Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 17:07:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/08_2023/6vmd_21240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/08_2023/6vmd_21240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/08_2023/6vmd_21240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/08_2023/6vmd_21240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/08_2023/6vmd_21240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/08_2023/6vmd_21240_updated.pdb" } resolution = 4.53 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 106 5.16 5 C 17268 2.51 5 N 4746 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D GLU 428": "OE1" <-> "OE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E GLU 428": "OE1" <-> "OE2" Residue "E TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 467": "OD1" <-> "OD2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 100": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ASP 55": "OD1" <-> "OD2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ASP 80": "OD1" <-> "OD2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "e ARG 120": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ASP 49": "OD1" <-> "OD2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g ASP 196": "OD1" <-> "OD2" Residue "g GLU 206": "OE1" <-> "OE2" Residue "g PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 261": "OE1" <-> "OE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "g GLU 352": "OE1" <-> "OE2" Residue "g GLU 355": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 27501 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "B" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3862 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2504 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 310} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.40, per 1000 atoms: 0.49 Number of scatterers: 27501 At special positions: 0 Unit cell: (155.76, 148.68, 128.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 14 15.00 O 5367 8.00 N 4746 7.00 C 17268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.84 Conformation dependent library (CDL) restraints added in 4.2 seconds 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 24 sheets defined 40.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 removed outlier: 4.101A pdb=" N ARG A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.585A pdb=" N LEU A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.556A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 296 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.590A pdb=" N ASN A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.245A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 484 through 504 Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.719A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 3.665A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 301 removed outlier: 5.132A pdb=" N ARG B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 374 through 396 removed outlier: 5.552A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.842A pdb=" N VAL B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.737A pdb=" N VAL B 454 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG B 455 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 461 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 465 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 466 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 484 through 502 removed outlier: 3.992A pdb=" N GLU B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.718A pdb=" N GLN C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 299 removed outlier: 4.226A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 296 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 374 through 398 removed outlier: 3.812A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 removed outlier: 4.110A pdb=" N GLN C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 4.100A pdb=" N MET C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 484 through 503 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.818A pdb=" N ILE D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 246 through 262 removed outlier: 4.604A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 312 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.012A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 4.196A pdb=" N LYS D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 407 removed outlier: 5.218A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 471 through 474 removed outlier: 3.774A pdb=" N PHE D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 178 through 191 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.821A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 345 removed outlier: 3.691A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.305A pdb=" N LYS E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 408 removed outlier: 4.892A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 406 " --> pdb=" O GLN E 402 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 408 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 430 Processing helix chain 'E' and resid 452 through 462 Processing helix chain 'E' and resid 471 through 473 No H-bonds generated for 'chain 'E' and resid 471 through 473' Processing helix chain 'E' and resid 480 through 495 removed outlier: 3.595A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 No H-bonds generated for 'chain 'F' and resid 154 through 157' Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 243 through 246 No H-bonds generated for 'chain 'F' and resid 243 through 246' Processing helix chain 'F' and resid 249 through 262 removed outlier: 3.567A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 345 removed outlier: 3.628A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 383 through 405 removed outlier: 4.564A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 430 Processing helix chain 'F' and resid 438 through 440 No H-bonds generated for 'chain 'F' and resid 438 through 440' Processing helix chain 'F' and resid 452 through 462 Processing helix chain 'F' and resid 480 through 495 removed outlier: 4.342A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 88 removed outlier: 3.926A pdb=" N TYR d 78 " --> pdb=" O THR d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 105 removed outlier: 3.692A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 