Starting phenix.real_space_refine on Sun Aug 4 21:08:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lx3_30004/08_2024/6lx3_30004.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lx3_30004/08_2024/6lx3_30004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lx3_30004/08_2024/6lx3_30004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lx3_30004/08_2024/6lx3_30004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lx3_30004/08_2024/6lx3_30004.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lx3_30004/08_2024/6lx3_30004.cif" } resolution = 3.15 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 7264 2.51 5 N 1981 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 254": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "C TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 363": "OE1" <-> "OE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ASP 468": "OD1" <-> "OD2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 66": "OD1" <-> "OD2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J GLU 75": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 104": "OD1" <-> "OD2" Residue "P TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 196": "OD1" <-> "OD2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "P TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 244": "OE1" <-> "OE2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 370": "OE1" <-> "OE2" Residue "P GLU 384": "OE1" <-> "OE2" Residue "P GLU 400": "OE1" <-> "OE2" Residue "P PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 428": "OD1" <-> "OD2" Residue "P GLU 474": "OE1" <-> "OE2" Residue "P TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11503 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain breaks: 3 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1570 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 15, 'TRANS': 190} Chain breaks: 3 Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1613 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain breaks: 4 Chain: "D" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1697 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 17, 'TRANS': 205} Chain breaks: 1 Chain: "J" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Chain: "P" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3964 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 485} Chain breaks: 5 Time building chain proxies: 6.66, per 1000 atoms: 0.58 Number of scatterers: 11503 At special positions: 0 Unit cell: (148.212, 104.328, 158.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2196 8.00 N 1981 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.02 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.04 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 202 " distance=2.03 Simple disulfide: pdb=" SG CYS P 239 " - pdb=" SG CYS P 307 " distance=2.02 Simple disulfide: pdb=" SG CYS P 253 " - pdb=" SG CYS P 261 " distance=2.04 Simple disulfide: pdb=" SG CYS P 353 " - pdb=" SG CYS P 423 " distance=2.03 Simple disulfide: pdb=" SG CYS P 367 " - pdb=" SG CYS P 377 " distance=2.03 Simple disulfide: pdb=" SG CYS P 464 " - pdb=" SG CYS P 526 " distance=2.04 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 36 sheets defined 9.1% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.797A pdb=" N LEU A 361 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.517A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.722A pdb=" N TRP B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 311 through 316' Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.663A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.828A pdb=" N LYS C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 Processing helix chain 'D' and resid 311 through 318 removed outlier: 4.205A pdb=" N TRP D 315 " --> pdb=" O CYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.571A pdb=" N GLY D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.741A pdb=" N SER P 87 " --> pdb=" O GLN P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 197 removed outlier: 3.508A pdb=" N ALA P 197 " --> pdb=" O LEU P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 removed outlier: 3.778A pdb=" N VAL P 245 " --> pdb=" O GLY P 242 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA P 246 " --> pdb=" O PRO P 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 242 through 246' Processing helix chain 'P' and resid 414 through 418 removed outlier: 3.842A