Starting phenix.real_space_refine on Tue Feb 20 09:51:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/02_2024/6vmd_21240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/02_2024/6vmd_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_21240/02_2024/6vmd_21240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/02_2024/6vmd_21240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/02_2024/6vmd_21240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vmd_21240/02_2024/6vmd_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.13, 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: 12.19 Conformation dependent library (CDL) restraints added in 5.4 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: 6.52 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: 8.45 Time building geometry restraints manager: 12.92 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: 2.100 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: 6.490 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 74.760 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.970 ------------------------------------------------------------------------------- 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 : 3.797 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: A 147 LEU cc_start: 0.8908 (tp) cc_final: 0.8222 (mt) REVERT: A 157 MET cc_start: 0.8592 (ptp) cc_final: 0.7921 (mmt) REVERT: A 276 LEU cc_start: 0.9172 (tp) cc_final: 0.8939 (tp) REVERT: A 314 MET cc_start: 0.8101 (mmm) cc_final: 0.7579 (mmm) REVERT: A 338 ILE cc_start: 0.9350 (mm) cc_final: 0.9111 (mt) REVERT: A 351 ASN cc_start: 0.8598 (t0) cc_final: 0.8190 (t0) REVERT: A 376 MET cc_start: 0.8789 (tpp) cc_final: 0.8509 (mmp) REVERT: A 436 MET cc_start: 0.8677 (ptp) cc_final: 0.8099 (ptp) REVERT: A 498 MET cc_start: 0.8896 (ttm) cc_final: 0.8511 (mtp) REVERT: B 236 GLN cc_start: 0.9148 (mt0) cc_final: 0.8910 (mt0) REVERT: B 251 MET cc_start: 0.7596 (tpt) cc_final: 0.7009 (tpt) REVERT: B 314 MET cc_start: 0.7908 (tpt) cc_final: 0.6968 (tpt) REVERT: B 323 GLN cc_start: 0.8614 (mp-120) cc_final: 0.8311 (mm110) REVERT: C 235 LEU cc_start: 0.9417 (mt) cc_final: 0.9201 (mt) REVERT: C 474 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8889 (mm-30) REVERT: D 256 MET cc_start: 0.8680 (mmt) cc_final: 0.8413 (mmp) REVERT: D 488 MET cc_start: 0.9184 (tmm) cc_final: 0.8928 (tmm) REVERT: E 79 MET cc_start: 0.9180 (mmt) cc_final: 0.8940 (mmp) REVERT: E 239 MET cc_start: 0.8624 (mmm) cc_final: 0.8195 (mmm) REVERT: E 247 MET cc_start: 0.8686 (tpp) cc_final: 0.8423 (tpp) REVERT: F 79 MET cc_start: 0.8503 (mpp) cc_final: 0.8029 (mpp) REVERT: F 89 MET cc_start: 0.8622 (ttm) cc_final: 0.8314 (mtp) REVERT: d 139 GLN cc_start: 0.9279 (mm110) cc_final: 0.8964 (mp10) REVERT: d 250 MET cc_start: 0.4386 (mmt) cc_final: 0.3183 (mtm) REVERT: g 62 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8729 (tm-30) REVERT: g 66 LEU cc_start: 0.8732 (mt) cc_final: 0.8095 (tt) REVERT: g 133 PHE cc_start: 0.8726 (t80) cc_final: 0.8383 (t80) REVERT: g 346 GLN cc_start: 0.8520 (mm110) cc_final: 0.8038 (mt0) outliers start: 23 outliers final: 12 residues processed: 335 average time/residue: 0.3899 time to fit residues: 209.4067 Evaluate side-chains 224 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 3.469 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.0870 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- 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 351 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 359 ASN B 409 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 468 ASN D 19 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN E 472 GLN F 19 ASN F 25 GLN F 193 HIS F 225 GLN F 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27883 Z= 0.188 Angle : 0.669 9.745 37786 Z= 0.344 Chirality : 0.044 0.203 4447 Planarity : 0.005 0.065 4912 Dihedral : 8.787 101.244 4023 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.18 % Favored : 91.65 % Rotamer: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.73 % 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: -2.77 (0.13), residues: 3558 helix: -0.81 (0.13), residues: 1437 sheet: -2.41 (0.21), residues: 466 loop : -2.60 (0.14), residues: 1655 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 0.008 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 