Starting phenix.real_space_refine on Thu Dec 14 06:43:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/12_2023/6vmd_21240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/12_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_21240/12_2023/6vmd_21240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/12_2023/6vmd_21240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/12_2023/6vmd_21240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/12_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: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 15.26, per 1000 atoms: 0.55 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: 11.43 Conformation dependent library (CDL) restraints added in 5.0 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: 6.22 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: 9.16 Time building geometry restraints manager: 11.86 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: 15678 22.35 - 44.70: 1273 44.70 - 67.05: 169 67.05 - 89.40: 61 89.40 - 111.74: 1 Dihedral angle restraints: 17182 sinusoidal: 6940 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 17179 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: 1.050 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: 6.620 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 73.010 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.660 ------------------------------------------------------------------------------- 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 : 16.576 111.745 10605 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 % Allowed : 15.57 % Favored : 83.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 15 HIS 0.013 0.002 HIS B 295 PHE 0.030 0.003 PHE E 430 TYR 0.021 0.003 TYR A 464 ARG 0.017 0.001 ARG F 277 *********************** 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 : 3.477 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: 0.3885 time to fit residues: 208.3209 Evaluate side-chains 216 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 4.040 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2411 time to fit residues: 10.1302 ------------------------------------------------------------------------------- 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 295 HIS 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 133 HIS ** 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 238 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: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27883 Z= 0.186 Angle : 0.674 9.686 37786 Z= 0.348 Chirality : 0.045 0.258 4447 Planarity : 0.005 0.065 4912 Dihedral : 8.784 101.064 4023 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.12 % Favored : 91.71 % Rotamer: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % 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: -2.78 (0.13), residues: 3558 helix: -0.85 (0.13), residues: 1439 sheet: -2.37 (0.21), residues: 466 loop : -2.60 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.004 0.001 HIS F 193 PHE 0.025 0.001 PHE C 482 TYR 0.018 0.001 TYR D 362 ARG 0.010 0.000 ARG A 462 *********************** 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 317 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 312 time to evaluate : 3.420 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: 317 average time/residue: 0.4130 time to fit residues: 206.4775 Evaluate side-chains 201 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2380 time to fit residues: 5.2220 ------------------------------------------------------------------------------- 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: 1.9990 chunk 100 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 322 optimal weight: 0.5980 chunk 348 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 chunk 320 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 259 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN 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 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** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 25 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27883 Z= 0.179 Angle : 0.642 9.924 37786 Z= 0.332 Chirality : 0.044 0.205 4447 Planarity : 0.004 0.058 4912 Dihedral : 8.397 96.129 4023 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 0.20 % Allowed : 5.20 % Favored : 94.60 % 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: -2.21 (0.13), residues: 3558 helix: -0.32 (0.13), residues: 1443 sheet: -1.98 (0.22), residues: 463 loop : -2.36 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 57 HIS 0.003 0.001 HIS d 141 PHE 0.047 0.001 PHE B 213 TYR 0.015 0.001 TYR B 330 ARG 0.009 0.000 ARG A 22 *********************** 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 293 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 287 time to evaluate : 3.393 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: 6 outliers final: 3 residues processed: 292 average time/residue: 0.3802 time to fit residues: 181.2462 Evaluate side-chains 200 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 3.705 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2821 time to fit residues: 5.9407 ------------------------------------------------------------------------------- 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: 3.9990 chunk 167 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 324 optimal weight: 0.8980 chunk 343 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 398 GLN ** B 164 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 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 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** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2428 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= 0.229 Angle : 0.650 9.876 37786 Z= 0.336 Chirality : 0.044 0.177 4447 Planarity : 0.004 0.056 4912 Dihedral : 8.260 97.481 4023 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.94 % Favored : 90.92 % Rotamer: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % 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: -1.88 (0.14), residues: 3558 helix: -0.03 (0.13), residues: 1437 sheet: -1.77 (0.23), residues: 452 loop : -2.20 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 57 HIS 0.004 0.001 HIS F 384 PHE 0.033 0.002 PHE g 284 TYR 0.014 0.001 TYR g 167 ARG 0.010 0.000 ARG C 141 *********************** 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 275 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 270 time to evaluate : 3.080 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: 5 outliers final: 2 residues processed: 275 average time/residue: 0.3918 time to fit residues: 176.6967 Evaluate side-chains 194 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 3.575 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2892 time to fit residues: 5.5993 ------------------------------------------------------------------------------- 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: 0.7980 chunk 194 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 307 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 295 HIS B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** 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** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27883 Z= 0.166 Angle : 0.622 10.767 37786 Z= 0.317 Chirality : 0.044 0.254 4447 Planarity : 0.004 0.054 4912 Dihedral : 7.966 90.500 4023 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.93 % Rotamer: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % 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: -1.67 (0.14), residues: 3558 helix: 0.11 (0.14), residues: 1445 sheet: -1.57 (0.24), residues: 455 loop : -2.09 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 57 HIS 0.006 0.001 HIS B 43 PHE 0.023 0.001 PHE g 133 TYR 0.012 0.001 TYR g 167 ARG 0.009 0.000 ARG D 248 *********************** 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 273 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 270 time to evaluate : 3.432 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: 3 outliers final: 2 residues processed: 273 average time/residue: 0.3951 time to fit residues: 175.3612 Evaluate side-chains 195 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2684 time to fit residues: 5.2432 ------------------------------------------------------------------------------- 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: 4.9990 chunk 309 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 201 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** 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 141 