removed outlier: 3.907A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN d 147 " --> pdb=" O ALA d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 173 removed outlier: 3.780A pdb=" N VAL d 158 " --> pdb=" O ILE d 155 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP d 167 " --> pdb=" O GLU d 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL d 168 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE d 172 " --> pdb=" O PHE d 169 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 201 Processing helix chain 'd' and resid 237 through 248 removed outlier: 5.249A pdb=" N GLU d 242 " --> pdb=" O LYS d 239 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU d 248 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 104 removed outlier: 4.477A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 130 removed outlier: 4.142A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 99 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 134 through 151 removed outlier: 3.685A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 164 through 170 Processing helix chain 'g' and resid 188 through 203 Processing helix chain 'g' and resid 288 through 362 removed outlier: 3.515A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 4.388A pdb=" N ALA g 362 " --> pdb=" O ALA g 358 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.507A pdb=" N GLY A 30 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 317 through 321 removed outlier: 7.248A pdb=" N GLU A 166 " --> pdb=" O PRO A 318 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL A 320 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY A 341 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE A 169 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 343 " --> pdb=" O ILE A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.600A pdb=" N CYS A 194 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 195 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 39 through 43 removed outlier: 5.892A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.656A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 196 removed outlier: 7.262A pdb=" N HIS B 256 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL B 195 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 258 " --> pdb=" O VAL B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.676A pdb=" N THR C 31 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS C 43 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN C 66 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'C' and resid 224 through 227 removed outlier: 8.615A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 258 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 313 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE C 259 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C 315 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 23 through 27 removed outlier: 6.804A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 47 through 49 Processing sheet with id= L, first strand: chain 'D' and resid 197 through 199 removed outlier: 6.239A pdb=" N LEU D 269 " --> pdb=" O VAL D 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 23 through 27 removed outlier: 6.329A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 65 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 197 through 199 removed outlier: 3.877A pdb=" N ALA E 233 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 268 through 272 Processing sheet with id= P, first strand: chain 'F' and resid 91 through 93 removed outlier: 6.827A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= R, first strand: chain 'F' and resid 348 through 352 removed outlier: 7.509A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY F 172 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL F 268 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE F 324 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 198 " --> pdb=" O LEU F 269 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'd' and resid 177 through 182 removed outlier: 6.911A pdb=" N ARG d 208 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL d 180 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS d 210 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N SER d 182 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL d 212 " --> pdb=" O SER d 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'd' and resid 222 through 225 Processing sheet with id= U, first strand: chain 'e' and resid 48 through 52 removed outlier: 3.525A pdb=" N ALA e 61 " --> pdb=" O GLU e 82 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'g' and resid 119 through 122 removed outlier: 5.777A pdb=" N THR g 156 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL g 122 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE g 158 " --> pdb=" O VAL g 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'g' and resid 211 through 216 removed outlier: 3.521A pdb=" N HIS g 228 " --> pdb=" O MET g 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS g 216 " --> pdb=" O ASP g 224 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP g 224 " --> pdb=" O LYS g 216 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'g' and resid 251 through 257 998 hydrogen bonds defined for protein. 2856 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: 7.99 Time building geometry restraints manager: 12.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9292 1.34 - 1.46: 5561 1.46 - 1.59: 12809 1.59 - 1.71: 21 1.71 - 1.83: 200 Bond restraints: 27883 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.12e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.98e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 ... (remaining 27878 not shown) Histogram of bond angle deviations from ideal: 97.38 - 105.96: 679 105.96 - 114.54: 16801 114.54 - 123.12: 18726 123.12 - 131.69: 1554 131.69 - 140.27: 26 Bond angle restraints: 37786 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 114.74 25.13 1.00e+00 1.00e+00 6.31e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.18 22.69 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 114.63 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.21e+02 ... (remaining 37781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 15584 22.35 - 44.70: 1256 44.70 - 67.05: 161 67.05 - 89.40: 56 89.40 - 111.74: 1 Dihedral angle restraints: 17058 sinusoidal: 6816 harmonic: 10242 Sorted by residual: dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.28 -52.72 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -132.27 -47.73 0 5.00e+00 4.00e-02 9.11e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -134.50 -45.50 0 5.00e+00 4.00e-02 8.28e+01 ... (remaining 17055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3708 0.080 - 0.159: 676 0.159 - 0.239: 55 0.239 - 0.319: 6 0.319 - 0.398: 2 Chirality restraints: 4447 Sorted by residual: chirality pdb=" CB ILE e 23 " pdb=" CA ILE e 23 " pdb=" CG1 ILE e 23 " pdb=" CG2 ILE e 23 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ARG B 355 " pdb=" N ARG B 355 " pdb=" C ARG B 355 " pdb=" CB ARG B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE D 189 " pdb=" CA ILE D 189 " pdb=" CG1 ILE D 189 " pdb=" CG2 ILE D 189 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4444 not shown) Planarity restraints: 4912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR e 9 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO e 10 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO e 10 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO e 10 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 295 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C ALA D 295 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA D 295 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 296 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 338 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO D 339 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " 0.040 5.00e-02 4.00e+02 ... (remaining 4909 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3179 2.73 - 3.27: 29700 3.27 - 3.82: 50369 3.82 - 4.36: 56465 4.36 - 4.90: 91307 Nonbonded interactions: 231020 Sorted by model distance: nonbonded pdb=" OG1 THR B 177 " pdb=" O2B ATP B 600 " model vdw 2.192 2.440 nonbonded pdb=" O LEU D 47 " pdb=" OG1 THR D 62 " model vdw 2.202 2.440 nonbonded pdb=" O ASP F 366 " pdb=" OG SER F 370 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR D 179 " pdb=" O1G ATP D 601 " model vdw 2.227 2.440 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.236 2.440 ... (remaining 231015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 503 or resid 600)) selection = (chain 'B' and (resid 6 through 503 or resid 600)) selection = (chain 'C' and (resid 6 through 503 or resid 600)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 7.300 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 69.230 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.089 27883 Z= 0.521 Angle : 1.159 25.129 37786 Z= 0.697 Chirality : 0.060 0.398 4447 Planarity : 0.007 0.080 4912 Dihedral : 16.431 111.745 10481 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.12 % Favored : 89.74 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.12), residues: 3558 helix: -2.19 (0.11), residues: 1441 sheet: -2.82 (0.20), residues: 466 loop : -2.96 (0.13), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 315 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 335 average time/residue: 0.3874 time to fit residues: 207.4214 Evaluate side-chains 216 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 3.205 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2370 time to fit residues: 9.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 423 GLN A 495 GLN B 66 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 323 GLN B 359 ASN B 409 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 468 ASN D 19 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN E 472 GLN F 19 ASN F 25 GLN F 193 HIS F 225 GLN F 389 GLN F 402 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN d 247 GLN e 56 GLN ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 ASN g 184 ASN g 192 GLN g 228 HIS ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN g 346 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 27883 Z= 0.181 Angle : 0.668 9.539 37786 Z= 0.344 Chirality : 0.045 0.233 4447 Planarity : 0.005 0.064 4912 Dihedral : 7.446 100.572 3899 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.87 % Favored : 91.96 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.13), residues: 3558 helix: -0.81 (0.13), residues: 1440 sheet: -2.35 (0.21), residues: 466 loop : -2.59 (0.14), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 313 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 318 average time/residue: 0.4163 time to fit residues: 209.6486 Evaluate side-chains 206 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2405 time to fit residues: 5.0911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 219 optimal weight: 0.1980 chunk 88 optimal weight: 8.9990 chunk 322 optimal weight: 0.8980 chunk 348 optimal weight: 0.7980 chunk 287 optimal weight: 0.9980 chunk 320 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 25 GLN F 238 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 27883 Z= 0.169 Angle : 0.639 10.082 37786 Z= 0.329 Chirality : 0.044 0.199 4447 Planarity : 0.004 0.058 4912 Dihedral : 6.988 95.439 3899 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.34 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3558 helix: -0.28 (0.13), residues: 1441 sheet: -1.96 (0.23), residues: 462 loop : -2.38 (0.14), residues: 1655 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 290 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 293 average time/residue: 0.3877 time to fit residues: 185.6865 Evaluate side-chains 202 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2730 time to fit residues: 5.4792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 35 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 324 optimal weight: 1.9990 chunk 343 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 chunk 92 optimal weight: 0.0050 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN F 25 GLN F 264 ASN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 27883 Z= 0.175 Angle : 0.622 10.123 37786 Z= 0.320 Chirality : 0.044 0.178 4447 Planarity : 0.004 0.055 4912 Dihedral : 6.684 90.158 3899 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.32 % Favored : 91.54 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.12 % 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: -1.81 (0.14), residues: 3558 helix: 0.03 (0.14), residues: 1443 sheet: -1.68 (0.24), residues: 454 loop : -2.19 (0.15), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 281 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 285 average time/residue: 0.4017 time to fit residues: 186.1692 Evaluate side-chains 193 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 3.417 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2762 time to fit residues: 5.