Starting phenix.real_space_refine on Tue Mar 19 05:43:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plu_13502/03_2024/7plu_13502_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plu_13502/03_2024/7plu_13502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plu_13502/03_2024/7plu_13502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plu_13502/03_2024/7plu_13502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plu_13502/03_2024/7plu_13502_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plu_13502/03_2024/7plu_13502_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 148 5.16 5 C 14821 2.51 5 N 3949 2.21 5 O 4361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "D TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 792": "NH1" <-> "NH2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23288 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.23, per 1000 atoms: 0.53 Number of scatterers: 23288 At special positions: 0 Unit cell: (169.6, 208.82, 177.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 6 15.00 Mg 3 11.99 O 4361 8.00 N 3949 7.00 C 14821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.04 Conformation dependent library (CDL) restraints added in 4.0 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 5460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 27 sheets defined 48.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.546A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.751A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.608A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 301 through 315 removed outlier: 4.156A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 480 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.547A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 removed outlier: 3.721A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.595A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 653 removed outlier: 3.871A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.733A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.567A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 5.377A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.594A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.775A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.841A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.757A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 4.324A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.629A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.180A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.787A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.725A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.105A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.585A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 139 through 152 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 169 through 184 Processing helix chain 'D' and resid 192 through 206 removed outlier: 3.727A pdb=" N ASN D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 260 through 268 Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.579A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 301 through 315 removed outlier: 4.073A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 336 Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 368 through 376 removed outlier: 3.999A pdb=" N CYS D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 423 Processing helix chain 'D' and resid 449 through 479 Processing helix chain 'D' and resid 484 through 486 No H-bonds generated for 'chain 'D' and resid 484 through 486' Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.591A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 499 " --> pdb=" O CYS D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 514 removed outlier: 3.792A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.667A pdb=" N SER D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 630 through 633 No H-bonds generated for 'chain 'D' and resid 630 through 633' Processing helix chain 'D' and resid 636 through 653 removed outlier: 3.889A pdb=" N ALA D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 684 removed outlier: 3.779A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 removed outlier: 3.736A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 714 removed outlier: 5.376A