Starting phenix.real_space_refine on Sat Aug 10 18:53:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk5_32559/08_2024/7wk5_32559.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk5_32559/08_2024/7wk5_32559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk5_32559/08_2024/7wk5_32559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk5_32559/08_2024/7wk5_32559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk5_32559/08_2024/7wk5_32559.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk5_32559/08_2024/7wk5_32559.cif" } resolution = 3.66 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= 0.006 sd= 0.108 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 143 5.16 5 C 18942 2.51 5 N 4926 2.21 5 O 5590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D GLU 748": "OE1" <-> "OE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "D GLU 1031": "OE1" <-> "OE2" Residue "D GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1001} Chain breaks: 7 Chain: "D" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Time building chain proxies: 16.23, per 1000 atoms: 0.55 Number of scatterers: 29601 At special positions: 0 Unit cell: (149.741, 134.439, 234.995, 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 143 16.00 O 5590 8.00 N 4926 7.00 C 18942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 5.5 seconds 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 24.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.640A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.023A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.992A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.474A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.842A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.644A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.878A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 3.503A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.731A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.568A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 279' Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.621A pdb=" N LYS A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.719A pdb=" N PHE A 327 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.504A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 3.732A pdb=" N ASP A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.623A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.716A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 422' Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.859A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.503A pdb=" N TYR A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.594A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.648A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 508' Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.847A pdb=" N TYR A 515 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 removed outlier: 3.942A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 removed outlier: 3.504A pdb=" N ALA A 550 " --> pdb=" O SER A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 551 through 559 removed outlier: 4.147A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.608A pdb=" N LEU A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.908A pdb=" N ASN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.758A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.694A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.798A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.551A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 782 removed outlier: 3.570A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 3.709A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.537A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.582A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.860A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.649A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.659A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.654A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.883A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.038A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 4.104A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.869A pdb=" N SER C 637 " --> pdb=" O ARG C 634 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.782A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.791A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 removed outlier: 3.705A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.648A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.622A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 910 removed outlier: 3.586A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.626A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.606A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.543A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.645A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.708A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.128A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.506A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.823A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 408' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.647A pdb=" N HIS D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 506 " --> pdb=" O VAL D 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 506' Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.781A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 737 through 742' Processing helix chain 'D' and resid 753 through 757 removed outlier: 3.603A pdb=" N TYR D 756 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 757 " --> pdb=" O LEU D 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 753 through 757' Processing helix chain 'D' and resid 758 through 782 removed outlier: 3.969A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 776 " --> pdb=" O VAL D 772 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.782A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 825 " --> pdb=" O LEU D 821 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.647A pdb=" N ILE D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.657A pdb=" N MET D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.728A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 918' Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.508A pdb=" N GLY D 932 " --> pdb=" O ASN D 928 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER D 939 " --> pdb=" O GLN D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.197A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.564A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 1032 removed outlier: 4.216A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.486A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.662A pdb=" N THR B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.538A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.741A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.816A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.658A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.007A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.683A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.689A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 453 removed outlier: 4.027A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.607A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.347A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B1065 " --> pdb=" O