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 307 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 389 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 27883 Z= 0.171 Angle : 0.626 10.582 37786 Z= 0.320 Chirality : 0.044 0.244 4447 Planarity : 0.004 0.054 4912 Dihedral : 6.511 85.893 3899 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.87 % Favored : 92.02 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -1.63 (0.14), residues: 3558 helix: 0.19 (0.14), residues: 1443 sheet: -1.61 (0.23), residues: 465 loop : -2.10 (0.15), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 275 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 280 average time/residue: 0.3643 time to fit residues: 169.5111 Evaluate side-chains 193 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2701 time to fit residues: 5.1730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 115 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 343 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 398 GLN B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 27883 Z= 0.269 Angle : 0.674 10.166 37786 Z= 0.346 Chirality : 0.044 0.198 4447 Planarity : 0.004 0.053 4912 Dihedral : 6.592 91.604 3899 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.02 % Favored : 90.84 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -1.56 (0.14), residues: 3558 helix: 0.28 (0.14), residues: 1436 sheet: -1.59 (0.24), residues: 464 loop : -2.08 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 256 average time/residue: 0.3891 time to fit residues: 165.4989 Evaluate side-chains 186 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2903 time to fit residues: 5.3879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 331 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 195 optimal weight: 0.1980 chunk 250 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 289 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 342 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 157 optimal weight: 0.0970 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 141 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 27883 Z= 0.162 Angle : 0.637 11.605 37786 Z= 0.321 Chirality : 0.044 0.206 4447 Planarity : 0.004 0.065 4912 Dihedral : 6.362 84.204 3899 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.41 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3558 helix: 0.46 (0.14), residues: 1436 sheet: -1.41 (0.24), residues: 453 loop : -1.97 (0.15), residues: 1669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 280 average time/residue: 0.3775 time to fit residues: 173.1161 Evaluate side-chains 193 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2999 time to fit residues: 4.7376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 211 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 233 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN B 43 HIS B 66 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 67 GLN F 25 GLN d 141 HIS ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 27883 Z= 0.357 Angle : 0.750 10.631 37786 Z= 0.385 Chirality : 0.046 0.250 4447 Planarity : 0.005 0.058 4912 Dihedral : 6.726 97.578 3899 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.72 % Favored : 90.13 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -1.52 (0.14), residues: 3558 helix: 0.27 (0.13), residues: 1438 sheet: -1.46 (0.24), residues: 455 loop : -2.04 (0.15), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.3924 time to fit residues: 161.5968 Evaluate side-chains 178 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 301 optimal weight: 0.0980 chunk 317 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 66 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN F 25 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 95 ASN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 27883 Z= 0.185 Angle : 0.663 16.759 37786 Z= 0.334 Chirality : 0.045 0.203 4447 Planarity : 0.004 0.057 4912 Dihedral : 6.581 92.367 3899 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.93 % Favored : 91.96 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.30 (0.14), residues: 3558 helix: 0.42 (0.14), residues: 1441 sheet: -1.33 (0.25), residues: 432 loop : -1.91 (0.15), residues: 1685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3687 time to fit residues: 159.4077 Evaluate side-chains 189 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 3.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 209 optimal weight: 8.9990 chunk 337 optimal weight: 0.0870 chunk 205 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 353 optimal weight: 0.9990 chunk 325 optimal weight: 0.6980 chunk 281 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN F 188 ASN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 27883 Z= 0.187 Angle : 0.659 16.382 37786 Z= 0.332 Chirality : 0.044 0.222 4447 Planarity : 0.004 0.053 4912 Dihedral : 6.454 91.255 3899 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.25 (0.14), residues: 3558 helix: 0.50 (0.14), residues: 1441 sheet: -1.38 (0.24), residues: 456 loop : -1.90 (0.15), residues: 1661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3599 time to fit residues: 151.8255 Evaluate side-chains 193 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 223 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 78 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 164 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042081 restraints weight = 186173.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043412 restraints weight = 115635.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044369 restraints weight = 79376.938| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 27883 Z= 0.163 Angle : 0.646 14.646 37786 Z= 0.323 Chirality : 0.044 0.204 4447 Planarity : 0.004 0.058 4912 Dihedral : 6.294 88.524 3899 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.50 % Favored : 92.38 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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 (0.14), residues: 3558 helix: 0.64 (0.14), residues: 1432 sheet: -1.31 (0.24), residues: 461 loop : -1.87 (0.15), residues: 1665 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.54 seconds wall clock time: 84 minutes 43.41 seconds (5083.41 seconds total)