Starting phenix.real_space_refine on Tue Feb 20 09:39:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/02_2024/6voi_21265_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/02_2024/6voi_21265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/02_2024/6voi_21265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/02_2024/6voi_21265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/02_2024/6voi_21265_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/02_2024/6voi_21265_updated.pdb" } resolution = 4.03 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= 0.003 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 105 5.16 5 C 17265 2.51 5 N 4745 2.21 5 O 5368 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 GLU 52": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D ASP 467": "OD1" <-> "OD2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E ARG 277": "NH1" <-> "NH2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E GLU 416": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 453": "OE1" <-> "OE2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 481": "OD1" <-> "OD2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 273": "OD1" <-> "OD2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F ASP 347": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F GLU 416": "OE1" <-> "OE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ASP 154": "OD1" <-> "OD2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 208": "OD1" <-> "OD2" Residue "g GLU 283": "OE1" <-> "OE2" Residue "g ASP 293": "OD1" <-> "OD2" Residue "g TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ASP 80": "OD1" <-> "OD2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27497 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: "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: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} 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: "g" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2508 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} 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: "A" 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: "B" 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: 14.94, per 1000 atoms: 0.54 Number of scatterers: 27497 At special positions: 0 Unit cell: (131.04, 145.6, 137.28, 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 105 16.00 P 14 15.00 O 5368 8.00 N 4745 7.00 C 17265 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.44 Conformation dependent library (CDL) restraints added in 5.4 seconds 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 23 sheets defined 40.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 4.396A pdb=" N ILE A 12 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.766A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 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 removed outlier: 3.821A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.569A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (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 291 through 299 Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 368 through 371 removed outlier: 3.575A pdb=" N ALA A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.859A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.916A pdb=" N ALA A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.220A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 448 No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.839A pdb=" N SER A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 504 removed outlier: 3.881A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.623A pdb=" N ILE C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) 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 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 221 removed outlier: 3.891A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 221' 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 291 through 299 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 374 through 394 removed outlier: 4.386A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.732A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 442 removed outlier: 4.200A pdb=" N MET C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 484 through 503 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.872A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 233 through 251 Proline residue: B 240 - end of helix removed outlier: 3.938A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 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 299 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' 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 376 through 395 Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'B' and resid 431 through 442 removed outlier: 3.840A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 4.087A pdb=" N VAL B 454 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG B 455 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 459 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 465 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.682A 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 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 249 through 263 removed outlier: 3.875A 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 305 through 312 removed outlier: 4.010A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.164A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 377 through 405 removed outlier: 6.964A pdb=" N GLU D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N GLU D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N HIS D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.039A 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 451 through 462 removed outlier: 4.186A pdb=" N ARG D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 474 No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 480 through 493 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: 3.520A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 300 through 310 removed outlier: 4.565A pdb=" N SER E 303 " --> pdb=" O PRO E 300 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR E 304 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 306 " --> pdb=" O SER E 303 " (cutoff:3.500A) 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 343 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' 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 401 Processing helix chain 'E' and resid 409 through 412 No H-bonds generated for 'chain 'E' and resid 409 through 412' Processing helix chain 'E' and resid 418 through 430 Processing helix chain 'E' and resid 451 through 463 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 494 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 180 through 192 removed outlier: 4.988A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' 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 Processing helix chain 'F' and resid 275 through 289 removed outlier: 4.853A pdb=" N ALA F 281 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 310 removed outlier: 4.657A pdb=" N SER F 303 " --> pdb=" O PRO F 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR F 304 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 305 " --> pdb=" O LEU F 302 " (cutoff:3.500A) 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 340 No H-bonds generated for 'chain 'F' and resid 337 through 340' Processing helix chain 'F' and resid 342 through 345 No H-bonds generated for 