Starting phenix.real_space_refine on Thu Jan 18 23:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c77_30294/01_2024/7c77_30294.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c77_30294/01_2024/7c77_30294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c77_30294/01_2024/7c77_30294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c77_30294/01_2024/7c77_30294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c77_30294/01_2024/7c77_30294.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c77_30294/01_2024/7c77_30294.pdb" } resolution = 3.3 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 36 5.16 5 C 6317 2.51 5 N 1603 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 497": "OD1" <-> "OD2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 463": "OD1" <-> "OD2" Residue "B GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9762 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5616 Classifications: {'peptide': 700} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 670} Chain: "B" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3869 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 21, 'TRANS': 461} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.75, per 1000 atoms: 0.59 Number of scatterers: 9762 At special positions: 0 Unit cell: (136.95, 171.81, 94.62, 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 36 16.00 O 1806 8.00 N 1603 7.00 C 6317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 678 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 368 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1001 " - " ASN A 58 " " NAG A1002 " - " ASN A 125 " " NAG A1003 " - " ASN A 197 " " NAG A1004 " - " ASN A 248 " " NAG A1005 " - " ASN A 253 " " NAG A1006 " - " ASN A 292 " " NAG A1016 " - " ASN A 668 " " NAG A1017 " - " ASN A 663 " " NAG B 601 " - " ASN B 251 " " NAG C 1 " - " ASN A 414 " " NAG D 1 " - " ASN A 425 " " NAG E 1 " - " ASN A 399 " " NAG F 1 " - " ASN A 508 " " NAG G 1 " - " ASN B 272 " Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 40.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 4.032A pdb=" N THR A 73 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.899A pdb=" N GLN A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.747A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.617A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.771A pdb=" N LYS A 273 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.845A pdb=" N TRP A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.818A pdb=" N TRP A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Proline residue: A 633 - end of helix removed outlier: 4.530A pdb=" N ASN A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 removed outlier: 6.437A pdb=" N TRP A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.669A pdb=" N HIS A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 676' Processing helix chain 'A' and resid 702 through 727 removed outlier: 3.562A pdb=" N ILE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 89 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.667A pdb=" N THR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.622A pdb=" N MET B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 199 Proline residue: B 163 - end of helix removed outlier: 4.841A pdb=" N VAL B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 213 through 235 removed outlier: 3.986A pdb=" N VAL B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.846A pdb=" N THR B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 307 Processing helix chain 'B' and resid 312 through 321 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 339 through 359 Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 374 through 395 removed outlier: 3.726A pdb=" N VAL B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.053A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 461 removed outlier: 3.826A pdb=" N TYR B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 488 Processing helix chain 'B' and resid 494 through 517 removed outlier: 3.842A pdb=" N ALA B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 517 " --> pdb=" O TRP