pdb=" N VAL D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 735 Processing helix chain 'D' and resid 739 through 741 No H-bonds generated for 'chain 'D' and resid 739 through 741' Processing helix chain 'D' and resid 755 through 791 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.606A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 removed outlier: 3.791A pdb=" N GLU F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.837A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.721A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 4.370A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.671A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 318 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.181A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 346 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.778A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 removed outlier: 3.651A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.504A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 19 Processing helix chain 'E' and resid 29 through 38 removed outlier: 4.272A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 78 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.315A pdb=" N PHE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 removed outlier: 3.580A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 removed outlier: 3.800A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.834A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.726A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 4.317A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.608A pdb=" N PHE G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 284 Processing helix chain 'G' and resid 290 through 295 Processing helix chain 'G' and resid 302 through 305 Processing helix chain 'G' and resid 309 through 318 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.152A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY G 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 346 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 354 removed outlier: 3.784A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 removed outlier: 3.658A pdb=" N GLU G 364 " --> pdb=" O GLN G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 373 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.724A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.108A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= D, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= E, first strand: chain 'A' and resid 700 through 703 Processing sheet with id= F, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.497A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.684A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= I, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.418A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= L, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 16 removed outlier: 3.765A pdb=" N LEU D 40 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.924A pdb=" N GLN D 157 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 163 " --> pdb=" O ILE D 438 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 377 through 382 Processing sheet with id= P, first strand: chain 'D' and resid 547 through 551 Processing sheet with id= Q, first strand: chain 'D' and resid 700 through 703 Processing sheet with id= R, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.556A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.681A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 18 " --> pdb=" O ASP F 11 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 65 through 69 Processing sheet with id= U, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.470A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'E' and resid 26 through 28 Processing sheet with id= X, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.628A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 65 through 69 Processing sheet with id= Z, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.485A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 238 through 241 974 hydrogen bonds defined for protein. 