316 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 313 time to evaluate : 3.495 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 REVERT: A 138 MET cc_start: 0.9324 (pmm) cc_final: 0.9094 (pmm) REVERT: A 147 LEU cc_start: 0.8899 (tp) cc_final: 0.8553 (tp) REVERT: A 157 MET cc_start: 0.8712 (ptp) cc_final: 0.8462 (ptt) REVERT: A 251 MET cc_start: 0.8167 (ptp) cc_final: 0.7734 (ppp) REVERT: A 314 MET cc_start: 0.8084 (mmm) cc_final: 0.7674 (mmm) REVERT: A 351 ASN cc_start: 0.8434 (t0) cc_final: 0.7841 (t0) REVERT: A 460 GLU cc_start: 0.8155 (tt0) cc_final: 0.7608 (mt-10) REVERT: B 131 GLU cc_start: 0.8735 (mp0) cc_final: 0.8369 (tp30) REVERT: C 182 ASP cc_start: 0.7895 (m-30) cc_final: 0.7676 (m-30) REVERT: C 251 MET cc_start: 0.8787 (ttt) cc_final: 0.8566 (ttt) REVERT: D 64 GLU cc_start: 0.5909 (tp30) cc_final: 0.5337 (tp30) REVERT: D 183 MET cc_start: 0.8792 (mmp) cc_final: 0.8437 (mmm) REVERT: D 256 MET cc_start: 0.8750 (mmt) cc_final: 0.8507 (mmp) REVERT: D 488 MET cc_start: 0.9221 (tmm) cc_final: 0.8989 (tmm) REVERT: E 79 MET cc_start: 0.9267 (mmt) cc_final: 0.8952 (mmp) REVERT: E 239 MET cc_start: 0.8650 (mmm) cc_final: 0.8397 (mmm) REVERT: E 247 MET cc_start: 0.8598 (tpp) cc_final: 0.8352 (tpp) REVERT: F 79 MET cc_start: 0.8751 (mpp) cc_final: 0.7937 (mpp) REVERT: F 89 MET cc_start: 0.8392 (ttm) cc_final: 0.7537 (tmm) REVERT: F 199 PHE cc_start: 0.7774 (t80) cc_final: 0.7354 (t80) REVERT: d 139 GLN cc_start: 0.9316 (mm110) cc_final: 0.9022 (mp10) REVERT: d 250 MET cc_start: 0.4251 (mmt) cc_final: 0.3292 (mtm) REVERT: e 95 THR cc_start: 0.8814 (t) cc_final: 0.8410 (p) REVERT: g 66 LEU cc_start: 0.8524 (mt) cc_final: 0.8099 (tt) REVERT: g 133 PHE cc_start: 0.8515 (t80) cc_final: 0.8051 (t80) REVERT: g 346 GLN cc_start: 0.8544 (mm110) cc_final: 0.7867 (mt0) outliers start: 3 outliers final: 0 residues processed: 316 average time/residue: 0.4078 time to fit residues: 204.0761 Evaluate side-chains 209 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.365 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 20.0000 chunk 268 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 322 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 287 optimal weight: 0.7980 chunk 320 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 259 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 323 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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** ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27883 Z= 0.173 Angle : 0.635 9.839 37786 Z= 0.328 Chirality : 0.044 0.206 4447 Planarity : 0.004 0.057 4912 Dihedral : 8.405 96.325 4023 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.49 % Favored : 91.37 % Rotamer: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.04 % 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: -2.20 (0.13), residues: 3558 helix: -0.27 (0.13), residues: 1440 sheet: -2.04 (0.23), residues: 454 loop : -2.38 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 57 HIS 0.003 0.001 HIS C 295 PHE 0.015 0.001 PHE E 271 TYR 0.014 0.001 TYR C 237 ARG 0.011 0.000 ARG F 277 *********************** 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 295 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 291 time to evaluate : 3.497 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: A 147 LEU cc_start: 0.8928 (tp) cc_final: 0.8659 (tp) REVERT: A 157 MET cc_start: 0.8685 (ptp) cc_final: 0.8346 (ptt) REVERT: A 251 MET cc_start: 0.7908 (ptp) cc_final: 0.7418 (ptm) REVERT: A 314 MET cc_start: 0.8184 (mmm) cc_final: 0.7664 (mmm) REVERT: A 460 GLU cc_start: 0.8332 (tt0) cc_final: 0.7532 (mt-10) REVERT: A 498 MET cc_start: 0.8845 (mtm) cc_final: 0.8254 (mtp) REVERT: B 131 GLU cc_start: 0.8730 (mp0) cc_final: 0.8402 (tp30) REVERT: B 251 MET cc_start: 0.7346 (tpt) cc_final: 0.6723 (tpt) REVERT: B 314 MET cc_start: 0.7713 (tpt) cc_final: 0.7167 (tpt) REVERT: B 355 ARG cc_start: 0.8984 (mmp-170) cc_final: 0.8122 (mmm160) REVERT: C 182 ASP cc_start: 0.7877 (m-30) cc_final: 0.7647 (m-30) REVERT: C 235 LEU cc_start: 0.9355 (mt) cc_final: 0.9138 (mt) REVERT: C 251 MET cc_start: 0.8824 (ttt) cc_final: 0.8606 (ttt) REVERT: D 44 TYR cc_start: 0.8732 (m-80) cc_final: 0.8066 (m-80) REVERT: D 64 GLU cc_start: 0.6023 (tp30) cc_final: 0.5520 (tp30) REVERT: D 183 MET