B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.475A pdb=" N LEU A 57 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N SER A 199 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ALA A 226 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG A 201 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 228 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 203 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 486 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 592 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 616 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.929A pdb=" N LEU A 187 " --> pdb=" O GLU A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 264 removed outlier: 3.888A pdb=" N THR A 264 " --> pdb=" O ASP A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.747A pdb=" N LEU A 314 " --> pdb=" O ASN A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.712A pdb=" N GLN A 471 " --> pdb=" O GLN A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 648 through 649 removed outlier: 7.343A pdb=" N LEU A 677 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 687 " --> pdb=" O CYS A 678 " (cutoff:3.500A) 348 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: 2.96 Time building geometry restraints manager: 4.26 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: 3018 1.34 - 1.46: 1809 1.46 - 1.58: 5107 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 9991 Sorted by residual: bond pdb=" N ALA B 506 " pdb=" CA ALA B 506 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.19e-02 7.06e+03 6.48e+00 bond pdb=" CA ALA B 506 " pdb=" C ALA B 506 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.27e-02 6.20e+03 4.33e+00 bond pdb=" C ALA B 506 " pdb=" O ALA B 506 " ideal model delta sigma weight residual 1.236 1.257 -0.021 1.15e-02 7.56e+03 3.21e+00 bond pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.01e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.48e+00 ... (remaining 9986 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.46: 257 106.46 - 113.39: 5571 113.39 - 120.31: 3617 120.31 - 127.23: 4026 127.23 - 134.15: 109 Bond angle restraints: 13580 Sorted by residual: angle pdb=" C SER B 510 " pdb=" N TYR B 511 " pdb=" CA TYR B 511 " ideal model delta sigma weight residual 120.54 124.87 -4.33 1.35e+00 5.49e-01 1.03e+01 angle pdb=" CA GLY B 266 " pdb=" C GLY B 266 " pdb=" N ILE B 267 " ideal model delta sigma weight residual 114.23 116.75 -2.52 8.80e-01 1.29e+00 8.17e+00 angle pdb=" CA SER B 510 " pdb=" C SER B 510 " pdb=" N TYR B 511 " ideal model delta sigma weight residual 117.39 114.08 3.31 1.24e+00 6.50e-01 7.14e+00 angle pdb=" C TRP A 547 " pdb=" N LYS A 548 " pdb=" CA LYS A 548 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.69e+00 angle pdb=" CA VAL B 275 " pdb=" C VAL B 275 " pdb=" N LEU B 276 " ideal model delta sigma weight residual 116.60 120.16 -3.56 1.45e+00 4.76e-01 6.04e+00 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 5534 21.71 - 43.42: 568 43.42 - 65.13: 74 65.13 - 86.85: 22 86.85 - 108.56: 4 Dihedral angle restraints: 6202 sinusoidal: 2730 harmonic: 3472 Sorted by residual: dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 38 " pdb=" CB CYS A 38 " ideal model delta sinusoidal sigma weight residual -86.00 -24.67 -61.33 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -51.65 -34.35 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CB CYS B 260 " pdb=" SG CYS B 260 " pdb=" SG CYS B 368 " pdb=" CB CYS B 368 " ideal model delta sinusoidal sigma weight residual 93.00 125.81 -32.81 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 6199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1364 0.055 - 0.109: 226 0.109 - 0.163: 21 0.163 - 0.218: 1 0.218 - 0.272: 1 Chirality restraints: 1613 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C2 NAG A1002 " pdb=" C1 NAG A1002 " pdb=" C3 NAG A1002 " pdb=" N2 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1610 not shown) Planarity restraints: 1694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 207 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO B 208 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 506 