2676 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: 7.96 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3886 1.32 - 1.44: 6274 1.44 - 1.56: 13375 1.56 - 1.69: 9 1.69 - 1.81: 242 Bond restraints: 23786 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.452 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.452 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.456 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.199 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 23781 not shown) Histogram of bond angle deviations from ideal: 96.85 - 104.75: 458 104.75 - 112.66: 12101 112.66 - 120.56: 11223 120.56 - 128.46: 8193 128.46 - 136.37: 172 Bond angle restraints: 32147 Sorted by residual: angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 110.42 11.28 1.80e+00 3.09e-01 3.93e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 110.72 10.98 1.80e+00 3.09e-01 3.72e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.01 10.69 1.80e+00 3.09e-01 3.52e+01 angle pdb=" N TRP I 1 " pdb=" CA TRP I 1 " pdb=" CB TRP I 1 " ideal model delta sigma weight residual 110.50 100.89 9.61 1.70e+00 3.46e-01 3.20e+01 angle pdb=" N TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.50 101.48 9.02 1.70e+00 3.46e-01 2.81e+01 ... (remaining 32142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 14000 32.11 - 64.21: 270 64.21 - 96.32: 69 96.32 - 128.43: 3 128.43 - 160.53: 6 Dihedral angle restraints: 14348 sinusoidal: 5871 harmonic: 8477 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 100.53 -160.53 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 100.43 -160.43 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 100.37 -160.37 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 14345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2678 0.053 - 0.106: 679 0.106 - 0.159: 145 0.159 - 0.212: 16 0.212 - 0.265: 2 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA CYS I 5 " pdb=" N CYS I 5 " pdb=" C CYS I 5 " pdb=" CB CYS I 5 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA CYS J 5 " pdb=" N CYS J 5 " pdb=" C CYS J 5 " pdb=" CB CYS J 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3517 not shown) Planarity restraints: 4112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 278 " -0.080 9.50e-02 1.11e+02 4.75e-02 1.31e+01 pdb=" NE ARG D 278 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 278 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG D 278 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 278 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.080 9.50e-02 1.11e+02 4.77e-02 1.30e+01 pdb=" NE ARG A 278 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 213 " -0.078 9.50e-02 1.11e+02 4.70e-02 1.30e+01 pdb=" NE ARG D 213 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 213 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG D 213 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 213 " 0.017 2.00e-02 2.50e+03 ... (remaining 4109 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 6 2.03 - 2.75: 2464 2.75 - 3.47: 33333 3.47 - 4.18: 55069 4.18 - 4.90: 99202 Nonbonded interactions: 190074 Sorted by model distance: nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.314 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.315 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.316 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.729 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.729 3.620 ... (remaining 190069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.830 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: 8.150 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 61.340 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 23786 Z= 0.303 Angle : 0.850 15.815 32147 Z= 0.488 Chirality : 0.049 0.265 3520 Planarity : 0.007 0.076 4112 Dihedral : 14.781 160.535 8888 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.88 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 2841 helix: -1.71 (0.11), residues: 1390 sheet: 0.21 (0.25), residues: 363 loop : -0.22 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP H 1 HIS 0.012 0.002 HIS A 418 PHE 0.054 0.002 PHE A 564 TYR 0.033 0.004 TYR A 102 ARG 0.061 0.009 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 MET cc_start: 0.8029 (mtm) cc_final: 0.7567 (mtp) REVERT: C 246 GLN cc_start: 0.7848 (mt0) cc_final: 0.7603 (tt0) REVERT: D 487 ILE cc_start: 0.8189 (tt) cc_final: 0.6672 (tt) REVERT: E 110 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7529 (mmt90) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.4105 time to fit residues: 241.4351 Evaluate side-chains 203 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 166 optimal weight: 0.0770 chunk 258 optimal weight: 5.