cc_start: 0.8767 (mmp) cc_final: 0.8509 (mmm) REVERT: D 488 MET cc_start: 0.9198 (tmm) cc_final: 0.8978 (tmm) REVERT: E 79 MET cc_start: 0.9257 (mmt) cc_final: 0.8932 (mmp) REVERT: E 239 MET cc_start: 0.8688 (mmm) cc_final: 0.8464 (mmm) REVERT: E 247 MET cc_start: 0.8564 (tpp) cc_final: 0.8328 (tpp) REVERT: E 374 MET cc_start: 0.8378 (mmm) cc_final: 0.8149 (mmm) REVERT: F 79 MET cc_start: 0.8697 (mpp) cc_final: 0.7928 (mpp) REVERT: F 199 PHE cc_start: 0.7786 (t80) cc_final: 0.7559 (t80) REVERT: F 405 ILE cc_start: 0.9283 (pt) cc_final: 0.9068 (pt) REVERT: F 488 MET cc_start: 0.9200 (tmm) cc_final: 0.8932 (tmm) REVERT: d 139 GLN cc_start: 0.9315 (mm110) cc_final: 0.8998 (mp10) REVERT: d 250 MET cc_start: 0.4191 (mmt) cc_final: 0.3277 (mtm) REVERT: g 66 LEU cc_start: 0.8667 (mt) cc_final: 0.7957 (tt) REVERT: g 284 PHE cc_start: 0.8464 (m-10) cc_final: 0.8047 (m-10) REVERT: g 295 LEU cc_start: 0.9355 (mt) cc_final: 0.8982 (mt) REVERT: g 346 GLN cc_start: 0.8461 (mm110) cc_final: 0.7982 (mt0) outliers start: 4 outliers final: 1 residues processed: 294 average time/residue: 0.3680 time to fit residues: 176.8830 Evaluate side-chains 207 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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: 1.9990 chunk 242 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 324 optimal weight: 0.9990 chunk 343 optimal weight: 0.0060 chunk 169 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 264 ASN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN ** 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: 0.8298 moved from start: 0.2479 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= 0.173 Angle : 0.617 10.211 37786 Z= 0.318 Chirality : 0.044 0.243 4447 Planarity : 0.004 0.055 4912 Dihedral : 8.113 91.170 4023 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.26 % Favored : 91.60 % Rotamer: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.41 % 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: -1.83 (0.14), residues: 3558 helix: 0.02 (0.13), residues: 1444 sheet: -1.74 (0.24), residues: 442 loop : -2.20 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 57 HIS 0.004 0.001 HIS F 384 PHE 0.045 0.001 PHE B 213 TYR 0.013 0.001 TYR D 298 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 284 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 3.474 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: A 147 LEU cc_start: 0.8944 (tp) cc_final: 0.8642 (tp) REVERT: A 157 MET cc_start: 0.8724 (ptp) cc_final: 0.7901 (mmt) REVERT: A 251 MET cc_start: 0.8064 (ptp) cc_final: 0.7631 (ppp) REVERT: A 314 MET cc_start: 0.8220 (mmm) cc_final: 0.7699 (mmm) REVERT: A 460 GLU cc_start: 0.8436 (tt0) cc_final: 0.7997 (mp0) REVERT: A 498 MET cc_start: 0.8761 (mtm) cc_final: 0.8022 (mtp) REVERT: B 131 GLU cc_start: 0.8714 (mp0) cc_final: 0.8424 (tp30) REVERT: B 251 MET cc_start: 0.7358 (tpt) cc_final: 0.6799 (tpt) REVERT: B 314 MET cc_start: 0.7663 (tpt) cc_final: 0.7123 (tpt) REVERT: B 355 ARG cc_start: 0.8930 (mmp-170) cc_final: 0.8173 (mmm160) REVERT: C 182 ASP cc_start: 0.7800 (m-30) cc_final: 0.7553 (m-30) REVERT: C 251 MET cc_start: 0.8860 (ttt) cc_final: 0.8637 (ttt) REVERT: C 295 HIS cc_start: 0.8921 (m90) cc_final: 0.8644 (m90) REVERT: D 44 TYR cc_start: 0.8711 (m-80) cc_final: 0.8057 (m-80) REVERT: D 183 MET cc_start: 0.8741 (mmp) cc_final: 0.8533 (mmm) REVERT: D 488 MET cc_start: 0.9186 (tmm) cc_final: 0.8964 (tmm) REVERT: E 79 MET cc_start: 0.9287 (mmt) cc_final: 0.8952 (mmp) REVERT: E 247 MET cc_start: 0.8578 (tpp) cc_final: 0.8349 (tpp) REVERT: E 335 THR cc_start: 0.8598 (t) cc_final: 0.7692 (t) REVERT: F 79 MET cc_start: 0.8723 (mpp) cc_final: 0.7879 (mpp) REVERT: F 167 LYS cc_start: 0.9291 (mppt) cc_final: 0.8953 (mtmm) REVERT: F 488 MET cc_start: 0.9254 (tmm) cc_final: 0.8985 (tmm) REVERT: d 250 MET cc_start: 0.4584 (mmt) cc_final: 0.3513 (mtm) REVERT: g 66 LEU cc_start: 0.8393 (mt) cc_final: 0.7999 (tt) REVERT: g 284 PHE cc_start: 0.8337 (m-10) cc_final: 0.8033 (m-10) REVERT: g 295 LEU cc_start: 0.9368 (mt) cc_final: 0.9117 (mt) REVERT: g 346 GLN cc_start: 0.8396 (mm110) cc_final: 0.7912 (mt0) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.3697 time to fit residues: 172.1150 Evaluate side-chains 203 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.160 ------------------------------------------------------------------------------- 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: 2.9990 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 255 optimal weight: 8.9990 chunk 141 optimal weight: 0.0870 chunk 292 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 307 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.9966 ------------------------------------------------------------------------------- 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 398 GLN B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** ** 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: 0.8285 moved from start: 0.2708 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= 0.165 Angle : 0.611 10.719 37786 Z= 0.312 Chirality : 0.043 0.188 4447 Planarity : 0.004 0.054 4912 Dihedral : 7.868 87.324 4023 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.98 % Favored : 91.91 % Rotamer: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.97 % 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: -1.60 (0.14), residues: 3558 helix: 0.20 (0.14), residues: 1446 sheet: -1.53 (0.24), residues: 451 loop : -2.09 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 57 HIS 0.010 0.001 HIS B 43 PHE 0.027 0.001 PHE B 213 TYR 0.011 0.001 TYR g 167 ARG 0.005 0.000 ARG B 140 *********************** 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 282 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 3.310 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: A 82 MET cc_start: 0.8437 (mpp) cc_final: 0.7778 (tpp) REVERT: A 147 LEU cc_start: 0.8932 (tp) cc_final: 0.8661 (tp) REVERT: A 157 MET cc_start: 0.8700 (ptp) cc_final: 0.8470 (ptt) REVERT: A 251 MET cc_start: 0.8062 (ptp) cc_final: 0.7640 (ppp) REVERT: A 314 MET cc_start: 0.8226 (mmm) cc_final: 0.7660 (mmm) REVERT: A 376 MET cc_start: 0.9001 (ptt) cc_final: 0.8762 (ptt) REVERT: A 460 GLU cc_start: 0.8422 (tt0) cc_final: 0.8001 (mp0) REVERT: A 498 MET cc_start: 0.8797 (mtm) cc_final: 0.8165 (mtp) REVERT: B 131 GLU cc_start: 0.8680 (mp0) cc_final: 0.8423 (tp30) REVERT: B 276 LEU cc_start: 0.9196 (tp) cc_final: 0.8354 (tp) REVERT: B 355 ARG cc_start: 0.8932 (mmp-170) cc_final: 0.8136 (mmm160) REVERT: C 182 ASP cc_start: 0.7756 (m-30) cc_final: 0.7548 (m-30) REVERT: C 295 HIS cc_start: 0.8923 (m90) cc_final: 0.8678 (m90) REVERT: C 376 MET cc_start: 0.8841 (mmp) cc_final: 0.8531 (mtt) REVERT: D 44 TYR cc_start: 0.8569 (m-80) cc_final: 0.8267 (m-80) REVERT: D 183 MET cc_start: 0.8762 (mmp) cc_final: 0.8507 (mmm) REVERT: D 247 MET cc_start: 0.8501 (ttt) cc_final: 0.8142 (tpp) REVERT: D 488 MET cc_start: 0.9170 (tmm) cc_final: 0.8958 (tmm) REVERT: E 59 MET cc_start: 0.8644 (ptp) cc_final: 0.8285 (ptp) REVERT: E 79 MET cc_start: 0.9125 (mmt) cc_final: 0.8810 (mmp) REVERT: E 247 MET cc_start: 0.8579 (tpp) cc_final: 0.8329 (tpp) REVERT: E 335 THR cc_start: 0.8586 (t) cc_final: 0.7814 (t) REVERT: F 79 MET cc_start: 0.8775 (mpp) cc_final: 0.7852 (mpp) REVERT: d 250 MET cc_start: 0.4553 (mmt) cc_final: 0.3341 (mtm) REVERT: g 66 LEU cc_start: 0.8632 (mt) cc_final: 0.7954 (tt) REVERT: g 295 LEU cc_start: 0.9376 (mt) cc_final: 0.9056 (mt) REVERT: g 323 MET cc_start: 0.9408 (mmp) cc_final: 0.8902 (mmm) REVERT: g 346 GLN cc_start: 0.8350 (mm110) cc_final: 0.8012 (mt0) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.3555 time to fit residues: 165.3252 Evaluate side-chains 197 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.271 ------------------------------------------------------------------------------- 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: 8.9990 chunk 309 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 343 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** A 372 GLN B 43 HIS B 66 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8339 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27883 Z= 0.251 Angle : 0.651 10.330 37786 Z= 0.336 Chirality : 0.044 0.198 4447 Planarity : 0.004 0.053 4912 Dihedral : 7.928 91.715 4023 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.94 % Favored : 90.92 % Rotamer: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % 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: -1.51 (0.14), residues: 3558 helix: 0.30 (0.14), residues: 1436 sheet: -1.45 (0.24), residues: 449 loop : -2.06 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 