.666 23.535 18296 Z= 0.346 Chirality : 0.046 0.183 1978 Planarity : 0.004 0.048 2373 Dihedral : 6.350 48.795 1814 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.91 % Favored : 87.03 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.66 (0.19), residues: 1604 helix: -2.55 (0.33), residues: 171 sheet: -2.07 (0.25), residues: 360 loop : -2.69 (0.18), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1996 time to fit residues: 27.3870 Evaluate side-chains 52 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13493 Z= 0.282 Angle : 0.668 23.531 18296 Z= 0.344 Chirality : 0.046 0.182 1978 Planarity : 0.004 0.048 2373 Dihedral : 6.259 48.578 1814 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.59 % Favored : 87.34 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.43 (0.19), residues: 1604 helix: -2.41 (0.33), residues: 173 sheet: -1.92 (0.25), residues: 365 loop : -2.53 (0.18), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.669 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.1967 time to fit residues: 26.9453 Evaluate side-chains 54 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 397 GLN ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 631 HIS ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 13493 Z= 0.170 Angle : 0.609 16.674 18296 Z= 0.318 Chirality : 0.045 0.277 1978 Planarity : 0.004 0.047 2373 Dihedral : 5.900 48.038 1814 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.09 (0.20), residues: 1604 helix: -2.17 (0.34), residues: 173 sheet: -1.66 (0.26), residues: 368 loop : -2.29 (0.19), residues: 1063 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2214 time to fit residues: 28.9845 Evaluate side-chains 54 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8223 > 50: distance: 80 - 95: 37.207 distance: 84 - 89: 34.202 distance: 85 - 103: 30.184 distance: 89 - 90: 57.737 distance: 90 - 91: 40.242 distance: 90 - 93: 44.256 distance: 91 - 92: 38.761 distance: 93 - 94: 44.916 distance: 95 - 96: 56.002 distance: 96 - 97: 40.200 distance: 96 - 99: 39.060 distance: 97 - 98: 39.814 distance: 97 - 103: 51.131 distance: 99 - 100: 38.634 distance: 100 - 101: 55.964 distance: 100 - 102: 69.857 distance: 103 - 104: 7.421 distance: 104 - 105: 56.438 distance: 104 - 107: 39.554 distance: 105 - 106: 39.728 distance: 105 - 111: 55.856 distance: 107 - 108: 39.341 distance: 108 - 109: 39.387 distance: 108 - 110: 40.146 distance: 111 - 112: 56.108 distance: 112 - 113: 68.602 distance: 112 - 115: 39.992 distance: 113 - 114: 40.440 distance: 113 - 123: 38.655 distance: 115 - 116: 67.877 distance: 117 - 119: 41.129 distance: 119 - 121: 57.924 distance: 120 - 121: 69.444 distance: 121 - 122: 5.729 distance: 123 - 124: 40.811 distance: 124 - 125: 55.593 distance: 124 - 127: 56.661 distance: 125 - 126: 56.195 distance: 125 - 131: 70.536 distance: 127 - 128: 56.708 distance: 127 - 129: 38.552 distance: 128 - 130: 67.806 distance: 131 - 132: 55.553 distance: 132 - 133: 56.749 distance: 133 - 134: 56.798 distance: 133 - 138: 38.736 distance: 135 - 136: 39.080 distance: 135 - 137: 58.001 distance: 138 - 139: 42.232 distance: 139 - 140: 61.385 distance: 140 - 141: 57.557 distance: 142 - 143: 69.197 distance: 143 - 144: 56.521 distance: 143 - 146: 39.840 distance: 144 - 150: 56.974 distance: 146 - 147: 40.913 distance: 147 - 148: 69.624 distance: 147 - 149: 39.538 distance: 150 - 151: 68.922 distance: 151 - 152: 38.785 distance: 151 - 154: 40.976 distance: 152 - 153: 40.005 distance: 152 - 159: 41.100 distance: 154 - 155: 38.864 distance: 156 - 157: 39.508 distance: 159 - 160: 43.276 distance: 159 - 165: 38.823 distance: 160 - 161: 37.480 distance: 160 - 163: 60.036 distance: 161 - 162: 49.122 distance: 161 - 166: 29.202 distance: 163 - 164: 40.589 distance: 164 - 165: 66.189