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 463 GLN A 464 GLN A 481 GLN A 497 ASN A 594 GLN A 775 GLN C 59 GLN C 121 GLN C 162 ASN C 296 ASN B 75 GLN B 147 HIS D 156 ASN D 264 GLN D 307 ASN D 398 ASN D 406 HIS D 463 GLN D 464 GLN D 481 GLN D 497 ASN D 639 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 280 ASN F 296 ASN E 75 GLN G 121 GLN G 296 ASN G 297 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23786 Z= 0.387 Angle : 0.680 7.150 32147 Z= 0.353 Chirality : 0.046 0.205 3520 Planarity : 0.005 0.058 4112 Dihedral : 9.647 175.252 3232 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.45 % Allowed : 5.76 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 2841 helix: 0.16 (0.13), residues: 1392 sheet: 0.44 (0.25), residues: 399 loop : 0.74 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP I 1 HIS 0.011 0.002 HIS E 147 PHE 0.040 0.002 PHE A 564 TYR 0.019 0.002 TYR A 259 ARG 0.007 0.001 ARG G 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: B 89 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: F 325 MET cc_start: 0.8221 (mmp) cc_final: 0.7999 (mmt) REVERT: G 101 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7162 (p-80) outliers start: 36 outliers final: 13 residues processed: 242 average time/residue: 0.3472 time to fit residues: 131.2466 Evaluate side-chains 177 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 259 optimal weight: 0.6980 chunk 280 optimal weight: 0.4980 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 594 GLN C 59 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 125 ASN D 310 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23786 Z= 0.216 Angle : 0.563 6.901 32147 Z= 0.289 Chirality : 0.042 0.211 3520 Planarity : 0.004 0.050 4112 Dihedral : 9.045 176.035 3232 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.33 % Allowed : 7.57 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2841 helix: 0.77 (0.14), residues: 1380 sheet: 0.51 (0.26), residues: 375 loop : 0.91 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 79 HIS 0.008 0.001 HIS E 147 PHE 0.025 0.001 PHE D 564 TYR 0.014 0.001 TYR A 259 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.7894 (tpp) cc_final: 0.7679 (tpp) REVERT: B 89 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: E 110 ARG cc_start: 0.8107 (mmt-90) cc_final: 0.7280 (mmt90) outliers start: 33 outliers final: 18 residues processed: 208 average time/residue: 0.3322 time to fit residues: 111.1347 Evaluate side-chains 174 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 246 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS A 458 ASN A 743 GLN B 8 GLN D 455 ASN D 743 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23786 Z= 0.390 Angle : 0.623 7.168 32147 Z= 0.319 Chirality : 0.045 0.234 3520 Planarity : 0.004 0.051 4112 Dihedral : 8.885 176.944 3232 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.85 % Allowed : 8.26 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2841 helix: 0.94 (0.14), residues: 1356 sheet: 0.31 (0.26), residues: 399 loop : 0.74 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 79 HIS 0.009 0.001 HIS A 418 PHE 0.039 0.002 PHE D 564 TYR 0.018 0.002 TYR A 259 ARG 0.006 0.001 ARG G 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 163 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.7980 (tpp) cc_final: 0.7726 (tpp) REVERT: C 101 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7327 (p-80) REVERT: B 36 MET cc_start: 0.6448 (tpp) cc_final: 0.6099 (tpp) REVERT: B 89 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: E 19 PHE cc_start: 0.6893 (t80) cc_final: 0.6517 (t80) outliers start: 46 outliers final: 29 residues processed: 200 average time/residue: 0.3237 time to fit residues: 106.6453 Evaluate side-chains 180 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 113 optimal weight: 40.0000 chunk 235 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 247 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 455 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23786 Z= 0.343 Angle : 0.594 10.153 32147 Z= 0.302 Chirality : 0.044 0.251 3520 Planarity : 0.004 0.047 4112 Dihedral : 8.699 178.291 3232 