15 HIS 0.009 0.001 HIS B 43 PHE 0.015 0.002 PHE F 199 TYR 0.028 0.001 TYR B 330 ARG 0.008 0.001 ARG A 366 *********************** 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 264 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 3.344 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: A 82 MET cc_start: 0.8238 (mpp) cc_final: 0.7703 (tpp) REVERT: A 147 LEU cc_start: 0.8898 (tp) cc_final: 0.8611 (tp) REVERT: A 157 MET cc_start: 0.8726 (ptp) cc_final: 0.8445 (ptt) REVERT: A 251 MET cc_start: 0.8121 (ptp) cc_final: 0.7764 (ppp) REVERT: A 314 MET cc_start: 0.8302 (mmm) cc_final: 0.7659 (mmm) REVERT: A 376 MET cc_start: 0.8990 (ptt) cc_final: 0.8747 (ptt) REVERT: A 460 GLU cc_start: 0.8572 (tt0) cc_final: 0.8066 (mp0) REVERT: A 498 MET cc_start: 0.8798 (mtm) cc_final: 0.8261 (mtp) REVERT: B 131 GLU cc_start: 0.8747 (mp0) cc_final: 0.8440 (tp30) REVERT: B 251 MET cc_start: 0.7551 (tpt) cc_final: 0.7276 (tpt) REVERT: C 219 MET cc_start: 0.8181 (mpp) cc_final: 0.7878 (mpp) REVERT: C 295 HIS cc_start: 0.8975 (m90) cc_final: 0.8677 (m90) REVERT: D 488 MET cc_start: 0.9148 (tmm) cc_final: 0.8915 (tmm) REVERT: E 32 ASP cc_start: 0.7071 (m-30) cc_final: 0.6753 (m-30) REVERT: E 79 MET cc_start: 0.9104 (mmt) cc_final: 0.8739 (mmp) REVERT: E 89 MET cc_start: 0.8233 (tpt) cc_final: 0.8019 (tpt) REVERT: E 247 MET cc_start: 0.8520 (tpp) cc_final: 0.8168 (tpp) REVERT: E 269 LEU cc_start: 0.9315 (tp) cc_final: 0.8972 (tt) REVERT: E 306 MET cc_start: 0.8688 (mmm) cc_final: 0.8287 (mmm) REVERT: E 335 THR cc_start: 0.8666 (t) cc_final: 0.8119 (t) REVERT: F 79 MET cc_start: 0.8748 (mpp) cc_final: 0.7859 (mpp) REVERT: d 250 MET cc_start: 0.4377 (mmt) cc_final: 0.3279 (mtm) REVERT: g 66 LEU cc_start: 0.8654 (mt) cc_final: 0.7950 (tt) REVERT: g 295 LEU cc_start: 0.9380 (mt) cc_final: 0.9030 (mt) REVERT: g 346 GLN cc_start: 0.8430 (mm110) cc_final: 0.7958 (mt0) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.3659 time to fit residues: 159.0519 Evaluate side-chains 190 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.419 ------------------------------------------------------------------------------- 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: 0.9990 chunk 38 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 289 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 342 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 295 HIS ** 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 434 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 141 GLN F 25 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8306 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27883 Z= 0.190 Angle : 0.640 11.227 37786 Z= 0.326 Chirality : 0.044 0.251 4447 Planarity : 0.004 0.078 4912 Dihedral : 7.833 89.700 4023 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.79 % Favored : 92.10 % Rotamer: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.96 % 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: -1.35 (0.14), residues: 3558 helix: 0.40 (0.14), residues: 1437 sheet: -1.43 (0.25), residues: 451 loop : -1.91 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 57 HIS 0.014 0.001 HIS B 43 PHE 0.027 0.001 PHE g 168 TYR 0.019 0.001 TYR D 44 ARG 0.011 0.000 ARG B 41 *********************** 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 275 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 3.236 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: A 147 LEU cc_start: 0.8920 (tp) cc_final: 0.8634 (tp) REVERT: A 157 MET cc_start: 0.8655 (ptp) cc_final: 0.8003 (mmt) REVERT: A 251 MET cc_start: 0.8168 (ptp) cc_final: 0.7884 (ppp) REVERT: A 274 MET cc_start: 0.8457 (mtt) cc_final: 0.8128 (mtt) REVERT: A 314 MET cc_start: 0.8270 (mmm) cc_final: 0.7652 (mmm) REVERT: A 343 ILE cc_start: 0.9451 (pt) cc_final: 0.9032 (mt) REVERT: A 376 MET cc_start: 0.8968 (ptt) cc_final: 0.8709 (ptt) REVERT: A 460 GLU cc_start: 0.8514 (tt0) cc_final: 0.7993 (mp0) REVERT: A 498 MET cc_start: 0.8832 (mtm) cc_final: 0.8323 (mtp) REVERT: B 131 GLU cc_start: 0.8737 (mp0) cc_final: 0.8434 (tp30) REVERT: B 285 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8389 (pm20) REVERT: C 77 MET cc_start: 0.8177 (ttp) cc_final: 0.7874 (ttm) REVERT: C 219 MET cc_start: 0.8123 (mpp) cc_final: 0.7865 (mpp) REVERT: C 251 MET cc_start: 0.8388 (tpt) cc_final: 