'chain 'F' and resid 342 through 345' Processing helix chain 'F' and resid 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 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 382 through 408 removed outlier: 4.750A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 417 through 430 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.565A pdb=" N LEU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 474 Processing helix chain 'F' and resid 480 through 495 removed outlier: 3.776A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 88 Processing helix chain 'd' and resid 92 through 106 Processing helix chain 'd' and resid 109 through 115 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 155 through 173 removed outlier: 5.479A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE d 169 " --> pdb=" O GLU d 166 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 237 through 248 Processing helix chain 'g' and resid 44 through 99 Proline residue: g 84 - end of helix removed outlier: 3.691A pdb=" N TYR g 94 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 110 No H-bonds generated for 'chain 'g' and resid 108 through 110' Processing helix chain 'g' and resid 133 through 150 Processing helix chain 'g' and resid 162 through 168 Processing helix chain 'g' and resid 188 through 203 Processing helix chain 'g' and resid 288 through 361 removed outlier: 4.522A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 3.736A pdb=" N SER g 311 " --> pdb=" O ALA g 307 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN g 361 " --> pdb=" O VAL g 357 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 103 Processing helix chain 'e' and resid 108 through 130 removed outlier: 3.909A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 43 removed outlier: 6.674A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 194 through 198 removed outlier: 6.697A pdb=" N LEU A 258 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 197 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE A 260 " --> pdb=" O VAL A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 31 through 35 removed outlier: 6.655A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.084A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 317 through 321 removed outlier: 7.049A pdb=" N GLU C 166 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL C 320 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 168 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE C 343 " --> pdb=" O ILE C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= G, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= H, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= I, first strand: chain 'B' and resid 52 through 54 removed outlier: 4.239A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= K, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.677A pdb=" N LEU B 258 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER B 313 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 259 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR B 315 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 22 through 27 removed outlier: 6.556A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 92 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'E' and resid 25 through 27 removed outlier: 6.660A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 197 through 200 removed outlier: 6.111A pdb=" N LEU E 269 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY E 200 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE E 271 " --> pdb=" O GLY E 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.934A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 167 through 169 removed outlier: 7.301A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL F 268 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE F 324 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 200 through 202 removed outlier: 7.201A pdb=" N VAL F 235 " --> pdb=" O GLY F 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'd' and resid 180 through 182 Processing sheet with id= T, first strand: chain 'g' and resid 119 through 122 removed outlier: 6.132A pdb=" N THR g 156 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL g 122 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE g 158 " --> pdb=" O VAL g 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.555A pdb=" N THR g 265 " --> pdb=" O THR g 258 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'e' and resid 67 through 69 removed outlier: 6.078A pdb=" N ASN e 4 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE e 76 " --> pdb=" O ASN e 4 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS e 6 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL e 7 " --> pdb=" O TRP e 15 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR e 9 " --> pdb=" O SER e 13 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER e 13 " --> pdb=" O THR e 9 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'e' and resid 21 through 23 removed outlier: 3.565A pdb=" N GLU e 21 " --> pdb=" O ARG e 52 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG e 50 " --> pdb=" O ILE e 23 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2691 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: 8.21 Time building geometry restraints manager: 12.12 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: 9313 1.34 - 1.46: 5491 1.46 - 1.58: 12854 1.58 - 1.71: 23 1.71 - 1.83: 198 Bond restraints: 27879 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.65e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.26e+01 ... (remaining 27874 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.85: 526 104.85 - 112.67: 14990 112.67 - 120.49: 11971 120.49 - 128.31: 10212 128.31 - 136.13: 82 Bond angle restraints: 37781 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.30 22.57 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.15 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 121.51 18.36 1.00e+00 1.00e+00 3.37e+02 ... (remaining 37776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.14: 16290 27.14 - 54.29: 805 54.29 - 81.43: 67 81.43 - 108.57: 14 108.57 - 135.71: 3 Dihedral angle restraints: 17179 sinusoidal: 6940 harmonic: 10239 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 -130.96 -49.04 0 5.00e+00 4.00e-02 9.62e+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 -133.84 -46.16 0 5.00e+00 4.00e-02 8.52e+01 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 -139.18 -40.82 0 5.00e+00 4.00e-02 6.67e+01 ... (remaining 17176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3461 0.054 - 0.108: 835 0.108 - 0.161: 130 0.161 - 0.215: 16 0.215 - 0.269: 4 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CB ILE g 239 " pdb=" CA ILE g 239 " pdb=" CG1 ILE g 239 " pdb=" CG2 ILE g 239 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE e 31 " pdb=" CA ILE e 31 " pdb=" CG1 ILE e 31 " pdb=" CG2 ILE e 31 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE e 69 " pdb=" CA ILE e 69 " pdb=" CG1 ILE e 69 " pdb=" CG2 ILE e 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4443 not shown) Planarity restraints: 4912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C LYS B 176 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG g 83 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO g 84 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO g 84 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO g 84 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 241 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO D 242 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 242 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 242 " 0.033 5.00e-02 4.00e+02 ... (remaining 4909 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 807 2.69 - 3.25: 29365 3.25 - 3.80: 44818 3.80 - 4.35: 58955 4.35 - 4.90: 96956 Nonbonded interactions: 230901 Sorted by model distance: nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.142 2.520 nonbonded pdb=" O ILE A 193 " pdb=" OG1 THR A 257 " model vdw 2.153 2.440 nonbonded pdb=" O LEU A 53 " pdb=" OG1 THR A 92 " model vdw 2.159 2.440 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.199 2.520 nonbonded pdb=" OG1 THR d 181 " pdb=" OG1 THR d 222 " model vdw 2.203 2.440 ... (remaining 230896 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: 2.820 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: 11.170 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 73.070 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 27879 Z= 0.336 Angle : 0.946 22.569 37781 Z= 0.602 Chirality : 0.048 0.269 4446 Planarity : 0.005 0.063 4912 Dihedral : 15.346 135.715 10604 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.73 % Favored : 91.96 % Rotamer: Outliers : 0.24 % Allowed : 7.68 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.86 (0.12), residues: 3557 helix: -1.75 (0.11), residues: 1421 sheet: -3.82 (0.18), residues: 451 loop : -2.90 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 15 HIS 0.004 0.001 HIS F 345 PHE 0.019 0.002 PHE B 472 TYR 0.013 0.001 TYR g 94 ARG 0.022 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 752 time to evaluate : 3.270 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 131 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 191 ASN cc_start: 0.7230 (t0) cc_final: 0.6834 (t0) REVERT: A 237 TYR cc_start: 0.8916 (t80) cc_final: 0.8713 (t80) REVERT: A 389 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8405 (tm-30) REVERT: C 14 ARG cc_start: 0.5852 (mmm160) cc_final: 0.5234 (mpt-90) REVERT: C 237 TYR cc_start: 0.8766 (t80) cc_final: 0.8528 (t80) REVERT: C 251 MET cc_start: 0.7923 (ttp) cc_final: 0.7510 (ttp) REVERT: C 300 GLU cc_start: 0.8592 (tt0) cc_final: 0.8382 (tp30) REVERT: C 314 MET cc_start: 0.8597 (ttp) cc_final: 0.8374 (ttt) REVERT: C 348 ASP cc_start: 0.7481 (m-30) cc_final: 0.6956 (m-30) REVERT: C 449 LEU cc_start: 0.7993 (mt) cc_final: 0.7690 (tp) REVERT: B 110 ASN cc_start: 0.8522 (t0) cc_final: 0.8224 (t0) REVERT: B 157 MET cc_start: 0.7650 (mpp) cc_final: 0.7324 (mpp) REVERT: B 164 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 422 LYS cc_start: 0.7436 (pttp) cc_final: 0.7058 (ptmt) REVERT: B 489 LEU cc_start: 0.6955 (pp) cc_final: 0.6638 (pp) REVERT: B 495 GLN cc_start: 0.5786 (mm110) cc_final: 0.5583 (tm-30) REVERT: D 79 MET cc_start: 0.8966 (mmp) cc_final: 0.8256 (mmm) REVERT: D 121 LEU cc_start: 0.8598 (pp) cc_final: 0.7917 (pt) REVERT: D 178 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7618 (ttpp) REVERT: D 256 MET cc_start: 0.8153 (ttm) cc_final: 0.7709 (mtt) REVERT: D 283 SER cc_start: 0.8492 (t) cc_final: 0.8091 (p) REVERT: E 20 LEU cc_start: 0.7291 (mt) cc_final: 0.6940 (tt) REVERT: E 39 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7786 (mmmm) REVERT: E 64 GLU cc_start: 0.8248 (pp20) cc_final: 0.7816 (pp20) REVERT: E 89 MET cc_start: 0.8639 (mtt) cc_final: 0.8164 (mtp) REVERT: E 155 VAL cc_start: 0.9199 (t) cc_final: 0.8996 (t) REVERT: E 191 LYS cc_start: 0.8361 (tptm) cc_final: 0.8122 (ttpt) REVERT: E 206 THR cc_start: 0.8679 (m) cc_final: 0.7904 (m) REVERT: E 214 MET cc_start: 0.7840 (mmt) cc_final: 0.7278 (tpp) REVERT: E 218 GLU cc_start: 0.6611 (pt0) cc_final: 0.6285 (pt0) REVERT: E 238 GLN cc_start: 0.7035 (mt0) cc_final: 0.6536 (mp10) REVERT: E 306 MET cc_start: 0.8478 (tmm) cc_final: 0.7235 (tmm) REVERT: E 310 GLN cc_start: 0.8005 (mt0) cc_final: 0.7620 (mt0) REVERT: E 313 ILE cc_start: 0.8542 (mm) cc_final: 0.8221 (mt) REVERT: F 63 CYS cc_start: 0.8227 (m) cc_final: 0.7905 (m) REVERT: F 184 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6679 (tm-30) REVERT: F 386 GLU cc_start: 0.7870 (tp30) cc_final: 0.7650 (tp30) REVERT: F 399 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7934 (ttmm) REVERT: d 72 ASP cc_start: 0.6324 (m-30) cc_final: 0.6064 (m-30) REVERT: d 92 LEU cc_start: 0.5172 (tp) cc_final: 0.4858 (pt) REVERT: d 169 PHE cc_start: 0.7366 (t80) cc_final: 0.7087 (t80) REVERT: d 171 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8340 (ttmm) REVERT: d 208 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7717 (ttp-110) REVERT: d 239 LYS cc_start: 0.5689 (mttt) cc_final: 0.4945 (ttpt) REVERT: g 100 LEU cc_start: 0.7092 (pp) cc_final: 0.6828 (pp) REVERT: g 136 MET cc_start: 0.8050 (tpt) cc_final: 0.7603 (ttp) REVERT: g 139 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6494 (mptt) REVERT: g 144 ARG cc_start: 0.6377 (mmm160) cc_final: 0.5665 (tpp80) REVERT: g 263 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7198 (ttmt) REVERT: e 20 LYS cc_start: 0.6083 (tptp) cc_final: 0.5697 (ttpt) REVERT: e 37 HIS cc_start: 0.7308 (t-90) cc_final: 0.6910 (t-90) REVERT: e 63 MET cc_start: 0.4653 (mmm) cc_final: 0.4279 (mmp) REVERT: e 91 GLU cc_start: 0.6898 (tp30) cc_final: 0.5947 (pm20) outliers start: 7 outliers final: 3 residues processed: 757 average time/residue: 0.4355 time to fit residues: 501.6027 Evaluate side-chains 523 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 520 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 0.9990 chunk 269 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 173 GLN B 188 GLN B 201 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN F 67 GLN ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27879 Z= 0.266 Angle : 0.690 9.389 37781 Z= 0.353 Chirality : 0.046 0.240 4446 Planarity : 0.005 0.069 4912 Dihedral : 8.749 122.883 4022 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.52 % Favored : 91.17 % Rotamer: Outliers : 0.10 % Allowed : 6.46 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.13), residues: 3557 helix: -0.60 (0.13), residues: 1405 sheet: -3.40 (0.20), residues: 450 loop : -2.39 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 15 HIS 0.004 0.001 HIS F 345 PHE 0.030 0.002 PHE B 292 TYR 0.015 0.002 TYR g 94 ARG 0.007 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 638 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7658 (m) cc_final: 0.7449 (m) REVERT: A 52 GLU cc_start: 0.8292 (tt0) cc_final: 0.8044 (tt0) REVERT: A 131 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 191 ASN cc_start: 0.7174 (t0) cc_final: 0.6770 (t0) REVERT: A 447 ASP cc_start: 0.7334 (t0) cc_final: 0.6862 (t0) REVERT: C 14 ARG cc_start: 0.5698 (mmm160) cc_final: 0.5146 (mpt-90) REVERT: C 49 MET cc_start: 0.8367 (mtm) cc_final: 0.8138 (mtt) REVERT: C 52 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7973 (mt-10) REVERT: C 251 MET cc_start: 0.7920 (ttp) cc_final: 0.7513 (ttp) REVERT: C 348 ASP cc_start: 0.7527 (m-30) cc_final: 0.6958 (m-30) REVERT: B 110 ASN cc_start: 0.8481 (t0) cc_final: 0.8248 (p0) REVERT: B 157 MET cc_start: 0.7535 (mpp) cc_final: 0.7307 (mpp) REVERT: B 164 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 259 ILE cc_start: 0.9217 (tt) cc_final: 0.8977 (tt) REVERT: B 285 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 422 LYS cc_start: 0.7249 (pttp) cc_final: 0.7047 (ptmt) REVERT: D 83 ASP cc_start: 0.7532 (m-30) cc_final: 0.7272 (m-30) REVERT: D 121 LEU cc_start: 0.8705 (pp) cc_final: 0.8432 (pp) REVERT: D 247 MET cc_start: 0.8156 (ttp) cc_final: 0.7766 (ttp) REVERT: D 283 SER cc_start: 0.8393 (t) cc_final: 0.8045 (p) REVERT: E 20 LEU cc_start: 0.7210 (mt) cc_final: 0.6873 (tp) REVERT: E 39 LYS cc_start: 0.8396 (mmtm) cc_final: 0.7880 (mmmm) REVERT: E 64 GLU cc_start: 0.8389 (pp20) cc_final: 0.8090 (pp20) REVERT: E 89 MET cc_start: 0.8596 (mtt) cc_final: 0.8179 (mtp) REVERT: E 147 SER cc_start: 0.7738 (m) cc_final: 0.7533 (t) REVERT: E 155 VAL cc_start: 0.9151 (t) cc_final: 0.8855 (t) REVERT: E 191 LYS cc_start: 0.8323 (tptm) cc_final: 0.8066 (ttpt) REVERT: E 206 THR cc_start: 0.8565 (m) cc_final: 0.7896 (m) REVERT: E 238 GLN cc_start: 0.6948 (mt0) cc_final: 0.6581 (mp10) REVERT: E 247 MET cc_start: 0.8230 (ttp) cc_final: 0.7873 (ttp) REVERT: E 306 MET cc_start: 0.8166 (tmm) cc_final: 0.7514 (tmm) REVERT: E 310 GLN cc_start: 0.8107 (mt0) cc_final: 0.7891 (mt0) REVERT: E 313 ILE cc_start: 0.8526 (mm) cc_final: 0.8189 (mt) REVERT: E 488 MET cc_start: 0.7268 (ppp) cc_final: 0.6418 (ppp) REVERT: F 71 ASN cc_start: 0.7706 (t0) cc_final: 0.7440 (t0) REVERT: F 127 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7352 (mtm180) REVERT: F 184 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6720 (tm-30) REVERT: F 216 MET cc_start: 0.8008 (mmp) cc_final: 0.7448 (mmm) REVERT: F 399 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7848 (ttmm) REVERT: F 475 TYR cc_start: 0.8745 (t80) cc_final: 0.8471 (t80) REVERT: d 92 LEU cc_start: 0.5080 (tp) cc_final: 0.4792 (pt) REVERT: d 239 LYS cc_start: 0.5530 (mttt) cc_final: 0.4817 (ttpt) REVERT: g 121 MET cc_start: 0.7898 (ppp) cc_final: 0.7653 (ppp) REVERT: g 136 MET cc_start: 0.8030 (tpt) cc_final: 0.7655 (ttp) REVERT: g 139 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6489 (mptt) REVERT: g 155 TYR cc_start: 0.6223 (p90) cc_final: 0.5778 (p90) REVERT: g 187 THR cc_start: 0.7224 (m) cc_final: 0.6963 (p) REVERT: e 3 LEU cc_start: 0.5571 (mp) cc_final: 0.5348 (mt) REVERT: e 37 HIS cc_start: 0.7258 (t-90) cc_final: 0.6878 (t-90) outliers start: 3 outliers final: 1 residues processed: 640 average time/residue: 0.3963 time to fit residues: 401.8978 Evaluate side-chains 509 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 508 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 268 optimal weight: 0.2980 chunk 219 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 287 optimal weight: 0.0020 chunk 320 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 201 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 148 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27879 Z= 0.254 Angle : 0.674 10.051 37781 Z= 0.340 Chirality : 0.045 0.242 4446 Planarity : 0.005 0.059 4912 Dihedral : 8.585 119.687 4022 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.24 % Favored : 91.45 % Rotamer: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 3557 helix: -0.19 (0.13), residues: 1411 sheet: -3.25 (0.20), residues: 445 loop : -2.17 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 57 HIS 0.012 0.002 HIS g 228 PHE 0.024 0.001 PHE B 292 TYR 0.039 0.002 TYR A 445 ARG 0.008 0.000 ARG g 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 634 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8234 (tt0) cc_final: 0.7833 (tt0) REVERT: A 107 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7478 (mmt-90) REVERT: A 191 ASN cc_start: 0.7156 (t0) cc_final: 0.6812 (t0) REVERT: A 215 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6696 (pt0) REVERT: A 413 ARG cc_start: 0.7021 (tpp80) cc_final: 0.6689 (tpp80) REVERT: A 447 ASP cc_start: 0.7261 (t0) cc_final: 0.6676 (t0) REVERT: C 14 ARG cc_start: 0.5637 (mmm160) cc_final: 0.5059 (mpt-90) REVERT: C 68 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7049 (mt-10) REVERT: C 251 MET cc_start: 0.7965 (ttp) cc_final: 0.7480 (ttp) REVERT: C 314 MET cc_start: 0.8690 (ttt) cc_final: 0.8343 (ttt) REVERT: C 348 ASP cc_start: 0.7561 (m-30) cc_final: 0.6986 (m-30) REVERT: C 386 GLU cc_start: 0.7817 (tp30) cc_final: 0.7174 (tt0) REVERT: C 451 LEU cc_start: 0.7886 (mt) cc_final: 0.7685 (mt) REVERT: B 157 MET cc_start: 0.7459 (mpp) cc_final: 0.7140 (mpp) REVERT: B 164 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8271 (tm-30) REVERT: B 422 LYS cc_start: 0.7242 (pttp) cc_final: 0.6990 (ptmt) REVERT: D 25 GLN cc_start: 0.8068 (tt0) cc_final: 0.7699 (tt0) REVERT: D 83 ASP cc_start: 0.7616 (m-30) cc_final: 0.7363 (m-30) REVERT: D 157 ASP cc_start: 0.8919 (t70) cc_final: 0.8440 (t70) REVERT: D 247 MET cc_start: 0.8062 (ttp) cc_final: 0.7705 (ttp) REVERT: D 283 SER cc_start: 0.8364 (t) cc_final: 0.8017 (p) REVERT: D 451 LEU cc_start: 0.6610 (tp) cc_final: 0.6205 (tp) REVERT: E 20 LEU cc_start: 0.7102 (mt) cc_final: 0.6772 (tp) REVERT: E 39 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7827 (mmmm) REVERT: E 64 GLU cc_start: 0.8306 (pp20) cc_final: 0.7688 (pp20) REVERT: E 89 MET cc_start: 0.8666 (mtt) cc_final: 0.8214 (mtp) REVERT: E 191 LYS cc_start: 0.8370 (tptm) cc_final: 0.8075 (ttpt) REVERT: E 206 THR cc_start: 0.8496 (m) cc_final: 0.7881 (m) REVERT: E 218 GLU cc_start: 0.6586 (pt0) cc_final: 0.6379 (pt0) REVERT: E 238 GLN cc_start: 0.6922 (mt0) cc_final: 0.6524 (mp10) REVERT: E 247 MET cc_start: 0.8347 (ttp) cc_final: 0.8080 (ttp) REVERT: E 306 MET cc_start: 0.8241 (tmm) cc_final: 0.7604 (tmm) REVERT: E 313 ILE cc_start: 0.8565 (mm) cc_final: 0.8239 (mt) REVERT: E 488 MET cc_start: 0.6972 (ppp) cc_final: 0.6770 (ppp) REVERT: F 71 ASN cc_start: 0.7706 (t0) cc_final: 0.7433 (t0) REVERT: F 86 THR cc_start: 0.7497 (m) cc_final: 0.7264 (m) REVERT: F 89 MET cc_start: 0.8302 (mtm) cc_final: 0.8017 (mtt) REVERT: F 184 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6883 (tm-30) REVERT: F 216 MET cc_start: 0.8086 (mmp) cc_final: 0.7448 (mmm) REVERT: F 399 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7837 (ttmm) REVERT: d 96 ASN cc_start: 0.8102 (t0) cc_final: 0.7783 (t0) REVERT: d 239 LYS cc_start: 0.5617 (mttt) cc_final: 0.4936 (ttpt) REVERT: g 136 MET cc_start: 0.8009 (tpt) cc_final: 0.7690 (ttp) REVERT: g 139 LYS cc_start: 0.7176 (ttpt) cc_final: 0.6442 (mptt) REVERT: g 187 THR cc_start: 0.7136 (m) cc_final: 0.6886 (p) REVERT: e 37 HIS cc_start: 0.7227 (t-90) cc_final: 0.6844 (t-90) REVERT: e 63 MET cc_start: 0.5038 (mmm) cc_final: 0.4608 (mmm) outliers start: 2 outliers final: 1 residues processed: 636 average time/residue: 0.3962 time to fit residues: 404.1519 Evaluate side-chains 480 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 479 time to evaluate : 2.988 ------------------------------------------------------------------------------- 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: 0.8980 chunk 242 optimal weight: 0.0670 chunk 167 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 216 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 92 optimal weight: 0.0270 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN e 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27879 Z= 0.200 Angle : 0.650 10.554 37781 Z= 0.326 Chirality : 0.044 0.258 4446 Planarity : 0.004 0.072 4912 Dihedral : 8.338 115.815 4022 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.93 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3557 helix: 0.17 (0.14), residues: 1404 sheet: -3.08 (0.22), residues: 434 loop : -1.94 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 PHE 0.023 0.001 PHE B 292 TYR 0.024 0.001 TYR A 445 ARG 0.010 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8341 (tt0) cc_final: 0.7996 (tt0) REVERT: A 191 ASN cc_start: 0.7070 (t0) cc_final: 0.6789 (t0) REVERT: A 215 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6781 (pt0) REVERT: A 413 ARG cc_start: 0.6935 (tpp80) cc_final: 0.6626 (tpp80) REVERT: A 447 ASP cc_start: 0.7140 (t0) cc_final: 0.6534 (t0) REVERT: C 14 ARG cc_start: 0.5640 (mmm160) cc_final: 0.5035 (mpt-90) REVERT: C 65 LEU cc_start: 0.9247 (mp) cc_final: 0.8884 (mt) REVERT: C 157 MET cc_start: 0.6298 (ptm) cc_final: 0.6081 (ptm) REVERT: C 251 MET cc_start: 0.7790 (ttp) cc_final: 0.7279 (ttp) REVERT: C 314 MET cc_start: 0.8618 (ttt) cc_final: 0.8233 (ttt) REVERT: C 348 ASP cc_start: 0.7491 (m-30) cc_final: 0.6971 (m-30) REVERT: C 386 GLU cc_start: 0.7802 (tp30) cc_final: 0.7192 (tt0) REVERT: C 451 LEU cc_start: 0.7996 (mt) cc_final: 0.7670 (mt) REVERT: C 456 LYS cc_start: 0.8322 (pttt) cc_final: 0.8099 (pttm) REVERT: B 157 MET cc_start: 0.7354 (mpp) cc_final: 0.7074 (mpp) REVERT: B 164 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 259 ILE cc_start: 0.9181 (tt) cc_final: 0.8959 (tt) REVERT: B 422 LYS cc_start: 0.7157 (pttp) cc_final: 0.6896 (ptmt) REVERT: D 25 GLN cc_start: 0.8030 (tt0) cc_final: 0.7677 (tt0) REVERT: D 83 ASP cc_start: 0.7649 (m-30) cc_final: 0.7415 (m-30) REVERT: D 157 ASP cc_start: 0.8896 (t70) cc_final: 0.8389 (t70) REVERT: D 247 MET cc_start: 0.7964 (ttp) cc_final: 0.7548 (ttp) REVERT: D 259 TYR cc_start: 0.8972 (t80) cc_final: 0.8717 (t80) REVERT: D 283 SER cc_start: 0.8314 (t) cc_final: 0.8068 (p) REVERT: D 306 MET cc_start: 0.8256 (tpp) cc_final: 0.7924 (tpt) REVERT: D 451 LEU cc_start: 0.6670 (tp) cc_final: 0.6302 (tp) REVERT: E 20 LEU cc_start: 0.6992 (mt) cc_final: 0.6719 (tp) REVERT: E 39 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7808 (mmmm) REVERT: E 191 LYS cc_start: 0.8336 (tptm) cc_final: 0.8063 (ttpt) REVERT: E 206 THR cc_start: 0.8410 (m) cc_final: 0.7865 (m) REVERT: E 238 GLN cc_start: 0.6752 (mt0) cc_final: 0.6375 (mp10) REVERT: E 247 MET cc_start: 0.8271 (ttp) cc_final: 0.8021 (ttp) REVERT: E 273 ASP cc_start: 0.8417 (t0) cc_final: 0.8082 (t70) REVERT: E 306 MET cc_start: 0.8106 (tmm) cc_final: 0.7422 (tmm) REVERT: E 313 ILE cc_start: 0.8448 (mm) cc_final: 0.8193 (mt) REVERT: F 43 ILE cc_start: 0.8840 (mt) cc_final: 0.8632 (mt) REVERT: F 63 CYS cc_start: 0.8605 (m) cc_final: 0.8395 (m) REVERT: F 71 ASN cc_start: 0.7795 (t0) cc_final: 0.7486 (t0) REVERT: F 184 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6967 (tm-30) REVERT: F 216 MET cc_start: 0.8168 (mmp) cc_final: 0.7512 (mmm) REVERT: F 399 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7796 (ttmm) REVERT: d 239 LYS cc_start: 0.5534 (mttt) cc_final: 0.4573 (ttpt) REVERT: g 136 MET cc_start: 0.7994 (tpt) cc_final: 0.7696 (ttp) REVERT: g 139 LYS cc_start: 0.7057 (ttpt) cc_final: 0.6239 (mptt) REVERT: g 187 THR cc_start: 0.7281 (m) cc_final: 0.6948 (p) REVERT: g 315 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6876 (tm-30) REVERT: e 37 HIS cc_start: 0.7218 (t-90) cc_final: 0.6828 (t-90) REVERT: e 63 MET cc_start: 0.5001 (mmm) cc_final: 0.4647 (mmm) REVERT: e 72 ASN cc_start: 0.3703 (m-40) cc_final: 0.3486 (m110) REVERT: e 73 GLU cc_start: 0.7250 (mp0) cc_final: 0.6996 (mp0) REVERT: e 91 GLU cc_start: 0.6802 (tp30) cc_final: 0.5669 (pm20) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.3896 time to fit residues: 394.9169 Evaluate side-chains 495 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 292 optimal weight: 0.2980 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 389 GLN A 398 GLN A 497 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN F 25 GLN F 402 GLN ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27879 Z= 0.248 Angle : 0.662 10.887 37781 Z= 0.332 Chirality : 0.045 0.234 4446 Planarity : 0.004 0.049 4912 Dihedral : 8.218 113.132 4022 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.69 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.75 (0.14), residues: 3557 helix: 0.29 (0.14), residues: 1403 sheet: -3.04 (0.21), residues: 454 loop : -1.86 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 PHE 0.022 0.002 PHE B 292 TYR 0.017 0.001 TYR A 445 ARG 0.007 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 3.085 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 191 ASN cc_start: 0.7105 (t0) cc_final: 0.6827 (t0) REVERT: A 342 GLN cc_start: 0.8999 (pm20) cc_final: 0.8368 (pm20) REVERT: C 14 ARG cc_start: 0.5642 (mmm160) cc_final: 0.5034 (mpt-90) REVERT: C 219 MET cc_start: 0.8487 (tpp) cc_final: 0.8176 (tpp) REVERT: C 251 MET cc_start: 0.7987 (ttp) cc_final: 0.7482 (ttp) REVERT: C 314 MET cc_start: 0.8715 (ttt) cc_final: 0.8231 (ttt) REVERT: C 386 GLU cc_start: 0.7766 (tp30) cc_final: 0.7251 (tt0) REVERT: C 451 LEU cc_start: 0.7956 (mt) cc_final: 0.7738 (mt) REVERT: B 157 MET cc_start: 0.7359 (mpp) cc_final: 0.7012 (mpp) REVERT: B 164 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 422 LYS cc_start: 0.7189 (pttp) cc_final: 0.6914 (ptmt) REVERT: D 25 GLN cc_start: 0.8056 (tt0) cc_final: 0.7659 (tt0) REVERT: D 149 PHE cc_start: 0.6032 (t80) cc_final: 0.5724 (t80) REVERT: D 157 ASP cc_start: 0.8831 (t70) cc_final: 0.8438 (t70) REVERT: D 247 MET cc_start: 0.7787 (ttp) cc_final: 0.7399 (ttp) REVERT: D 259 TYR cc_start: 0.8888 (t80) cc_final: 0.8579 (t80) REVERT: D 263 VAL cc_start: 0.8942 (t) cc_final: 0.8698 (t) REVERT: D 283 SER cc_start: 0.8312 (t) cc_final: 0.8054 (p) REVERT: D 306 MET cc_start: 0.8286 (tpp) cc_final: 0.8015 (tpt) REVERT: D 451 LEU cc_start: 0.6759 (tp) cc_final: 0.6411 (tp) REVERT: E 20 LEU cc_start: 0.6938 (mt) cc_final: 0.6674 (tp) REVERT: E 39 LYS cc_start: 0.8332 (mmtm) cc_final: 0.7824 (mmmm) REVERT: E 89 MET cc_start: 0.8820 (mtt) cc_final: 0.8600 (mtt) REVERT: E 191 LYS cc_start: 0.8385 (tptm) cc_final: 0.8111 (ttpt) REVERT: E 206 THR cc_start: 0.8457 (m) cc_final: 0.8103 (m) REVERT: E 214 MET cc_start: 0.8060 (mmt) cc_final: 0.7583 (tpp) REVERT: E 247 MET cc_start: 0.8353 (ttp) cc_final: 0.7942 (ttp) REVERT: E 306 MET cc_start: 0.8220 (tmm) cc_final: 0.7545 (tmm) REVERT: E 313 ILE cc_start: 0.8389 (mm) cc_final: 0.8132 (mt) REVERT: F 43 ILE cc_start: 0.8912 (mt) cc_final: 0.8645 (mt) REVERT: F 71 ASN cc_start: 0.7844 (t0) cc_final: 0.7541 (t0) REVERT: F 184 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6868 (tm-30) REVERT: F 218 GLU cc_start: 0.6616 (pp20) cc_final: 0.6276 (pp20) REVERT: F 284 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7455 (mt-10) REVERT: F 343 PHE cc_start: 0.8502 (m-80) cc_final: 0.8169 (m-80) REVERT: d 239 LYS cc_start: 0.5480 (mttt) cc_final: 0.4835 (ttpt) REVERT: g 91 GLU cc_start: 0.6895 (pt0) cc_final: 0.6671 (pt0) REVERT: g 133 PHE cc_start: 0.7699 (t80) cc_final: 0.7334 (t80) REVERT: g 136 MET cc_start: 0.8004 (tpt) cc_final: 0.7724 (ttp) REVERT: g 139 LYS cc_start: 0.7067 (ttpt) cc_final: 0.6226 (mptt) REVERT: g 187 THR cc_start: 0.7213 (m) cc_final: 0.6932 (p) REVERT: g 264 LEU cc_start: 0.8812 (tt) cc_final: 0.8527 (tt) REVERT: g 272 LYS cc_start: 0.8713 (tptt) cc_final: 0.8476 (tppt) REVERT: g 315 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6915 (tm-30) REVERT: e 37 HIS cc_start: 0.7315 (t-90) cc_final: 0.6922 (t-90) REVERT: e 63 MET cc_start: 0.5025 (mmm) cc_final: 0.4632 (mmm) REVERT: e 72 ASN cc_start: 0.3674 (m-40) cc_final: 0.3416 (m110) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.3860 time to fit residues: 379.6713 Evaluate side-chains 498 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 3.451 ------------------------------------------------------------------------------- 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: 0.9980 chunk 309 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN d 227 ASN e 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27879 