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.93 % Allowed : 9.59 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2841 helix: 1.02 (0.14), residues: 1366 sheet: 0.22 (0.26), residues: 399 loop : 0.57 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 79 HIS 0.008 0.001 HIS A 418 PHE 0.028 0.002 PHE A 564 TYR 0.017 0.001 TYR A 259 ARG 0.004 0.001 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.7976 (tpp) cc_final: 0.7742 (tpp) REVERT: C 101 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7274 (p-80) REVERT: B 36 MET cc_start: 0.6472 (tpp) cc_final: 0.6126 (tpp) REVERT: D 132 MET cc_start: 0.7724 (tpp) cc_final: 0.7362 (tpt) REVERT: E 19 PHE cc_start: 0.7138 (t80) cc_final: 0.6794 (t80) REVERT: E 105 MET cc_start: 0.8093 (tpp) cc_final: 0.7891 (tpp) REVERT: E 110 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7601 (mmt180) REVERT: E 120 MET cc_start: 0.3531 (ptt) cc_final: 0.3148 (pmm) REVERT: G 246 GLN cc_start: 0.7620 (mt0) cc_final: 0.7377 (mt0) outliers start: 48 outliers final: 30 residues processed: 197 average time/residue: 0.3181 time to fit residues: 103.2893 Evaluate side-chains 185 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 54 optimal weight: 0.0270 chunk 161 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 455 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23786 Z= 0.244 Angle : 0.555 8.049 32147 Z= 0.281 Chirality : 0.042 0.249 3520 Planarity : 0.004 0.046 4112 Dihedral : 8.262 160.445 3232 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.53 % Allowed : 10.68 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2841 helix: 1.17 (0.14), residues: 1366 sheet: 0.21 (0.27), residues: 378 loop : 0.58 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 79 HIS 0.007 0.001 HIS A 418 PHE 0.019 0.001 PHE A 564 TYR 0.014 0.001 TYR A 259 ARG 0.005 0.000 ARG G 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.7891 (tpp) cc_final: 0.7654 (tpp) REVERT: B 36 MET cc_start: 0.6439 (tpp) cc_final: 0.6057 (tpp) REVERT: D 132 MET cc_start: 0.7914 (tpp) cc_final: 0.7637 (tpt) REVERT: D 439 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7810 (p90) REVERT: E 19 PHE cc_start: 0.7072 (t80) cc_final: 0.6759 (t80) REVERT: E 105 MET cc_start: 0.8139 (tpp) cc_final: 0.7913 (tpp) REVERT: E 110 ARG cc_start: 0.8022 (mmt180) cc_final: 0.7639 (mmt180) REVERT: E 120 MET cc_start: 0.3664 (ptt) cc_final: 0.3267 (pmm) outliers start: 38 outliers final: 26 residues processed: 192 average time/residue: 0.3234 time to fit residues: 101.6351 Evaluate side-chains 184 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 0.0060 chunk 31 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 274 optimal weight: 0.8980 chunk 171 optimal weight: 0.0770 chunk 167 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23786 Z= 0.144 Angle : 0.527 9.483 32147 Z= 0.265 Chirality : 0.041 0.236 3520 Planarity : 0.003 0.046 4112 Dihedral : 7.620 134.337 3232 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.17 % Allowed : 11.68 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 2841 helix: 1.35 (0.15), residues: 1366 sheet: 0.27 (0.27), residues: 374 loop : 0.62 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 79 HIS 0.006 0.001 HIS A 418 PHE 0.017 0.001 PHE E 93 TYR 0.010 0.001 TYR A 259 ARG 0.005 0.000 ARG G 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.6945 (ppp) cc_final: 0.6694 (ppp) REVERT: B 36 MET cc_start: 0.6418 (tpp) cc_final: 0.6042 (tpp) REVERT: E 19 PHE cc_start: 0.7067 (t80) cc_final: 0.6817 (t80) REVERT: E 110 ARG cc_start: 0.8014 (mmt180) cc_final: 0.7644 (mmt180) REVERT: E 120 MET cc_start: 0.3450 (ptt) cc_final: 0.3209 (pmm) outliers start: 29 outliers final: 24 residues processed: 189 average time/residue: 0.3608 time to fit residues: 112.2372 Evaluate side-chains 182 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 455 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23786 Z= 0.169 Angle : 0.531 9.537 32147 Z= 0.266 Chirality : 0.041 0.236 3520 Planarity : 0.003 0.043 4112 Dihedral : 7.345 124.573 3232 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.57 % Allowed : 11.56 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2841 helix: 1.50 (0.15), residues: 1346 sheet: 0.25 (0.26), residues: 395 loop : 0.58 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 79 HIS 0.006 0.001 HIS A 418 PHE 0.019 0.001 PHE E 93 