0.8060 (tpt) REVERT: C 295 HIS cc_start: 0.8988 (m90) cc_final: 0.8658 (m90) REVERT: D 247 MET cc_start: 0.8562 (tpp) cc_final: 0.8225 (tpp) REVERT: D 343 PHE cc_start: 0.8468 (m-80) cc_final: 0.7991 (m-80) REVERT: E 32 ASP cc_start: 0.7264 (m-30) cc_final: 0.6944 (m-30) REVERT: E 59 MET cc_start: 0.8780 (ptp) cc_final: 0.8360 (ptp) REVERT: E 79 MET cc_start: 0.9086 (mmt) cc_final: 0.8817 (mmp) REVERT: E 89 MET cc_start: 0.8204 (tpt) cc_final: 0.7948 (tpt) REVERT: E 247 MET cc_start: 0.8504 (tpp) cc_final: 0.8278 (tpp) REVERT: F 167 LYS cc_start: 0.9244 (mppt) cc_final: 0.9039 (mtmt) REVERT: F 405 ILE cc_start: 0.9236 (pt) cc_final: 0.9035 (pt) REVERT: d 250 MET cc_start: 0.4493 (mmt) cc_final: 0.3224 (mtm) REVERT: g 66 LEU cc_start: 0.8594 (mt) cc_final: 0.7914 (tt) REVERT: g 101 GLN cc_start: 0.7711 (pm20) cc_final: 0.7405 (pm20) REVERT: g 295 LEU cc_start: 0.9406 (mt) cc_final: 0.9065 (mt) REVERT: g 323 MET cc_start: 0.9413 (mmp) cc_final: 0.8931 (mmm) REVERT: g 346 GLN cc_start: 0.8400 (mm110) cc_final: 0.7954 (mt0) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3804 time to fit residues: 170.9251 Evaluate side-chains 197 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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: 10.0000 chunk 136 optimal weight: 0.0370 chunk 204 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 233 optimal weight: 0.0270 chunk 169 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 66 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 67 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 95 ASN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 340 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 27883 Z= 0.158 Angle : 0.634 11.809 37786 Z= 0.323 Chirality : 0.044 0.180 4447 Planarity : 0.004 0.053 4912 Dihedral : 7.608 89.454 4023 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.67 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3558 helix: 0.43 (0.14), residues: 1439 sheet: -1.31 (0.25), residues: 451 loop : -1.91 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 57 HIS 0.012 0.001 HIS B 43 PHE 0.021 0.001 PHE E 271 TYR 0.013 0.001 TYR E 298 ARG 0.006 0.000 ARG C 14 *********************** 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 277 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.306 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: A 157 MET cc_start: 0.8515 (ptp) cc_final: 0.8169 (ptt) REVERT: A 219 MET cc_start: 0.9145 (mmm) cc_final: 0.8640 (mpp) REVERT: A 251 MET cc_start: 0.8155 (ptp) cc_final: 0.7838 (ppp) REVERT: A 274 MET cc_start: 0.8603 (mtt) cc_final: 0.8149 (mtt) REVERT: A 314 MET cc_start: 0.8233 (mmm) cc_final: 0.7630 (mmm) REVERT: A 343 ILE cc_start: 0.9442 (pt) cc_final: 0.9023 (mt) REVERT: A 376 MET cc_start: 0.8958 (ptt) cc_final: 0.8655 (ptt) REVERT: A 460 GLU cc_start: 0.8462 (tt0) cc_final: 0.7940 (mp0) REVERT: A 498 MET cc_start: 0.8885 (mtm) cc_final: 0.8358 (mtp) REVERT: B 131 GLU cc_start: 0.8692 (mp0) cc_final: 0.8371 (tp30) REVERT: B 251 MET cc_start: 0.7279 (tpt) cc_final: 0.4624 (tpt) REVERT: C 77 MET cc_start: 0.8150 (ttp) cc_final: 0.7738 (ttm) REVERT: C 182 ASP cc_start: 0.7706 (m-30) cc_final: 0.7502 (m-30) REVERT: C 251 MET cc_start: 0.8130 (tpt) cc_final: 0.7703 (tpt) REVERT: C 295 HIS cc_start: 0.8946 (m90) cc_final: 0.8646 (m90) REVERT: D 247 MET cc_start: 0.8663 (tpp) cc_final: 0.8155 (tpp) REVERT: D 374 MET cc_start: 0.8942 (mmm) cc_final: 0.8459 (mmt) REVERT: E 32 ASP cc_start: 0.7204 (m-30) cc_final: 0.6860 (m-30) REVERT: E 59 MET cc_start: 0.8732 (ptp) cc_final: 0.8268 (ptp) REVERT: E 79 MET cc_start: 0.9052 (mmt) cc_final: 0.8816 (mmp) REVERT: E 89 MET cc_start: 0.7983 (tpt) cc_final: 0.7698 (tpt) REVERT: E 247 MET cc_start: 0.8496 (tpp) cc_final: 0.8280 (tpp) REVERT: E 335 THR cc_start: 0.8785 (t) cc_final: 0.8023 (t) REVERT: F 167 LYS cc_start: 0.9199 (mppt) cc_final: 0.8900 (mtmt) REVERT: d 225 TYR cc_start: 0.8060 (p90) cc_final: 0.7821 (p90) REVERT: d 250 MET cc_start: 0.4648 (mmt) cc_final: 0.3291 (mtm) REVERT: g 66 LEU cc_start: 0.8248 (mt) cc_final: 0.7862 (tt) REVERT: g 101 GLN cc_start: 0.7668 (pm20) cc_final: 0.7337 (pm20) REVERT: g 295 LEU cc_start: 0.9387 (mt) cc_final: 0.9116 (mt) REVERT: g 323 MET cc_start: 0.9352 (mmp) cc_final: 0.8891 (mmm) REVERT: g 346 GLN cc_start: 0.8322 (mm110) cc_final: 