pdb=" N ASP P 417 " --> pdb=" O THR P 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA P 418 " --> pdb=" O SER P 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 414 through 418' Processing helix chain 'P' and resid 467 through 471 removed outlier: 3.561A pdb=" N PHE P 470 " --> pdb=" O PRO P 467 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 471 " --> pdb=" O CYS P 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 467 through 471' Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.284A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 5.284A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 465 removed outlier: 6.798A pdb=" N VAL A 463 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.707A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.707A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 246 through 249 removed outlier: 3.735A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 352 Processing sheet with id=AB6, first strand: chain 'C' and resid 348 through 352 Processing sheet with id=AB7, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB8, first strand: chain 'C' and resid 457 through 458 removed outlier: 5.793A pdb=" N HIS C 457 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 460 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS D 457 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE J 37 " --> pdb=" O HIS D 457 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 459 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 461 through 463 removed outlier: 7.273A pdb=" N VAL J 41 " --> pdb=" O SER D 461 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 463 " --> pdb=" O VAL J 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 245 through 248 Processing sheet with id=AC2, first strand: chain 'D' and resid 278 through 281 Processing sheet with id=AC3, first strand: chain 'D' and resid 348 through 352 removed outlier: 5.346A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 348 through 352 removed outlier: 5.346A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'J' and resid 74 through 78 Processing sheet with id=AC7, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.652A pdb=" N VAL P 10 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER P 110 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER P 12 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS P 35 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER P 51 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP P 37 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'P' and resid 121 through 125 removed outlier: 6.627A pdb=" N TYR P 122 " --> pdb=" O GLN P 218 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU P 220 " --> pdb=" O TYR P 122 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL P 124 " --> pdb=" O LEU P 220 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN P 199 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN P 150 " --> pdb=" O GLN P 199 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 129 through 133 Processing sheet with id=AD3, first strand: chain 'P' and resid 225 through 230 removed outlier: 6.168A pdb=" N GLU P 225 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE P 327 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG P 304 " --> pdb=" O GLN P 255 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU P 252 " --> pdb=" O VAL P 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL P 265 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 235 through 240 removed outlier: 3.940A pdb=" N PHE P 290 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 340 through 344 removed outlier: 6.527A pdb=" N VAL P 341 " --> pdb=" O LYS P 438 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE P 440 " --> pdb=" O VAL P 341 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY P 343 " --> pdb=" O ILE P 440 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR P 433 " --> pdb=" O CYS P 423 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 348 through 354 Processing sheet with id=AD7, first strand: chain 'P' and resid 365 through 366 removed outlier: 3.637A pdb=" N VAL P 381 " --> pdb=" O TRP P 366 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 460 through 462 Processing sheet with id=AD9, first strand: chain 'P' and resid 486 through 487 removed outlier: 4.000A pdb=" N GLN P 486 " --> pdb=" O LYS P 479 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS P 479 " --> pdb=" O GLN P 486 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU P 536 " --> pdb=" O VAL P 528 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN P 530 " --> pdb=" O TYR P 534 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR P 534 " --> pdb=" O GLN P 530 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1032 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: 4.07 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3331 1.33 - 1.46: 2961 1.46 - 1.59: 5392 1.59 - 1.71: 0 1.71 - 1.84: 71 Bond restraints: 11755 Sorted by residual: bond pdb=" C ARG P 278 " pdb=" N ILE P 279 " ideal model delta sigma weight residual 1.327 1.293 0.034 9.50e-03 1.11e+04 1.25e+01 bond pdb=" C PHE B 345 " pdb=" N ARG B 346 " ideal model delta sigma weight residual 1.327 1.267 0.060 1.71e-02 3.42e+03 1.23e+01 bond pdb=" CB THR P 33 " pdb=" CG2 THR P 33 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CG LEU A 367 " pdb=" CD2 LEU A 367 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CD LYS P 35 " pdb=" CE LYS P 35 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.72e+00 ... (remaining 11750 not shown) Histogram of bond angle deviations from ideal: 96.95 - 104.85: 275 104.85 - 112.74: 6326 112.74 - 120.64: 5058 120.64 - 128.54: 4215 128.54 - 136.44: 124 Bond angle restraints: 15998 Sorted by residual: angle pdb=" C LEU J 78 " pdb=" N ASP J 79 " pdb=" CA ASP J 79 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" N VAL P 158 " pdb=" CA VAL P 158 " pdb=" C VAL P 158 " ideal model delta sigma weight residual 111.62 107.63 3.99 7.90e-01 1.60e+00 2.55e+01 angle pdb=" C SER J 88 " pdb=" N ASN J 89 " pdb=" CA ASN J 89 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" CA ASP J 131 " pdb=" CB ASP J 131 " pdb=" CG ASP J 131 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C CYS P 92 " pdb=" N GLY P 93 " pdb=" CA GLY P 93 " ideal model delta sigma weight residual 121.15 113.62 7.53 1.80e+00 3.09e-01 1.75e+01 ... (remaining 15993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6208 17.89 - 35.77: 744 35.77 - 53.66: 139 53.66 - 71.54: 26 71.54 - 89.43: 11 Dihedral angle restraints: 7128 sinusoidal: 2843 harmonic: 4285 Sorted by residual: dihedral pdb=" CB CYS P 253 " pdb=" SG CYS P 253 " pdb=" SG CYS P 261 " pdb=" CB CYS P 261 " ideal model delta sinusoidal sigma weight residual 93.00 12.34 80.66 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS P 367 " pdb=" SG CYS P 367 " pdb=" SG CYS P 377 " pdb=" CB CYS P 377 " ideal model delta sinusoidal sigma weight residual 93.00 169.80 -76.80 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS P 38 " pdb=" SG CYS P 38 " pdb=" SG CYS P 46 " pdb=" CB CYS P 46 " ideal model delta sinusoidal sigma weight residual 93.00 25.03 67.97 1 1.00e+01 1.00e-02 6.00e+01 ... (remaining 7125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1442 0.077 - 0.154: 337 0.154 - 0.230: 50 0.230 - 0.307: 13 0.307 - 0.384: 2 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CB VAL P 245 " pdb=" CA VAL P 245 " pdb=" CG1 VAL P 245 " pdb=" CG2 VAL P 245 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL P 76 " pdb=" CA VAL P 76 " pdb=" CG1 VAL P 76 " pdb=" CG2 VAL P 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL P 265 " pdb=" CA VAL P 265 " pdb=" CG1 VAL P 265 " pdb=" CG2 VAL P 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 1841 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 472 " 0.027 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR A 472 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 472 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 472 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 472 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 472 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 472 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 472 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " 0.051 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 283 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " -0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO C 283 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.046 5.00e-02 4.00e+02 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2872 2.79 - 3.32: 8927 3.32 - 3.85: 18193 3.85 - 4.37: 20751 4.37 - 4.90: 38206 Nonbonded interactions: 88949 Sorted by model distance: nonbonded pdb=" O SER P 195 " pdb=" OG SER P 195 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU C 403 " pdb=" OG1 THR C 410 " model vdw 2.267 3.040 nonbonded pdb=" O THR P 429 " pdb=" OG1 THR P 429 " model vdw 2.268 3.040 nonbonded pdb=" O SER J 50 " pdb=" OG SER J 50 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR D 282 " pdb=" OG1 THR D 322 " model vdw 2.308 3.040 ... (remaining 88944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 244 through 281 or resid 287 through 294 or resid 303 thro \ ugh 405 or resid 408 through 452 or resid 462)) selection = (chain 'B' and (resid 244 through 270 or resid 278 through 281 or resid 287 thro \ ugh 405 or resid 408 through 452 or resid 462)) selection = (chain 'C' and (resid 244 through 270 or resid 278 through 281 or resid 287 thro \ ugh 294 or resid 303 through 452 or resid 458)) selection = (chain 'D' and (resid 244 through 270 or resid 278 through 281 or resid 287 thro \ ugh 294 or resid 303 through 405 or resid 408 through 452 or resid 462)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 33.090 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.016 0.119 11755 Z= 1.021 Angle : 1.201 12.762 15998 Z= 0.633 Chirality : 0.069 0.384 1844 Planarity : 0.009 0.076 2043 Dihedral : 15.566 89.429 4286 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.40 % Allowed : 15.62 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.19), residues: 1444 helix: -4.54 (0.17), residues: 108 sheet: -1.45 (0.20), residues: 598 loop : -3.08 (0.18), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP P 431 HIS 0.010 0.002 HIS D 350 PHE 0.027 0.004 PHE D 374 TYR 0.058 0.004 TYR A 472 ARG 0.021 0.001 ARG J 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7489 (tpt90) REVERT: A 425 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7933 (mmtt) REVERT: B 433 MET cc_start: 0.7603 (ttm) cc_final: 0.7340 (ttp) REVERT: C 423 ASP cc_start: 0.8594 (t70) cc_final: 0.8162 (t0) REVERT: C 426 LYS cc_start: 0.8776 (pttt) cc_final: 0.8480 (pttp) REVERT: C 428 ASP cc_start: 0.8081 (m-30) cc_final: 0.7765 (m-30) REVERT: D 423 ASP cc_start: 0.8426 (t0) cc_final: 0.8171 (t0) REVERT: J 44 ASN cc_start: 0.8583 (t0) cc_final: 0.8171 (t0) REVERT: J 51 ASP cc_start: 0.8731 (t70) cc_final: 0.8505 (t0) REVERT: J 59 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.8111 (ttt90) REVERT: J 107 LYS cc_start: 0.8681 (tttm) cc_final: 0.8351 (ttmm) REVERT: P 173 ILE cc_start: 0.7701 (tt) cc_final: 0.7434 (tt) REVERT: P 191 GLN cc_start: 0.7555 (mt0) cc_final: 0.7090 (pt0) outliers start: 18 outliers final: 13 residues processed: 184 average time/residue: 0.3145 time to fit residues: 76.8583 Evaluate side-chains 161 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 516 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN C 362 ASN ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 457 HIS J 45 ASN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 GLN ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 412 GLN P 530 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11755 Z= 0.213 Angle : 0.638 11.966 15998 Z= 0.321 Chirality : 0.042 0.166 1844 Planarity : 0.006 0.054 2043 Dihedral : 6.304 40.656 1605 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.72 % Allowed : 18.18 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1444 helix: -3.35 (0.30), residues: 111 sheet: -0.92 (0.20), residues: 597 loop : -2.53 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 431 HIS 0.002 0.001 HIS D 457 PHE 0.015 0.001 PHE P 406 TYR 0.010 0.001 TYR J 103 ARG 0.007 0.000 ARG P 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8687 (tt0) cc_final: 0.8454 (tt0) REVERT: A 392 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7413 (tpt90) REVERT: B 433 MET cc_start: 0.7433 (ttm) cc_final: 0.7231 (ttp) REVERT: C 423 ASP cc_start: 0.8595 (t70) cc_final: 0.8049 (t0) REVERT: C 426 LYS cc_start: 0.8553 (pttt) cc_final: 0.8216 (pttp) REVERT: C 428 ASP cc_start: 0.7950 (m-30) cc_final: 0.7459 (m-30) REVERT: D 362 ASN cc_start: 0.7647 (t0) cc_final: 0.7376 (t0) REVERT: J 44 ASN cc_start: 0.8528 (t0) cc_final: 0.8192 (t0) REVERT: J 59 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8083 (ttt90) REVERT: J 107 LYS cc_start: 0.8579 (tttm) cc_final: 0.8182 (ttmm) REVERT: P 172 ARG cc_start: 0.6984 (mtm180) cc_final: 0.6492 (mtm180) REVERT: P 359 GLU cc_start: 0.7258 (pp20) cc_final: 0.6284 (pp20) REVERT: P 366 TRP cc_start: 0.9189 (OUTLIER) cc_final: 0.8649 (t60) REVERT: P 367 CYS cc_start: 0.5882 (t) cc_final: 0.5543 (t) outliers start: 35 