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C ALA B 506 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA B 506 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 507 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 118 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 119 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.025 5.00e-02 4.00e+02 ... (remaining 1691 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 969 2.75 - 3.29: 9757 3.29 - 3.82: 16278 3.82 - 4.36: 18331 4.36 - 4.90: 31933 Nonbonded interactions: 77268 Sorted by model distance: nonbonded pdb=" OH TYR B 248 " pdb=" O THR B 274 " model vdw 2.209 2.440 nonbonded pdb=" O SER A 373 " pdb=" OG SER A 404 " model vdw 2.269 2.440 nonbonded pdb=" O SER A 475 " pdb=" OG SER A 475 " model vdw 2.292 2.440 nonbonded pdb=" O HIS B 229 " pdb=" OG SER B 383 " model vdw 2.292 2.440 nonbonded pdb=" O ALA B 222 " pdb=" OG SER B 390 " model vdw 2.304 2.440 ... (remaining 77263 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.400 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: 2.250 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.320 Find NCS groups from input model: 0.220 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.003 0.035 9991 Z= 0.213 Angle : 0.668 7.030 13580 Z= 0.341 Chirality : 0.041 0.272 1613 Planarity : 0.004 0.065 1680 Dihedral : 16.649 108.557 3945 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 1.88 % Allowed : 12.15 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.63 (0.22), residues: 1179 helix: -0.89 (0.23), residues: 415 sheet: -1.91 (0.48), residues: 121 loop : -2.35 (0.21), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 547 HIS 0.005 0.000 HIS B 475 PHE 0.016 0.001 PHE A 692 TYR 0.017 0.001 TYR B 511 ARG 0.007 0.001 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 334 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8210 (mtmm) REVERT: A 364 ASP cc_start: 0.7916 (m-30) cc_final: 0.7662 (m-30) REVERT: A 365 ASP cc_start: 0.8190 (t0) cc_final: 0.7942 (t0) REVERT: A 398 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 448 LEU cc_start: 0.9238 (mt) cc_final: 0.9028 (mt) REVERT: A 660 ASN cc_start: 0.8055 (m-40) cc_final: 0.7853 (m-40) REVERT: B 478 GLN cc_start: 0.7325 (tt0) cc_final: 0.7019 (tt0) outliers start: 20 outliers final: 8 residues processed: 344 average time/residue: 0.1803 time to fit residues: 90.2697 Evaluate side-chains 294 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 285 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 497 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 182 ASN A 344 HIS A 418 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 475 HIS ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9991 Z= 0.304 Angle : 0.706 9.755 13580 Z= 0.338 Chirality : 0.046 0.232 1613 Planarity : 0.004 0.048 1680 Dihedral : 7.781 65.035 1709 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.90 % Allowed : 19.02 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.44 (0.24), residues: 1179 helix: 0.14 (0.25), residues: 444 sheet: -1.55 (0.48), residues: 116 loop : -1.68 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 476 HIS 0.007 0.001 HIS B 195 PHE 0.024 0.002 PHE B 347 TYR 0.018 0.002 TYR A 327 ARG 0.008 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 293 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8093 (mtmm) REVERT: A 364 ASP cc_start: 0.7666 (m-30) cc_final: 0.7322 (m-30) REVERT: A 644 ARG cc_start: 0.8108 (ptt90) cc_final: 0.7803 (ptt-90) REVERT: B 106 ASP cc_start: 0.7624 (t70) cc_final: 0.7262 (t0) REVERT: B 189 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8234 (mptt) REVERT: B 244 ASN cc_start: 0.8128 (m110) cc_final: 0.7756 (m110) REVERT: B 297 PHE cc_start: 0.8426 (t80) cc_final: 0.8166 (t80) REVERT: B 330 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 441 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8871 (mp) REVERT: B 478 GLN cc_start: 0.7613 (tt0) cc_final: 0.7315 (tt0) outliers start: 52 outliers final: 37 residues processed: 321 average time/residue: 0.1792 time to fit residues: 84.0501 Evaluate side-chains 316 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 