0.7845 (mt0) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.3720 time to fit residues: 168.9497 Evaluate side-chains 207 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.245 ------------------------------------------------------------------------------- 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: 4.9990 chunk 327 optimal weight: 3.9990 chunk 299 optimal weight: 0.0030 chunk 318 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- 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 B 66 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN F 25 GLN F 188 ASN F 325 GLN ** e 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8344 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27883 Z= 0.279 Angle : 0.680 11.180 37786 Z= 0.350 Chirality : 0.044 0.191 4447 Planarity : 0.004 0.063 4912 Dihedral : 7.748 91.684 4023 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.97 % Favored : 90.92 % Rotamer: Outliers : 0.03 % Allowed : 0.75 % Favored : 99.22 % 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: -1.32 (0.14), residues: 3558 helix: 0.43 (0.14), residues: 1437 sheet: -1.37 (0.24), residues: 461 loop : -1.93 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 15 HIS 0.011 0.001 HIS B 43 PHE 0.028 0.002 PHE g 133 TYR 0.017 0.002 TYR g 167 ARG 0.009 0.001 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 254 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.933 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: A 157 MET cc_start: 0.8495 (ptp) cc_final: 0.8088 (ptt) REVERT: A 219 MET cc_start: 0.9101 (mmm) cc_final: 0.7888 (mpp) REVERT: A 274 MET cc_start: 0.8589 (mtt) cc_final: 0.8187 (mtt) REVERT: A 314 MET cc_start: 0.8328 (mmm) cc_final: 0.7673 (mmm) REVERT: A 376 MET cc_start: 0.8950 (ptt) cc_final: 0.8620 (ptt) REVERT: A 460 GLU cc_start: 0.8607 (tt0) cc_final: 0.8026 (mp0) REVERT: A 498 MET cc_start: 0.8828 (mtm) cc_final: 0.8346 (mtp) REVERT: B 131 GLU cc_start: 0.8766 (mp0) cc_final: 0.8416 (tp30) REVERT: B 251 MET cc_start: 0.7411 (tpt) cc_final: 0.5420 (tpt) REVERT: B 314 MET cc_start: 0.7194 (mmp) cc_final: 0.6209 (mmm) REVERT: B 355 ARG cc_start: 0.8901 (mmp-170) cc_final: 0.8397 (mmm160) REVERT: C 77 MET cc_start: 0.8230 (ttp) cc_final: 0.7895 (ttm) REVERT: C 251 MET cc_start: 0.8188 (tpt) cc_final: 0.7792 (tpt) REVERT: C 295 HIS cc_start: 0.9025 (m90) cc_final: 0.8719 (m90) REVERT: D 79 MET cc_start: 0.8390 (ttp) cc_final: 0.7725 (tmm) REVERT: D 247 MET cc_start: 0.8695 (tpp) cc_final: 0.8230 (tpp) REVERT: D 256 MET cc_start: 0.8974 (mmm) cc_final: 0.8725 (mmp) REVERT: E 32 ASP cc_start: 0.7218 (m-30) cc_final: 0.6930 (m-30) REVERT: E 59 MET cc_start: 0.8728 (ptp) cc_final: 0.8232 (ptp) REVERT: E 79 MET cc_start: 0.9042 (mmt) cc_final: 0.8656 (mmp) REVERT: E 89 MET cc_start: 0.8222 (tpt) cc_final: 0.7903 (tpt) REVERT: E 247 MET cc_start: 0.8493 (tpp) cc_final: 0.8271 (tpp) REVERT: E 269 LEU cc_start: 0.9270 (tp) cc_final: 0.9036 (tt) REVERT: F 167 LYS cc_start: 0.9095 (mppt) cc_final: 0.8865 (mtmt) REVERT: d 225 TYR cc_start: 0.8194 (p90) cc_final: 0.7961 (p90) REVERT: d 250 MET cc_start: 0.4039 (mmt) cc_final: 0.2949 (mtm) REVERT: g 66 LEU cc_start: 0.8560 (mt) cc_final: 0.7880 (tt) REVERT: g 101 GLN cc_start: 0.7741 (pm20) cc_final: 0.7393 (pm20) REVERT: g 284 PHE cc_start: 0.8346 (m-10) cc_final: 0.8069 (m-10) REVERT: g 295 LEU cc_start: 0.9401 (mt) cc_final: 0.9063 (mt) REVERT: g 323 MET cc_start: 0.9428 (mmp) cc_final: 0.9010 (mmm) REVERT: g 346 GLN cc_start: 0.8300 (mm110) cc_final: 0.7918 (mt0) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.3611 time to fit residues: 153.0266 Evaluate side-chains 199 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.163 ------------------------------------------------------------------------------- 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: 10.0000 chunk 337 optimal weight: 0.1980 chunk 205 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 353 optimal weight: 1.9990 chunk 325 optimal weight: 0.3980 chunk 281 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 217 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 273 GLN A 372 GLN B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN D 67 GLN ** 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 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: 0.8283 