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 188 ASN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 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** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2961 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= 0.166 Angle : 0.622 10.969 37786 Z= 0.316 Chirality : 0.044 0.215 4447 Planarity : 0.004 0.052 4912 Dihedral : 7.754 89.830 4023 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % 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: -1.52 (0.14), residues: 3558 helix: 0.26 (0.14), residues: 1436 sheet: -1.50 (0.24), residues: 457 loop : -2.02 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 57 HIS 0.009 0.001 HIS B 43 PHE 0.035 0.001 PHE B 213 TYR 0.023 0.001 TYR D 259 ARG 0.005 0.000 ARG D 248 *********************** 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 281 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 3.321 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 outliers start: 2 outliers final: 1 residues processed: 281 average time/residue: 0.3907 time to fit residues: 177.9680 Evaluate side-chains 197 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 3.332 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2851 time to fit residues: 4.9664 ------------------------------------------------------------------------------- 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: 0.0770 chunk 38 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 342 optimal weight: 0.0040 chunk 214 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.0156 ------------------------------------------------------------------------------- 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 351 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 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 66 GLN D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 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 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** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3146 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= 0.169 Angle : 0.622 11.217 37786 Z= 0.316 Chirality : 0.044 0.208 4447 Planarity : 0.004 0.074 4912 Dihedral : 7.597 88.895 4023 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.79 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -1.42 (0.14), residues: 3558 helix: 0.33 (0.14), residues: 1436 sheet: -1.35 (0.24), residues: 455 loop : -1.99 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 57 HIS 0.013 0.001 HIS B 43 PHE 0.025 0.001 PHE E 278 TYR 0.019 0.001 TYR D 259 ARG 0.006 0.000 ARG D 248 *********************** 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 279 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.635 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: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3894 time to fit residues: 178.3422 Evaluate side-chains 199 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7369 ------------------------------------------------------------------------------- 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: 0.0470 chunk 136 optimal weight: 0.0980 chunk 204 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 overall best weight: 1.4280 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 67 GLN F 25 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 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** g 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3263 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= 0.181 Angle : 0.628 11.424 37786 Z= 0.320 Chirality : 0.044 0.189 4447 Planarity : 0.004 0.053 4912 Dihedral : 7.529 88.245 4023 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.74 % 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: -1.27 (0.14), residues: 3558 helix: 0.45 (0.14), residues: 1428 sheet: -1.29 (0.25), residues: 454 loop : -1.88 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 57 HIS 0.011 0.001 HIS B 43 PHE 0.022 0.001 PHE g 168 TYR 0.015 0.001 TYR D 259 ARG 0.006 0.000 ARG B 41 *********************** 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 272 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 3.304 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: 1 outliers final: 0 residues processed: 272 average time/residue: 0.3739 time to fit residues: 167.3987 Evaluate side-chains 195 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2086 ------------------------------------------------------------------------------- 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: 0.9980 chunk 299 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 273 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 ** 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** ** 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** g 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3292 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= 0.221 Angle : 0.648 11.530 37786 Z= 0.331 Chirality : 0.044 0.177 4447 Planarity : 0.004 0.053 4912 Dihedral : 7.587 87.678 4023 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.57 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.27 (0.14), residues: 3558 helix: 0.46 (0.14), residues: 1436 sheet: -1.29 (0.25), residues: 448 loop : -1.90 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 15 HIS 0.009 0.001 HIS B 43 PHE 0.021 0.001 PHE E 271 TYR 0.018 0.001 TYR g 167 ARG 0.006 0.000 ARG A 366 *********************** 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 257 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.320 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 outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3865 time to fit residues: 163.5225 Evaluate side-chains 190 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6173 ------------------------------------------------------------------------------- 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: 7.9990 chunk 337 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 217 optimal weight: 0.0770 chunk 172 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 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** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 273 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 170 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** g 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27883 Z= 0.177 Angle : 0.642 11.931 37786 Z= 0.322 Chirality : 0.044 0.193 4447 Planarity : 0.004 0.054 4912 Dihedral : 7.510 85.657 4023 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.13 (0.14), residues: 3558 helix: 0.63 (0.14), residues: 1425 sheet: -1.25 (0.25), residues: 448 loop : -1.84 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 15 HIS 0.010 0.001 HIS B 43 PHE 0.021 0.001 PHE E 271 TYR 0.016 0.001 TYR D 298 ARG 0.006 0.000 ARG B 94 ********************** 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 260 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.407 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: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3905 time to fit residues: 167.2059 Evaluate side-chains 196 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8958 ------------------------------------------------------------------------------- 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: 1.9990 chunk 300 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 282 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 71 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** 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 ** d 170 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** g 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.041907 restraints weight = 187851.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043231 restraints weight = 115758.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044190 restraints weight = 79160.883| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3529 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= 0.176 Angle : 0.630 11.816 37786 Z= 0.319 Chirality : 0.044 0.169 4447 Planarity : 0.004 0.071 4912 Dihedral : 7.422 84.549 4023 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.98 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.09 (0.14), residues: 3558 helix: 0.65 (0.14), residues: 1429 sheet: -1.20 (0.25), residues: 446 loop : -1.84 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 15 HIS 0.008 0.001 HIS B 43 PHE 0.020 0.001 PHE g 168 TYR 0.027 0.001 TYR D 213 ARG 0.005 0.000 ARG B 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4881.87 seconds wall clock time: 91 minutes 2.47 seconds (5462.47 seconds total)