TYR 0.011 0.001 TYR A 259 ARG 0.007 0.000 ARG G 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 MET cc_start: 0.8000 (mmm) cc_final: 0.7618 (mmm) REVERT: C 47 MET cc_start: 0.7124 (ppp) cc_final: 0.6811 (ppp) REVERT: B 36 MET cc_start: 0.6404 (tpp) cc_final: 0.6087 (tpp) REVERT: E 110 ARG cc_start: 0.8025 (mmt180) cc_final: 0.7655 (mmt180) REVERT: E 120 MET cc_start: 0.3738 (ptt) cc_final: 0.3452 (pmm) outliers start: 39 outliers final: 29 residues processed: 196 average time/residue: 0.3201 time to fit residues: 101.7136 Evaluate side-chains 186 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 6.9990 chunk 240 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 chunk 242 optimal weight: 30.0000 chunk 168 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23786 Z= 0.361 Angle : 0.616 10.708 32147 Z= 0.310 Chirality : 0.045 0.263 3520 Planarity : 0.004 0.044 4112 Dihedral : 7.700 133.857 3232 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.69 % Allowed : 11.89 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2841 helix: 1.33 (0.15), residues: 1359 sheet: 0.18 (0.26), residues: 395 loop : 0.41 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 340 HIS 0.006 0.001 HIS A 418 PHE 0.046 0.002 PHE B 12 TYR 0.018 0.001 TYR A 259 ARG 0.008 0.001 ARG G 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 152 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 715 MET cc_start: 0.8037 (mmm) cc_final: 0.7694 (mmm) REVERT: C 47 MET cc_start: 0.7149 (ppp) cc_final: 0.6741 (ppp) REVERT: B 36 MET cc_start: 0.6409 (tpp) cc_final: 0.6031 (tpp) REVERT: D 132 MET cc_start: 0.8092 (tpt) cc_final: 0.7876 (tpp) REVERT: D 790 MET cc_start: 0.0562 (tpp) cc_final: -0.0028 (ttt) REVERT: E 110 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7545 (mmt180) REVERT: E 120 MET cc_start: 0.3737 (ptt) cc_final: 0.3399 (pmm) outliers start: 42 outliers final: 32 residues processed: 186 average time/residue: 0.3138 time to fit residues: 97.6044 Evaluate side-chains 182 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN D 455 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23786 Z= 0.269 Angle : 0.581 9.950 32147 Z= 0.291 Chirality : 0.043 0.254 3520 Planarity : 0.004 0.045 4112 Dihedral : 7.535 130.695 3232 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.49 % Allowed : 11.97 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2841 helix: 1.37 (0.15), residues: 1350 sheet: 0.10 (0.27), residues: 378 loop : 0.41 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 79 HIS 0.007 0.001 HIS A 418 PHE 0.039 0.001 PHE B 12 TYR 0.015 0.001 TYR A 259 ARG 0.008 0.000 ARG G 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 715 MET cc_start: 0.7972 (mmm) cc_final: 0.7634 (mmm) REVERT: C 47 MET cc_start: 0.7162 (ppp) cc_final: 0.6682 (ppp) REVERT: E 110 ARG cc_start: 0.8003 (mmt180) cc_final: 0.7519 (mmt180) REVERT: E 120 MET cc_start: 0.3741 (ptt) cc_final: 0.3415 (pmm) outliers start: 37 outliers final: 34 residues processed: 182 average time/residue: 0.3096 time to fit residues: 93.1861 Evaluate side-chains 186 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 64, in __init__ weight = self.w, xray_structure = self.xray_structure) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 67.5631 > 50: distance: 419 - 420: 3.423 distance: 771 - 786: 3.203 distance: 793 - 4952: 3.212 distance: 808 - 4971: 3.004 distance: 811 - 4985: 3.052 distance: 917 - 946: 4.160 distance: 925 - 951: 11.219 distance: 947 - 948: 3.746 distance: 948 - 949: 4.527 distance: 948 - 951: 8.323 distance: 951 - 952: 14.395 distance: 952 - 953: 9.236 distance: 952 - 955: 21.619 distance: 953 - 954: 3.661 distance: 955 - 956: 15.343 distance: 956 - 957: 17.194 distance: 956 - 958: 34.317 distance: 957 - 959: 33.912 distance: 958 - 960: 24.170 distance: 959 - 961: 37.286 distance: 960 - 961: 11.728 distance: 961 - 962: 30.947 distance: 1010 - 1011: 14.231 distance: 1011 - 1012: 9.239 distance: 1011 - 1014: 24.166 distance: 1014 - 1015: 6.367 distance: 1015 - 1016: 47.844 distance: 1016 - 1017: 25.358 distance: 1020 - 1021: 3.064 distance: 1226 - 3383: 3.053 distance: 1326 - 1359: 3.008 distance: 1650 - 3378: 3.349 distance: 1659 - 1806: 3.252 distance: 1671 - 3363: 3.056 distance: 1674 - 3360: 3.167 distance: 1688 - 3351: 3.034 distance: 1927 - 1928: 3.026 distance: 1928 - 1929: 3.005 distance: 1929 - 