moved from start: 0.3365 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= 0.170 Angle : 0.655 17.283 37786 Z= 0.329 Chirality : 0.044 0.184 4447 Planarity : 0.004 0.055 4912 Dihedral : 7.634 87.581 4023 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -1.16 (0.14), residues: 3558 helix: 0.54 (0.14), residues: 1435 sheet: -1.24 (0.25), residues: 447 loop : -1.82 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 PHE 0.034 0.002 PHE g 133 TYR 0.028 0.001 TYR C 241 ARG 0.005 0.000 ARG E 378 ********************** 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 269 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.074 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: A 157 MET cc_start: 0.8443 (ptp) cc_final: 0.8036 (ptt) REVERT: A 219 MET cc_start: 0.9158 (mmm) cc_final: 0.7928 (mpp) REVERT: A 251 MET cc_start: 0.7203 (ppp) cc_final: 0.6938 (ppp) REVERT: A 314 MET cc_start: 0.7970 (mmm) cc_final: 0.7635 (mmm) REVERT: A 338 ILE cc_start: 0.8967 (mm) cc_final: 0.8597 (mm) REVERT: A 376 MET cc_start: 0.9004 (ptt) cc_final: 0.8759 (ptt) REVERT: A 498 MET cc_start: 0.8803 (mtm) cc_final: 0.8281 (mtp) REVERT: B 131 GLU cc_start: 0.8738 (mp0) cc_final: 0.8405 (tp30) REVERT: B 251 MET cc_start: 0.7560 (tpt) cc_final: 0.5910 (tpt) REVERT: B 314 MET cc_start: 0.7559 (mmp) cc_final: 0.6524 (mmm) REVERT: C 77 MET cc_start: 0.8261 (ttp) cc_final: 0.7900 (ttm) REVERT: C 251 MET cc_start: 0.8142 (tpt) cc_final: 0.7728 (tpt) REVERT: C 274 MET cc_start: 0.8810 (ptp) cc_final: 0.8468 (ptm) REVERT: D 247 MET cc_start: 0.8686 (tpp) cc_final: 0.8183 (tpp) REVERT: D 256 MET cc_start: 0.8953 (mmm) cc_final: 0.8658 (mmp) REVERT: D 343 PHE cc_start: 0.8276 (m-10) cc_final: 0.8009 (m-80) REVERT: D 374 MET cc_start: 0.8851 (mmm) cc_final: 0.8316 (mmt) REVERT: E 32 ASP cc_start: 0.7149 (m-30) cc_final: 0.6822 (m-30) REVERT: E 214 MET cc_start: 0.9004 (mpp) cc_final: 0.8484 (mpp) REVERT: E 239 MET cc_start: 0.8583 (mmm) cc_final: 0.8157 (mmp) REVERT: E 247 MET cc_start: 0.8468 (tpp) cc_final: 0.8241 (tpp) REVERT: E 269 LEU cc_start: 0.9301 (tp) cc_final: 0.9063 (tt) REVERT: E 335 THR cc_start: 0.8832 (t) cc_final: 0.8029 (t) REVERT: E 374 MET cc_start: 0.8316 (mmm) cc_final: 0.8039 (mmm) REVERT: F 167 LYS cc_start: 0.9032 (mppt) cc_final: 0.8773 (mtmt) REVERT: F 405 ILE cc_start: 0.9226 (pt) cc_final: 0.9021 (pt) REVERT: d 225 TYR cc_start: 0.8139 (p90) cc_final: 0.7932 (p90) REVERT: d 250 MET cc_start: 0.4450 (mmt) cc_final: 0.3117 (mtm) REVERT: g 66 LEU cc_start: 0.8539 (mt) cc_final: 0.7913 (tt) REVERT: g 101 GLN cc_start: 0.7674 (pm20) cc_final: 0.7333 (pm20) REVERT: g 284 PHE cc_start: 0.8300 (m-10) cc_final: 0.8025 (m-10) REVERT: g 295 LEU cc_start: 0.9391 (mt) cc_final: 0.9055 (mt) REVERT: g 323 MET cc_start: 0.9357 (mmp) cc_final: 0.8948 (mmm) REVERT: g 346 GLN cc_start: 0.8357 (mm110) cc_final: 0.7952 (mt0) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3609 time to fit residues: 161.3894 Evaluate side-chains 206 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.902 ------------------------------------------------------------------------------- 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: 0.2980 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 282 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 289 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 164 GLN C 334 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** 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 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.042627 restraints weight = 190014.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.043928 restraints weight = 117955.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044895 restraints weight = 81598.355| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27883 Z= 0.159 Angle : 0.644 13.331 37786 Z= 0.326 Chirality : 0.044 0.171 4447 Planarity : 0.004 0.054 4912 Dihedral : 7.463 86.789 4023 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3558 helix: 0.57 (0.14), residues: 1439 sheet: -1.29 (0.24), residues: 463 loop : -1.80 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 PHE 0.022 0.001 PHE A 501 TYR 0.017 0.001 TYR D 298 ARG 0.007 0.000 ARG A 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4752.83 seconds wall clock time: 88 minutes 51.41 seconds (5331.41 seconds total)