outliers final: 21 residues processed: 194 average time/residue: 0.2846 time to fit residues: 74.5862 Evaluate side-chains 167 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 109 optimal weight: 0.0030 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 GLN ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11755 Z= 0.275 Angle : 0.630 11.269 15998 Z= 0.313 Chirality : 0.042 0.157 1844 Planarity : 0.005 0.046 2043 Dihedral : 5.805 42.157 1597 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.73 % Allowed : 19.35 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1444 helix: -2.32 (0.39), residues: 112 sheet: -0.65 (0.21), residues: 597 loop : -2.17 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 431 HIS 0.002 0.001 HIS D 457 PHE 0.015 0.001 PHE P 406 TYR 0.012 0.001 TYR P 148 ARG 0.008 0.000 ARG P 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 GLN cc_start: 0.8670 (tt0) cc_final: 0.8421 (tt0) REVERT: A 392 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7420 (tpt90) REVERT: B 433 MET cc_start: 0.7397 (ttm) cc_final: 0.7144 (ttp) REVERT: C 423 ASP cc_start: 0.8564 (t70) cc_final: 0.8002 (t0) REVERT: C 426 LYS cc_start: 0.8552 (pttt) cc_final: 0.8166 (pttp) REVERT: C 428 ASP cc_start: 0.7982 (m-30) cc_final: 0.7352 (m-30) REVERT: J 44 ASN cc_start: 0.8528 (t0) cc_final: 0.8219 (t0) REVERT: J 107 LYS cc_start: 0.8613 (tttm) cc_final: 0.8199 (ttmm) REVERT: P 108 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6276 (mm-30) REVERT: P 359 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6471 (pp20) REVERT: P 366 TRP cc_start: 0.9158 (OUTLIER) cc_final: 0.8498 (t60) REVERT: P 536 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6943 (tm-30) outliers start: 48 outliers final: 32 residues processed: 193 average time/residue: 0.2901 time to fit residues: 75.8625 Evaluate side-chains 178 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 378 ASP Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 190 ASN Chi-restraints excluded: chain P residue 359 GLU Chi-restraints excluded: chain P residue 366 TRP Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 414 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 452 VAL Chi-restraints excluded: chain P residue 453 THR Chi-restraints excluded: chain P residue 460 LEU Chi-restraints excluded: chain P residue 536 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4974 > 50: distance: 73 - 77: 28.256 distance: 77 - 78: 21.478 distance: 78 - 79: 35.778 distance: 78 - 81: 34.690 distance: 79 - 80: 33.307 distance: 79 - 85: 30.603 distance: 81 - 82: 55.723 distance: 82 - 83: 22.542 distance: 82 - 84: 52.607 distance: 85 - 86: 12.995 distance: 85 - 180: 25.341 distance: 86 - 87: 40.470 distance: 86 - 89: 29.847 distance: 87 - 88: 35.160 distance: 87 - 91: 25.946 distance: 88 - 177: 24.722 distance: 89 - 90: 11.389 distance: 91 - 92: 20.535 distance: 92 - 93: 30.417 distance: 92 - 95: 27.135 distance: 93 - 94: 48.136 distance: 93 - 99: 39.558 distance: 95 - 96: 31.765 distance: 96 - 97: 29.922 distance: 96 - 98: 28.755 distance: 99 - 100: 10.493 distance: 100 - 101: 26.784 distance: 100 - 103: 47.966 distance: 101 - 102: 33.037 distance: 101 - 107: 25.887 distance: 103 - 104: 27.853 distance: 104 - 105: 22.747 distance: 104 - 106: 15.493 distance: 107 - 108: 34.322 distance: 108 - 109: 25.920 distance: 108 - 111: 27.988 distance: 109 - 110: 40.651 distance: 109 - 116: 11.780 distance: 111 - 112: 55.860 distance: 112 - 113: 16.381 distance: 113 - 114: 29.091 distance: 113 - 115: 20.430 distance: 116 - 117: 20.494 distance: 117 - 118: 39.329 distance: 117 - 120: 32.114 distance: 118 - 119: 39.947 distance: 118 - 125: 31.948 distance: 120 - 121: 34.488 distance: 121 - 122: 25.663 distance: 122 - 123: 6.315 distance: 122 - 124: 6.082 distance: 125 - 126: 28.734 distance: 125 - 131: 17.881 distance: 126 - 127: 14.050 distance: 126 - 129: 30.959 distance: 127 - 128: 28.779 distance: 127 - 132: 26.378 distance: 129 - 130: 13.050 distance: 130 - 131: 8.948 distance: 132 - 133: 35.593 distance: 133 - 134: 26.207 distance: 134 - 135: 30.989 distance: 134 - 136: 28.356 distance: 136 - 137: 20.194 distance: 137 - 138: 32.859 distance: 137 - 140: 16.532 distance: 138 - 139: 25.651 distance: 138 - 144: 18.433 distance: 140 - 141: 33.891 distance: 141 - 142: 22.479 distance: 141 - 143: 30.578 distance: 144 - 145: 29.149 distance: 145 - 146: 13.862 distance: 146 - 147: 47.015 distance: 146 - 148: 18.849