1930: 5.498 distance: 1929 - 1931: 5.664 distance: 1984 - 2022: 3.069 distance: 2025 - 2050: 3.681 distance: 2319 - 2349: 3.081 distance: 2328 - 2357: 3.011 distance: 2337 - 2364: 3.391 distance: 2339 - 2340: 3.885 distance: 2340 - 2341: 3.534 distance: 2345 - 2375: 3.808 distance: 2439 - 2471: 3.238 distance: 2465 - 2491: 3.420 distance: 2474 - 2502: 3.076 distance: 2477 - 2478: 4.464 distance: 2486 - 2521: 3.003 distance: 2505 - 2534: 3.517 distance: 2541 - 2572: 3.107 distance: 2746 - 2776: 3.012 distance: 2756 - 2758: 3.066 distance: 2759 - 2761: 3.448 distance: 2760 - 2761: 4.408 distance: 2789 - 2790: 9.399 distance: 2790 - 2791: 16.379 distance: 2814 - 2849: 3.160 distance: 3113 - 3149: 3.074 distance: 3221 - 3251: 3.057 distance: 3229 - 3260: 3.001 distance: 3239 - 3265: 3.002 distance: 3419 - 3422: 4.359 distance: 3422 - 3423: 4.373 distance: 3423 - 3424: 5.595 distance: 3424 - 3425: 7.852 distance: 3424 - 3426: 8.807 distance: 3450 - 3451: 3.367 distance: 3451 - 3452: 4.182 distance: 3451 - 3453: 4.432 distance: 3508 - 3538: 3.001 distance: 3525 - 3555: 3.020 distance: 3575 - 3607: 3.055 distance: 3700 - 3736: 3.085 distance: 3709 - 3744: 3.408 distance: 3741 - 3742: 3.521 distance: 4127 - 4161: 3.149 distance: 4324 - 4387: 3.018 distance: 4372 - 4373: 7.294 distance: 4372 - 4374: 7.752 distance: 4640 - 4669: 3.014 distance: 4828 - 4857: 3.013 distance: 4842 - 4873: 3.005 distance: 4868 - 4897: 3.208 distance: 4879 - 4880: 3.422 distance: 5137 - 5167: 3.038 distance: 5289 - 5739: 3.207 distance: 5306 - 5720: 3.012 distance: 5853 - 5886: 3.001 distance: 5861 - 5891: 3.074 distance: 5870 - 5896: 3.028 distance: 5894 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3.167 distance: 6684 - 6715: 3.025 distance: 6701 - 6739: 3.008 distance: 6732 - 6767: 3.025 distance: 7142 - 7168: 3.094 distance: 7156 - 7182: 3.031 distance: 7264 - 7305: 3.154 distance: 7298 - 7447: 3.221 distance: 7315 - 7428: 3.317 distance: 7318 - 7425: 3.380 distance: 7375 - 7377: 3.287 distance: 7514 - 7547: 3.000 distance: 7649 - 7678: 3.114 distance: 7716 - 7747: 3.056 distance: 7824 - 7855: 3.038 distance: 7850 - 7872: 3.096 distance: 7852 - 7853: 3.170 distance: 7918 - 8015: 3.020 distance: 8134 - 8155: 3.060 distance: 8243 - 8274: 3.183 distance: 8255 - 8282: 3.095 distance: 8475 - 8504: 3.227 distance: 8648 - 8649: 4.643 distance: 8649 - 8654: 3.227 distance: 8705 - 8729: 3.292 distance: 8740 - 8751: 3.053 distance: 8789 - 8810: 3.001 distance: 8954 - 8979: 3.046 distance: 9066 - 9067: 4.067 distance: 9066 - 9068: 4.738 distance: 9068 - 9070: 5.276 distance: 9074 - 9075: 5.400 distance: 9076 - 9077: 3.728 distance: 9077 - 9079: 3.463 distance: 9081 - 9082: 5.165 distance: 9082 - 9083: 4.585 distance: 9082 - 9085: 20.335 distance: 9083 - 9110: 4.369 distance: 9085 - 9086: 18.161 distance: 9086 - 9087: 28.531 distance: 9086 - 9089: 7.970 distance: 9087 - 9088: 49.806 distance: 9087 - 9093: 45.294 distance: 9088 - 9115: 31.756 distance: 9089 - 9090: 20.805 distance: 9090 - 9091: 12.379 distance: 9090 - 9092: 5.635 distance: 9093 - 9094: 27.189 distance: 9094 - 9095: 34.954 distance: 9094 - 9097: 40.577 distance: 9095 - 9096: 49.514 distance: 9095 - 9102: 31.572 distance: 9096 - 9124: 30.305 distance: 9097 - 9098: 56.132 distance: 9098 - 9099: 62.435 distance: 9099 - 9100: 18.694 distance: 9099 - 9101: 56.724 distance: 9102 - 9103: 14.831 distance: 9103 - 9104: 9.123 distance: 9103 - 9106: 7.571 distance: 9104 - 9105: 17.470 distance: 9104 - 9110: 18.105 distance: 9105 - 9135: 18.004 distance: 9106 - 9107: 23.978 distance: 9107 - 9108: 18.337 distance: 9107 - 9109: 8.661 distance: 9110 - 9111: 6.119 distance: 9117 - 9124: 3.591 distance: 9118 - 9149: 3.130 distance: 9125 - 9128: 3.624 distance: 9127 - 9154: 3.235 distance: 9129 - 9130: 3.683 distance: 9132 - 9134: 8.580 distance: 9133 - 9134: 13.707 distance: 9247 - 9527: 3.048 distance: 9281 - 9305: 3.080 distance: 9290 - 9312: 7.939 distance: 9296 - 9320: 4.742 distance: 9300 - 9331: 3.081 distance: 9307 - 9308: 3.461 distance: 9307 - 9312: 5.428 distance: 9308 - 9336: 4.432 distance: 9313 - 9314: 3.324 distance: 9313 - 9316: 6.452 distance: 9314 - 9315: 3.603 distance: 9316 - 9317: 6.874 distance: 9317 - 9318: 19.257 distance: 9318 - 9319: 13.953 distance: 9338 - 9344: 3.355 distance: 9395 - 9425: 3.126 distance: 9429 - 9431: 3.483 distance: 9539 - 9541: 3.047 distance: 9545 - 9580: 3.173 distance: 9583 - 9611: 3.494 distance: 9591 - 9620: 3.086 distance: 9597 - 9603: 7.710 distance: 9598 - 9625: 3.253 distance: 9599 - 9600: 4.912 distance: 9600 - 9601: 9.104 distance: 9601 - 9602: 3.997 distance: 9603 - 9604: 10.743 distance: 9604 - 9605: 3.262 distance: 9604 - 9607: 10.436 distance: 9607 - 9608: 15.528 distance: 9608 - 9609: 16.403 distance: 9608 - 9610: 19.928 distance: 9666 - 9697: 3.035 distance: 9773 - 9774: 3.158 distance: 9774 - 9775: 3.588 distance: 9788 - 9823: 3.189 distance: 9805 - 9838: 3.791 distance: 9817 - 9818: 3.389 distance: 9842 - 9844: 3.092 distance: 9857 - 9858: 4.287 distance: 9857 - 9859: 3.221 distance: 9860 - 9861: 4.392 distance: 9874 - 9877: 4.021 distance: 9878 - 9879: 4.193 distance: 9879 - 9880: 4.363 distance: 9880 - 9881: 4.720 distance: 9888 - 9889: 4.662 distance: 9918 - 9947: 3.001 distance: 10532 - 10538: 7.223 distance: 10538 - 10539: 17.294 distance: 10538 - 10544: 3.776 distance: 10539 - 10540: 27.093 distance: 10539 - 10542: 16.513 distance: 10540 - 10541: 21.928 distance: 10540 - 10545: 21.662 distance: 10542 - 10543: 3.210 distance: 10545 - 10546: 4.214 distance: 10545 - 10551: 6.320 distance: 10767 - 10799: 3.116 distance: 10888 - 10909: 3.044 distance: 10891 - 10906: 3.241 distance: 10913 - 15072: 3.093 distance: 10928 - 15091: 3.104 distance: 10931 - 15105: 3.084 distance: 11006 - 11008: 3.458 distance: 11075 - 11076: 3.549 distance: 11076 - 11077: 4.333 distance: 11076 - 11078: 7.203 distance: 11079 - 11081: 4.009 distance: 11080 - 11081: 6.384 distance: 11104 - 11105: 3.055 distance: 11104 - 11110: 4.356 distance: 11110 - 11111: 3.888 distance: 11112 - 11113: 4.559 distance: 11114 - 11115: 7.420 distance: 11115 - 11116: 16.795 distance: 11116 - 11117: 9.726 distance: 11118 - 11119: 4.077 distance: 11131 - 11134: 5.284 distance: 11134 - 11135: 3.705 distance: 11135 - 11136: 5.286 distance: 11315 - 13476: 3.021 distance: 11338 - 15081: 3.073 distance: 11346 - 13503: 3.302 distance: 11614 - 11643: 3.052 distance: 11779 - 11926: 3.483 distance: 11791 - 13483: 3.274 distance: 11794 - 13480: 3.151 distance: 11823 - 13451: 3.079 distance: 12114 - 12151: 3.079 distance: 12122 - 12159: 3.042 distance: 12133 - 12165: 3.418 distance: 12144 - 12145: 5.607 distance: 12145 - 12170: 7.456 distance: 12448 - 12477: 3.621 distance: 12457 - 12484: 3.617 distance: 12458 - 12459: 3.719 distance: 12459 - 12460: 6.958 distance: 12460 - 12461: 6.145 distance: 12465 - 12495: 3.285 distance: 12559 - 12591: 3.004 distance: 12567 - 12599: 3.079 distance: 12585 - 12611: 3.478 distance: 12597 - 12598: 3.695 distance: 12661 - 12692: 3.110 distance: 12731 - 12790: 3.055 distance: 13233 - 13269: 3.110 distance: 13242 - 13274: 3.007 distance: 13695 - 13727: 3.058 distance: 13721 - 13755: 3.148 distance: 13730 - 13763: 3.106 distance: 13750 - 13780: 3.364 distance: 13761 - 13762: 3.804 distance: 14196 - 14230: 3.043 distance: 14212 - 14244: 3.077 distance: 14247 - 14281: 3.156 distance: 14444 - 14507: 3.082 distance: 14447 - 14504: 3.168 distance: 14760 - 14789: 3.191 distance: 14970 - 15001: 3.011 distance: 15241 - 15270: 3.054 distance: 15409 - 15859: 3.479 distance: 15412 - 15856: 3.053 distance: 15426 - 15840: 3.018 distance: 15558 - 15559: 3.493 distance: 15560 - 15561: 5.103 distance: 15572 - 15573: 3.234 distance: 15573 - 15574: 3.114 distance: 15575 - 15576: 3.120 distance: 15576 - 15577: 3.135 distance: 15577 - 15578: 3.609 distance: 15577 - 15579: 3.599 distance: 15791 - 15845: 3.042 distance: 16033 - 16067: 3.004 distance: 16122 - 16156: 3.788 distance: 16124 - 16125: 4.069 distance: 16125 - 16126: 4.585 distance: 16141 - 16176: 4.019 distance: 16150 - 16187: 3.116 distance: 16168 - 16169: 4.361 distance: 16169 - 16172: 5.168 distance: 16172 - 16173: 6.168 distance: 16173 - 16174: 6.647 distance: 16174 - 16175: 8.184 distance: 16307 - 16400: 3.154 distance: 16323 - 16388: 3.365 distance: 16432 - 16683: 4.018 distance: 16439 - 16568: 3.056 distance: 16443 - 16668: 3.087 distance: 16591 - 16619: 3.080 distance: 16838 - 16876: 3.121 distance: 17088 - 17122: 3.159 distance: 17117 - 17146: 3.059 distance: 17125 - 17154: 3.068 distance: 17262 - 17288: 3.139 distance: 17354 - 17460: 3.424 distance: 17369 - 17443: 3.254 distance: 17384 - 17425: 3.073 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