Z= 0.297 Angle : 0.690 11.353 37781 Z= 0.347 Chirality : 0.046 0.278 4446 Planarity : 0.004 0.052 4912 Dihedral : 8.158 111.759 4022 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.33 % Favored : 90.47 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3557 helix: 0.26 (0.14), residues: 1413 sheet: -3.00 (0.21), residues: 460 loop : -1.77 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 57 HIS 0.009 0.001 HIS A 43 PHE 0.022 0.002 PHE B 292 TYR 0.015 0.002 TYR B 237 ARG 0.007 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.7192 (t0) cc_final: 0.6915 (t0) REVERT: C 14 ARG cc_start: 0.5692 (mmm160) cc_final: 0.5095 (mpt-90) REVERT: C 219 MET cc_start: 0.8526 (tpp) cc_final: 0.8166 (tpp) REVERT: C 251 MET cc_start: 0.7889 (ttp) cc_final: 0.7400 (ttp) REVERT: C 314 MET cc_start: 0.8723 (ttt) cc_final: 0.8262 (ttt) REVERT: C 386 GLU cc_start: 0.7717 (tp30) cc_final: 0.7221 (tt0) REVERT: B 157 MET cc_start: 0.7317 (mpp) cc_final: 0.7063 (mpp) REVERT: B 164 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 422 LYS cc_start: 0.7208 (pttp) cc_final: 0.6910 (ptmt) REVERT: D 25 GLN cc_start: 0.7999 (tt0) cc_final: 0.7651 (tt0) REVERT: D 64 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 157 ASP cc_start: 0.8841 (t70) cc_final: 0.8402 (t70) REVERT: D 247 MET cc_start: 0.7902 (ttp) cc_final: 0.7413 (ttp) REVERT: D 283 SER cc_start: 0.8416 (t) cc_final: 0.8043 (p) REVERT: D 306 MET cc_start: 0.8285 (tpp) cc_final: 0.8077 (tpt) REVERT: D 451 LEU cc_start: 0.6729 (tp) cc_final: 0.6421 (tp) REVERT: E 20 LEU cc_start: 0.7019 (mt) cc_final: 0.6711 (tp) REVERT: E 39 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7859 (mmmm) REVERT: E 191 LYS cc_start: 0.8423 (tptm) cc_final: 0.8136 (ttpt) REVERT: E 214 MET cc_start: 0.8000 (mmt) cc_final: 0.7437 (tpp) REVERT: E 247 MET cc_start: 0.8376 (ttp) cc_final: 0.8117 (ttp) REVERT: E 306 MET cc_start: 0.8276 (tmm) cc_final: 0.7712 (tmm) REVERT: E 310 GLN cc_start: 0.8027 (mt0) cc_final: 0.7700 (mt0) REVERT: E 313 ILE cc_start: 0.8404 (mm) cc_final: 0.8117 (mt) REVERT: E 475 TYR cc_start: 0.7858 (t80) cc_final: 0.7622 (t80) REVERT: F 71 ASN cc_start: 0.8006 (t0) cc_final: 0.7697 (t0) REVERT: F 86 THR cc_start: 0.7642 (m) cc_final: 0.7368 (m) REVERT: F 89 MET cc_start: 0.8221 (mtm) cc_final: 0.7983 (mtp) REVERT: F 184 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7057 (tm-30) REVERT: F 216 MET cc_start: 0.8285 (mmp) cc_final: 0.7605 (mmm) REVERT: F 218 GLU cc_start: 0.6766 (pp20) cc_final: 0.6506 (pp20) REVERT: F 306 MET cc_start: 0.8150 (tpt) cc_final: 0.7928 (tpt) REVERT: F 415 GLU cc_start: 0.6445 (mm-30) cc_final: 0.4805 (tp30) REVERT: F 476 LEU cc_start: 0.8641 (mm) cc_final: 0.8377 (mm) REVERT: F 492 MET cc_start: 0.7846 (mtt) cc_final: 0.7583 (mtp) REVERT: d 117 ASN cc_start: 0.7210 (t0) cc_final: 0.6803 (t0) REVERT: d 239 LYS cc_start: 0.5699 (mttt) cc_final: 0.4871 (ttpt) REVERT: g 133 PHE cc_start: 0.7698 (t80) cc_final: 0.7335 (t80) REVERT: g 136 MET cc_start: 0.8022 (tpt) cc_final: 0.7653 (ttp) REVERT: g 139 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6271 (mptt) REVERT: g 187 THR cc_start: 0.7242 (m) cc_final: 0.6961 (p) REVERT: g 211 GLU cc_start: 0.6299 (mt-10) cc_final: 0.5554 (mt-10) REVERT: g 272 LYS cc_start: 0.8718 (tptt) cc_final: 0.8485 (tppt) REVERT: e 37 HIS cc_start: 0.7373 (t-90) cc_final: 0.6979 (t-90) REVERT: e 63 MET cc_start: 0.5063 (mmm) cc_final: 0.4654 (mmm) REVERT: e 72 ASN cc_start: 0.3686 (m-40) cc_final: 0.3174 (m110) REVERT: e 111 GLN cc_start: 0.7350 (mt0) cc_final: 0.7136 (mt0) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.3993 time to fit residues: 378.9395 Evaluate side-chains 479 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.247 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 0.6980 chunk 195 optimal weight: 0.3980 chunk 250 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 289 optimal weight: 0.4980 chunk 191 optimal weight: 0.6980 chunk 342 optimal weight: 0.6980 chunk 214 optimal weight: 0.2980 chunk 208 optimal weight: 0.9980 chunk 157 optimal weight: 0.0170 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 201 GLN A 351 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN B 148 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN F 402 GLN d 144 ASN d 227 ASN g 361 ASN e 102 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27879 Z= 0.198 Angle : 0.654 12.044 37781 Z= 0.326 Chirality : 0.044 0.269 4446 Planarity : 0.004 0.048 4912 Dihedral : 7.918 110.950 4022 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.82 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3557 helix: 0.42 (0.14), residues: 1411 sheet: -2.99 (0.21), residues: 463 loop : -1.67 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 PHE 0.025 0.002 PHE B 292 TYR 0.022 0.001 TYR F 475 ARG 0.006 0.000 ARG F 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6628 (tm-30) REVERT: A 52 GLU cc_start: 0.8499 (tt0) cc_final: 0.8298 (tt0) REVERT: A 215 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6835 (pt0) REVERT: A 219 MET cc_start: 0.8309 (tpp) cc_final: 0.8005 (tpp) REVERT: C 14 ARG cc_start: 0.5672 (mmm160) cc_final: 0.5075 (mpt-90) REVERT: C 219 MET cc_start: 0.8365 (tpp) cc_final: 0.8010 (tpp) REVERT: C 251 MET cc_start: 0.7786 (ttp) cc_final: 0.7338 (ttp) REVERT: C 314 MET cc_start: 0.8515 (ttt) cc_final: 0.8122 (ttt) REVERT: C 386 GLU cc_start: 0.7561 (tp30) cc_final: 0.7230 (tt0) REVERT: B 12 ILE cc_start: 0.8757 (mm) cc_final: 0.8556 (tt) REVERT: B 123 THR cc_start: 0.7476 (p) cc_final: 0.7216 (m) REVERT: B 157 MET cc_start: 0.7017 (mpp) cc_final: 0.6762 (mpp) REVERT: B 164 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8212 (tm-30) REVERT: B 300 GLU cc_start: 0.8047 (tt0) cc_final: 0.7816 (tt0) REVERT: B 422 LYS cc_start: 0.7107 (pttp) cc_final: 0.6860 (ptmt) REVERT: B 436 MET cc_start: 0.6777 (tpp) cc_final: 0.6358 (tpt) REVERT: D 25 GLN cc_start: 0.7928 (tt0) cc_final: 0.7545 (tt0) REVERT: D 64 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7923 (mt-10) REVERT: D 157 ASP cc_start: 0.8754 (t70) cc_final: 0.8311 (t70) REVERT: D 208 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 247 MET cc_start: 0.7755 (ttp) cc_final: 0.7372 (ttp) REVERT: D 451 LEU cc_start: 0.6765 (tp) cc_final: 0.6426 (tp) REVERT: E 20 LEU cc_start: 0.6961 (mt) cc_final: 0.6639 (tp) REVERT: E 39 LYS cc_start: 0.8247 (mmtm) cc_final: 0.7816 (mmmm) REVERT: E 247 MET cc_start: 0.8434 (ttp) cc_final: 0.8216 (ttp) REVERT: E 306 MET cc_start: 0.8212 (tmm) cc_final: 0.7718 (tmm) REVERT: E 310 GLN cc_start: 0.7796 (mt0) cc_final: 0.7537 (mt0) REVERT: E 313 ILE cc_start: 0.8367 (mm) cc_final: 0.8063 (mt) REVERT: F 43 ILE cc_start: 0.8849 (mt) cc_final: 0.8636 (mt) REVERT: F 71 ASN cc_start: 0.7904 (t0) cc_final: 0.7565 (t0) REVERT: F 86 THR cc_start: 0.7392 (m) cc_final: 0.7142 (m) REVERT: F 216 MET cc_start: 0.8299 (mmp) cc_final: 0.7626 (mmm) REVERT: F 218 GLU cc_start: 0.6798 (pp20) cc_final: 0.6573 (pp20) REVERT: F 306 MET cc_start: 0.8099 (tpt) cc_final: 0.7875 (tpt) REVERT: F 374 MET cc_start: 0.8690 (mmt) cc_final: 0.8466 (mmt) REVERT: F 415 GLU cc_start: 0.6567 (mm-30) cc_final: 0.4985 (tp30) REVERT: F 492 MET cc_start: 0.7912 (mtt) cc_final: 0.7608 (mtp) REVERT: d 117 ASN cc_start: 0.7124 (t0) cc_final: 0.6750 (t0) REVERT: d 239 LYS cc_start: 0.5632 (mttt) cc_final: 0.5089 (ttpt) REVERT: g 136 MET cc_start: 0.7985 (tpt) cc_final: 0.7678 (ttp) REVERT: g 139 LYS cc_start: 0.7062 (ttpt) cc_final: 0.6193 (mptt) REVERT: g 187 THR cc_start: 0.7232 (m) cc_final: 0.6978 (p) REVERT: g 263 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7264 (mtpp) REVERT: g 272 LYS cc_start: 0.8650 (tptt) cc_final: 0.8446 (tppt) REVERT: e 1 MET cc_start: 0.4710 (ppp) cc_final: 0.3833 (ppp) REVERT: e 37 HIS cc_start: 0.7369 (t-90) cc_final: 0.6967 (t-90) REVERT: e 58 LEU cc_start: 0.5224 (pt) cc_final: 0.4969 (pp) REVERT: e 63 MET cc_start: 0.5052 (mmm) cc_final: 0.4674 (mmm) REVERT: e 111 GLN cc_start: 0.7250 (mt0) cc_final: 0.6972 (mt0) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.3878 time to fit residues: 389.1565 Evaluate side-chains 494 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 3.114 ------------------------------------------------------------------------------- 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: 1.9990 chunk 136 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 233 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 268 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN E 66 GLN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN ** F 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27879 Z= 0.263 Angle : 0.678 12.818 37781 Z= 0.338 Chirality : 0.045 0.219 4446 Planarity : 0.004 0.051 4912 Dihedral : 7.862 109.096 4022 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.46 % Favored : 91.31 % Rotamer: Outliers : 0.03 % Allowed : 1.67 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3557 helix: 0.42 (0.14), residues: 1403 sheet: -2.94 (0.21), residues: 476 loop : -1.63 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 57 HIS 0.008 0.001 HIS A 43 PHE 0.023 0.002 PHE B 292 TYR 0.021 0.002 TYR g 155 ARG 0.008 0.001 ARG d 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 593 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 425 GLN cc_start: 0.7331 (pt0) cc_final: 0.6323 (pp30) REVERT: C 14 ARG cc_start: 0.5689 (mmm160) cc_final: 0.5090 (mpt-90) REVERT: C 52 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 251 MET cc_start: 0.7815 (ttp) cc_final: 0.7340 (ttp) REVERT: C 314 MET cc_start: 0.8640 (ttt) cc_final: 0.8217 (ttt) REVERT: C 386 GLU cc_start: 0.7705 (tp30) cc_final: 0.7269 (tt0) REVERT: B 123 THR cc_start: 0.7466 (p) cc_final: 0.7238 (m) REVERT: B 157 MET cc_start: 0.7073 (mpp) cc_final: 0.6858 (mpp) REVERT: B 164 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 419 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5549 (mm-30) REVERT: B 422 LYS cc_start: 0.7142 (pttp) cc_final: 0.6913 (pttm) REVERT: B 436 MET cc_start: 0.6877 (tpp) cc_final: 0.6500 (tpt) REVERT: D 25 GLN cc_start: 0.7958 (tt0) cc_final: 0.7610 (tt0) REVERT: D 64 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8112 (mt-10) REVERT: D 157 ASP cc_start: 0.8768 (t70) cc_final: 0.8258 (t70) REVERT: D 247 MET cc_start: 0.7779 (ttp) cc_final: 0.7417 (ttp) REVERT: D 451 LEU cc_start: 0.6900 (tp) cc_final: 0.6475 (tp) REVERT: E 20 LEU cc_start: 0.7005 (mt) cc_final: 0.6674 (tp) REVERT: E 39 LYS cc_start: 0.8314 (mmtm) cc_final: 0.7822 (mmmm) REVERT: E 214 MET cc_start: 0.7888 (mmt) cc_final: 0.7460 (tpp) REVERT: E 247 MET cc_start: 0.8432 (ttp) cc_final: 0.8201 (ttp) REVERT: E 306 MET cc_start: 0.8259 (tmm) cc_final: 0.7870 (tmm) REVERT: E 310 GLN cc_start: 0.7904 (mt0) cc_final: 0.7512 (mt0) REVERT: E 313 ILE cc_start: 0.8357 (mm) cc_final: 0.8100 (mt) REVERT: F 43 ILE cc_start: 0.8883 (mt) cc_final: 0.8621 (mt) REVERT: F 71 ASN cc_start: 0.7989 (t0) cc_final: 0.7698 (t0) REVERT: F 184 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6918 (tm-30) REVERT: F 216 MET cc_start: 0.8351 (mmp) cc_final: 0.7645 (mmm) REVERT: F 306 MET cc_start: 0.8111 (tpt) cc_final: 0.7848 (tpt) REVERT: F 415 GLU cc_start: 0.6628 (mm-30) cc_final: 0.5054 (tp30) REVERT: F 492 MET cc_start: 0.7962 (mtt) cc_final: 0.7664 (mtp) REVERT: d 117 ASN cc_start: 0.7211 (t0) cc_final: 0.6817 (t0) REVERT: d 239 LYS cc_start: 0.5771 (mttt) cc_final: 0.5000 (ttpt) REVERT: g 136 MET cc_start: 0.7980 (tpt) cc_final: 0.7697 (ttp) REVERT: g 139 LYS cc_start: 0.7067 (ttpt) cc_final: 0.6210 (mptt) REVERT: g 187 THR cc_start: 0.7238 (m) cc_final: 0.6978 (p) REVERT: g 197 ASP cc_start: 0.6355 (t70) cc_final: 0.6010 (t70) REVERT: g 263 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7254 (tppp) REVERT: e 1 MET cc_start: 0.4796 (ppp) cc_final: 0.3989 (ppp) REVERT: e 37 HIS cc_start: 0.7426 (t-90) cc_final: 0.6993 (t-90) REVERT: e 58 LEU cc_start: 0.5272 (pt) cc_final: 0.4935 (pp) REVERT: e 63 MET cc_start: 0.5016 (mmm) cc_final: 0.4648 (mmm) REVERT: e 111 GLN cc_start: 0.7166 (mt0) cc_final: 0.6941 (mt0) outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 0.3772 time to fit residues: 360.1854 Evaluate side-chains 478 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 3.220 ------------------------------------------------------------------------------- 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: 1.9990 chunk 327 optimal weight: 3.9990 chunk 299 optimal weight: 0.8980 chunk 318 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 250 optimal weight: 0.0970 chunk 97 optimal weight: 0.0040 chunk 288 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 317 optimal weight: 0.0870 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 208 GLN A 389 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27879 Z= 0.199 Angle : 0.659 12.247 37781 Z= 0.327 Chirality : 0.044 0.252 4446 Planarity : 0.004 0.047 4912 Dihedral : 7.707 110.571 4022 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.31 % Favored : 92.49 % Rotamer: Outliers : 0.03 % Allowed : 1.05 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.41 (0.14), residues: 3557 helix: 0.53 (0.14), residues: 1405 sheet: -2.99 (0.21), residues: 478 loop : -1.54 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP e 15 HIS 0.009 0.001 HIS A 43 PHE 0.031 0.001 PHE D 343 TYR 0.026 0.001 TYR F 475 ARG 0.007 0.000 ARG d 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 607 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6574 (tm-30) REVERT: A 219 MET cc_start: 0.8274 (tpp) cc_final: 0.8073 (tpp) REVERT: A 342 GLN cc_start: 0.9014 (pm20) cc_final: 0.8049 (pt0) REVERT: A 425 GLN cc_start: 0.7187 (pt0) cc_final: 0.6246 (pp30) REVERT: C 14 ARG cc_start: 0.5633 (mmm160) cc_final: 0.5032 (mpt-90) REVERT: C 53 LEU cc_start: 0.8806 (pp) cc_final: 0.8603 (pp) REVERT: C 251 MET cc_start: 0.7824 (ttp) cc_final: 0.7369 (ttp) REVERT: C 314 MET cc_start: 0.8423 (ttt) cc_final: 0.8026 (ttt) REVERT: C 386 GLU cc_start: 0.7624 (tp30) cc_final: 0.7318 (tt0) REVERT: C 387 LEU cc_start: 0.7914 (mt) cc_final: 0.7293 (tt) REVERT: B 123 THR cc_start: 0.7504 (p) cc_final: 0.7197 (m) REVERT: B 164 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 259 ILE cc_start: 0.9194 (tt) cc_final: 0.8988 (tt) REVERT: B 415 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7351 (tp40) REVERT: B 422 LYS cc_start: 0.7082 (pttp) cc_final: 0.6863 (ptmt) REVERT: B 436 MET cc_start: 0.6804 (tpp) cc_final: 0.6442 (tpt) REVERT: D 25 GLN cc_start: 0.7951 (tt0) cc_final: 0.7579 (tt0) REVERT: D 64 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 157 ASP cc_start: 0.8671 (t70) cc_final: 0.8065 (t0) REVERT: D 247 MET cc_start: 0.7567 (ttp) cc_final: 0.7064 (ttp) REVERT: D 451 LEU cc_start: 0.6925 (tp) cc_final: 0.6306 (tp) REVERT: E 20 LEU cc_start: 0.6830 (mt) cc_final: 0.6405 (tt) REVERT: E 39 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7674 (mmmm) REVERT: E 59 MET cc_start: 0.6610 (mpp) cc_final: 0.6286 (mpp) REVERT: E 90 GLU cc_start: 0.8299 (mp0) cc_final: 0.7497 (tt0) REVERT: E 109 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7289 (mtm-85) REVERT: E 247 MET cc_start: 0.8394 (ttp) cc_final: 0.8118 (ttp) REVERT: E 273 ASP cc_start: 0.8136 (t70) cc_final: 0.7898 (t70) REVERT: E 306 MET cc_start: 0.8310 (tmm) cc_final: 0.7793 (tmm) REVERT: E 310 GLN cc_start: 0.7787 (mt0) cc_final: 0.7533 (mt0) REVERT: E 313 ILE cc_start: 0.8265 (mm) cc_final: 0.8037 (mt) REVERT: F 71 ASN cc_start: 0.7926 (t0) cc_final: 0.7652 (t0) REVERT: F 80 SER cc_start: 0.8685 (m) cc_final: 0.8323 (t) REVERT: F 198 VAL cc_start: 0.9202 (t) cc_final: 0.8983 (m) REVERT: F 216 MET cc_start: 0.8352 (mmp) cc_final: 0.8006 (mmm) REVERT: F 218 GLU cc_start: 0.6715 (pp20) cc_final: 0.6498 (pp20) REVERT: F 306 MET cc_start: 0.8024 (tpt) cc_final: 0.7796 (tpt) REVERT: F 415 GLU cc_start: 0.6634 (mm-30) cc_final: 0.5106 (tp30) REVERT: F 475 TYR cc_start: 0.8439 (t80) cc_final: 0.8237 (t80) REVERT: d 117 ASN cc_start: 0.7118 (t0) cc_final: 0.6765 (t0) REVERT: d 239 LYS cc_start: 0.5756 (mttt) cc_final: 0.5217 (ttpt) REVERT: g 87 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6653 (mt-10) REVERT: g 136 MET cc_start: 0.7973 (tpt) cc_final: 0.7677 (ttp) REVERT: g 139 LYS cc_start: 0.7032 (ttpt) cc_final: 0.6100 (mptt) REVERT: g 187 THR cc_start: 0.7201 (m) cc_final: 0.6968 (p) REVERT: g 263 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7283 (tppp) REVERT: g 323 MET cc_start: 0.7728 (mmt) cc_final: 0.7350 (mmt) REVERT: e 1 MET cc_start: 0.4653 (ppp) cc_final: 0.4062 (ppp) REVERT: e 37 HIS cc_start: 0.7402 (t-90) cc_final: 0.6974 (t-90) REVERT: e 63 MET cc_start: 0.4824 (mmm) cc_final: 0.4409 (mmm) REVERT: e 91 GLU cc_start: 0.6781 (tp30) cc_final: 0.5726 (pm20) REVERT: e 111 GLN cc_start: 0.7087 (mt0) cc_final: 0.6866 (mt0) outliers start: 1 outliers final: 0 residues processed: 608 average time/residue: 0.3749 time to fit residues: 366.5942 Evaluate side-chains 479 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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: 0.1980 chunk 337 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 0.0980 chunk 234 optimal weight: 0.5980 chunk 353 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 186 ASN A 201 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 434 GLN E 66 GLN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27879 Z= 0.217 Angle : 0.674 12.430 37781 Z= 0.334 Chirality : 0.045 0.213 4446 Planarity : 0.004 0.061 4912 Dihedral : 7.637 110.819 4022 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.98 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 3557 helix: 0.59 (0.14), residues: 1407 sheet: -2.86 (0.22), residues: 467 loop : -1.53 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 PHE 0.021 0.002 PHE D 343 TYR 0.042 0.002 TYR F 475 ARG 0.011 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6683 (mtp180) REVERT: A 47 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6626 (tm-30) REVERT: A 262 ASP cc_start: 0.8056 (t70) cc_final: 0.7767 (t70) REVERT: A 314 MET cc_start: 0.8534 (ttm) cc_final: 0.7938 (ttp) REVERT: A 342 GLN cc_start: 0.9045 (pm20) cc_final: 0.8110 (pt0) REVERT: A 425 GLN cc_start: 0.7178 (pt0) cc_final: 0.6230 (pp30) REVERT: C 14 ARG cc_start: 0.5647 (mmm160) cc_final: 0.5025 (mpt-90) REVERT: C 251 MET cc_start: 0.7859 (ttp) cc_final: 0.7344 (ttp) REVERT: C 314 MET cc_start: 0.8452 (ttt) cc_final: 0.8049 (ttt) REVERT: C 386 GLU cc_start: 0.7603 (tp30) cc_final: 0.7233 (tt0) REVERT: C 387 LEU cc_start: 0.7936 (mt) cc_final: 0.7377 (tt) REVERT: B 164 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 422 LYS cc_start: 0.7171 (pttp) cc_final: 0.6926 (ptmt) REVERT: B 436 MET cc_start: 0.6806 (tpp) cc_final: 0.6467 (tpt) REVERT: D 25 GLN cc_start: 0.7933 (tt0) cc_final: 0.7546 (tt0) REVERT: D 64 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8025 (mt-10) REVERT: D 157 ASP cc_start: 0.8690 (t70) cc_final: 0.8053 (t0) REVERT: D 247 MET cc_start: 0.7630 (ttp) cc_final: 0.7198 (ttp) REVERT: D 428 GLU cc_start: 0.7625 (pp20) cc_final: 0.7387 (pp20) REVERT: D 451 LEU cc_start: 0.7009 (tp) cc_final: 0.6482 (tp) REVERT: E 20 LEU cc_start: 0.6738 (mt) cc_final: 0.6483 (tp) REVERT: E 39 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7736 (mmmt) REVERT: E 44 TYR cc_start: 0.8344 (m-80) cc_final: 0.8124 (m-80) REVERT: E 59 MET cc_start: 0.6588 (mpp) cc_final: 0.6226 (mpp) REVERT: E 64 GLU cc_start: 0.8159 (pp20) cc_final: 0.7949 (pp20) REVERT: E 109 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7318 (mtm-85) REVERT: E 247 MET cc_start: 0.8385 (ttp) cc_final: 0.8173 (ttp) REVERT: E 273 ASP cc_start: 0.8105 (t70) cc_final: 0.7877 (t70) REVERT: E 306 MET cc_start: 0.8278 (tmm) cc_final: 0.7798 (tmm) REVERT: E 310 GLN cc_start: 0.7797 (mt0) cc_final: 0.7521 (mt0) REVERT: E 313 ILE cc_start: 0.8327 (mm) cc_final: 0.8101 (mt) REVERT: F 71 ASN cc_start: 0.7870 (t0) cc_final: 0.7595 (t0) REVERT: F 80 SER cc_start: 0.8729 (m) cc_final: 0.8358 (t) REVERT: F 216 MET cc_start: 0.8330 (mmp) cc_final: 0.7641 (mmm) REVERT: F 306 MET cc_start: 0.8049 (tpt) cc_final: 0.7766 (tpt) REVERT: F 415 GLU cc_start: 0.6606 (mm-30) cc_final: 0.5106 (tp30) REVERT: d 117 ASN cc_start: 0.7088 (t0) cc_final: 0.6735 (t0) REVERT: d 175 THR cc_start: 0.8536 (m) cc_final: 0.8114 (m) REVERT: d 208 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.6694 (mtm-85) REVERT: g 87 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6648 (mt-10) REVERT: g 136 MET cc_start: 0.7976 (tpt) cc_final: 0.7697 (ttp) REVERT: g 139 LYS cc_start: 0.7027 (ttpt) cc_final: 0.6113 (mptt) REVERT: g 187 THR cc_start: 0.7164 (m) cc_final: 0.6941 (p) REVERT: g 263 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7170 (tppp) REVERT: g 323 MET cc_start: 0.7575 (mmt) cc_final: 0.7278 (mmt) REVERT: e 1 MET cc_start: 0.4617 (ppp) cc_final: 0.4209 (ppp) REVERT: e 37 HIS cc_start: 0.7464 (t-90) cc_final: 0.6984 (t-90) REVERT: e 63 MET cc_start: 0.4728 (mmm) cc_final: 0.4378 (mmm) REVERT: e 91 GLU cc_start: 0.6789 (tp30) cc_final: 0.5730 (pm20) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.4018 time to fit residues: 383.0614 Evaluate side-chains 489 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 3.124 ------------------------------------------------------------------------------- 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: 0.9990 chunk 300 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 259 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 289 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 201 GLN A 389 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 186 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.143864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136714 restraints weight = 36933.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.134974 restraints weight = 67623.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134471 restraints weight = 65375.182| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27879 Z= 0.229 Angle : 0.671 12.452 37781 Z= 0.334 Chirality : 0.045 0.207 4446 Planarity : 0.004 0.048 4912 Dihedral : 7.598 110.442 4022 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.84 % Favored : 91.93 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.29 (0.14), residues: 3557 helix: 0.62 (0.14), residues: 1415 sheet: -2.92 (0.21), residues: 468 loop : -1.49 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.008 0.001 HIS A 43 PHE 0.023 0.002 PHE D 343 TYR 0.017 0.001 TYR B 237 ARG 0.009 0.001 ARG d 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6977.28 seconds wall clock time: 126 minutes 30.93 seconds (7590.93 seconds total)