108 GLN A 134 ASN A 344 HIS A 610 GLN B 85 GLN B 195 HIS B 467 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9991 Z= 0.163 Angle : 0.637 12.679 13580 Z= 0.297 Chirality : 0.044 0.233 1613 Planarity : 0.004 0.051 1680 Dihedral : 6.585 56.375 1706 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.33 % Allowed : 23.35 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.11 (0.24), residues: 1179 helix: 0.43 (0.25), residues: 444 sheet: -1.34 (0.50), residues: 116 loop : -1.50 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 476 HIS 0.006 0.001 HIS B 195 PHE 0.035 0.001 PHE B 347 TYR 0.019 0.001 TYR B 158 ARG 0.005 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 298 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8119 (mtmm) REVERT: A 364 ASP cc_start: 0.7658 (m-30) cc_final: 0.7356 (m-30) REVERT: A 644 ARG cc_start: 0.8085 (ptt90) cc_final: 0.7743 (ptt-90) REVERT: B 186 MET cc_start: 0.8071 (tpp) cc_final: 0.7445 (ttp) REVERT: B 189 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8135 (mptt) REVERT: B 244 ASN cc_start: 0.8139 (m110) cc_final: 0.7729 (m110) REVERT: B 297 PHE cc_start: 0.8436 (t80) cc_final: 0.8167 (t80) REVERT: B 370 MET cc_start: 0.7059 (pmm) cc_final: 0.6784 (pmm) REVERT: B 441 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8826 (mp) REVERT: B 478 GLN cc_start: 0.7378 (tt0) cc_final: 0.7077 (tt0) outliers start: 46 outliers final: 32 residues processed: 321 average time/residue: 0.1962 time to fit residues: 90.5079 Evaluate side-chains 315 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 282 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 547 TRP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 398 TRP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 505 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 52.9329 > 50: distance: 63 - 83: 6.711 distance: 67 - 87: 10.821 distance: 74 - 95: 24.392 distance: 78 - 83: 4.003 distance: 79 - 107: 7.789 distance: 84 - 85: 14.246 distance: 85 - 86: 9.151 distance: 85 - 87: 15.763 distance: 86 - 112: 19.594 distance: 87 - 88: 22.546 distance: 88 - 89: 25.336 distance: 88 - 91: 19.704 distance: 89 - 90: 13.146 distance: 89 - 95: 43.919 distance: 90 - 120: 20.491 distance: 91 - 92: 10.774 distance: 91 - 93: 27.587 distance: 92 - 94: 23.165 distance: 95 - 96: 11.711 distance: 96 - 97: 36.462 distance: 96 - 99: 26.287 distance: 97 - 98: 12.237 distance: 97 - 107: 25.958 distance: 98 - 131: 11.121 distance: 99 - 100: 21.594 distance: 100 - 101: 5.070 distance: 100 - 102: 9.494 distance: 101 - 103: 9.491 distance: 102 - 104: 13.702 distance: 103 - 105: 10.739 distance: 104 - 105: 7.104 distance: 105 - 106: 7.032 distance: 107 - 108: 11.147 distance: 108 - 109: 4.446 distance: 108 - 111: 7.374 distance: 109 - 110: 8.443 distance: 109 - 112: 3.911 distance: 110 - 138: 23.161 distance: 112 - 113: 7.747 distance: 113 - 114: 5.623 distance: 113 - 116: 11.689 distance: 114 - 115: 6.809 distance: 114 - 120: 6.654 distance: 115 - 144: 31.905 distance: 116 - 117: 16.714 distance: 117 - 118: 9.720 distance: 117 - 119: 18.098 distance: 120 - 121: 12.586 distance: 121 - 122: 7.078 distance: 121 - 124: 4.508 distance: 122 - 123: 4.851 distance: 122 - 131: 17.175 distance: 125 - 126: 3.264 distance: 125 - 127: 3.343 distance: 126 - 128: 3.782 distance: 127 - 129: 4.637 distance: 128 - 130: 4.298 distance: 129 - 130: 5.180 distance: 131 - 132: 3.715 distance: 132 - 133: 7.345 distance: 132 - 135: 9.220 distance: 133 - 134: 3.178 distance: 133 - 138: 10.425 distance: 135 - 136: 11.457 distance: 135 - 137: 8.845 distance: 138 - 139: 5.676 distance: 139 - 140: 20.009 distance: 139 - 142: 7.151 distance: 140 - 141: 15.728 distance: 140 - 144: 22.435 distance: 142 - 143: 22.171 distance: 144 - 145: 8.928 distance: 145 - 146: 32.048 distance: 145 - 148: 18.339 distance: 146 - 147: 48.899 distance: 146 - 151: 6.299 distance: 148 - 149: 6.971 distance: 148 - 150: 49.188 distance: 151 - 152: 18.287 distance: 152 - 153: 19.153 distance: 152 - 155: 8.392 distance: 153 - 154: 11.724 distance: 153 - 159: 8.328 distance: 155 - 156: 7.897 distance: 156 - 157: 7.976 distance: 156 - 158: 13.690