MET B1050 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.347A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.556A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.466A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.750A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.596A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.598A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.578A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.159A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.935A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.551A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.551A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.551A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.019A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.606A pdb=" N THR D 22 " --> pdb=" O PHE D 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.507A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 206 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 202 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.651A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.530A pdb=" N GLN D 239 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 311 through 319 removed outlier: 3.702A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR D 612 " --> pdb=" O CYS D 649 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.636A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.636A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.536A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.646A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.978A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 734 through 736 removed outlier: 3.521A pdb=" N THR D 859 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 5.451A pdb=" N VAL D1122 " --> pdb=" O PHE D1089 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE D1089 " --> pdb=" O VAL D1122 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY D1124 " --> pdb=" O ALA D1087 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2412 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: 13.68 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9365 1.34 - 1.47: 7599 1.47 - 1.59: 13156 1.59 - 1.72: 0 1.72 - 1.85: 194 Bond restraints: 30314 Sorted by residual: bond pdb=" CA ILE C 584 " pdb=" C ILE C 584 " ideal model delta sigma weight residual 1.526 1.474 0.051 1.01e-02 9.80e+03 2.59e+01 bond pdb=" N GLU C 583 " pdb=" CA GLU C 583 " ideal model delta sigma weight residual 1.456 1.397 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" CA ILE C 584 " pdb=" CB ILE C 584 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" CA LEU D 585 " pdb=" C LEU D 585 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" CA GLU C 583 " pdb=" C GLU C 583 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.23e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 98.01 - 106.01: 739 106.01 - 114.01: 16800 114.01 - 122.01: 17190 122.01 - 130.01: 6327 130.01 - 138.02: 157 Bond angle restraints: 41213 Sorted by residual: angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 112.90 105.56 7.34 9.60e-01 1.09e+00 5.85e+01 angle pdb=" C ALA A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta sigma weight residual 120.94 132.27 -11.33 1.90e+00 2.77e-01 3.55e+01 angle pdb=" N ILE D 584 " pdb=" CA ILE D 584 " pdb=" C ILE D 584 " ideal model delta sigma weight residual 109.30 102.36 6.94 1.25e+00 6.40e-01 3.08e+01 angle pdb=" C CYS B 480 " pdb=" N ASN B 481 " pdb=" CA ASN B 481 " ideal model delta sigma weight residual 122.46 130.11 -7.65 1.41e+00 5.03e-01 2.94e+01 angle pdb=" N VAL A 293 " pdb=" CA VAL A 293 " pdb=" C VAL A 293 " ideal model delta sigma weight residual 113.43 107.59 5.84 1.09e+00 8.42e-01 2.87e+01 ... (remaining 41208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16470 17.96 - 35.92: 1294 35.92 - 53.88: 227 53.88 - 71.85: 63 71.85 - 89.81: 23 Dihedral angle restraints: 18077 sinusoidal: 7135 harmonic: 10942 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.16 -87.16 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.65 84.65 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 18074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4108 0.091 - 0.182: 445 0.182 - 0.273: 47 0.273 - 0.364: 2 0.364 - 0.455: 1 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA GLN B1142 " pdb=" N GLN B1142 " pdb=" C GLN B1142 " pdb=" CB GLN B1142 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN C 481 " pdb=" N ASN C 481 " pdb=" C ASN C 481 " pdb=" CB ASN C 481 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4600 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.064 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 987 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.064 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO B 987 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.064 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO D 987 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.053 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 2 2.30 - 2.95: 12301 2.95 - 3.60: 38552 3.60 - 4.25: 67877 4.25 - 4.90: 110158 Nonbonded interactions: 228890 Sorted by model distance: nonbonded pdb=" CD1 ILE B 472 " pdb=" CE2 PHE B 490 " model vdw 1.646 3.760 nonbonded pdb=" CD1 ILE B 472 " pdb=" CZ PHE B 490 " model vdw 2.225 3.760 nonbonded pdb=" O SER C 758 " pdb=" OG SER C 758 " model vdw 2.335 3.040 nonbonded pdb=" O SER B 446 " pdb=" OG SER B 446 " model vdw 2.339 3.040 nonbonded pdb=" O ALA D 879 " pdb=" OG1 THR D 883 " model vdw 2.346 3.040 ... (remaining 228885 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 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 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: 2.240 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 85.730 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30314 Z= 0.306 Angle : 0.837 13.017 41213 Z= 0.486 Chirality : 0.054 0.455 4603 Planarity : 0.007 0.095 5332 Dihedral : 13.401 87.356 10901 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 5.81 % Favored : 93.92 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -4.59 (0.10), residues: 3700 helix: -5.13 (0.04), residues: 806 sheet: -1.55 (0.19), residues: 567 loop : -2.77 (0.10), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 302 HIS 0.005 0.001 HIS A 493 PHE 0.018 0.001 PHE B 347 TYR 0.022 0.001 TYR A 385 ARG 0.006 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 741 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2111 (tpt) cc_final: -0.3053 (ptp) REVERT: A 171 GLU cc_start: 0.5789 (tt0) cc_final: 0.5419 (mm-30) REVERT: A 190 MET cc_start: -0.0018 (ppp) cc_final: -0.1075 (ptt) REVERT: A 223 ILE cc_start: 0.3571 (mm) cc_final: 0.2477 (mm) REVERT: A 249 MET cc_start: 0.1231 (mmt) cc_final: 0.0043 (mtt) REVERT: A 431 ASP cc_start: 0.5078 (p0) cc_final: 0.4233 (p0) REVERT: A 566 TRP cc_start: -0.1016 (p-90) cc_final: -0.1593 (p-90) REVERT: B 41 LYS cc_start: 0.6654 (mttt) cc_final: 0.6016 (mmmt) REVERT: B 54 LEU cc_start: 0.7411 (tp) cc_final: 0.6347 (pp) REVERT: B 118 LEU cc_start: 0.8213 (mt) cc_final: 0.7953 (mt) REVERT: B 296 LEU cc_start: 0.7432 (tp) cc_final: 0.7076 (tp) REVERT: B 309 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8511 (tp30) REVERT: B 731 MET cc_start: 0.8178 (mtp) cc_final: 0.7728 (mtt) REVERT: B 751 ASN cc_start: 0.9134 (m-40) cc_final: 0.8932 (m-40) REVERT: B 755 GLN cc_start: 0.8254 (mt0) cc_final: 0.7835 (mp10) REVERT: B 770 ILE cc_start: 0.9044 (pt) cc_final: 0.8694 (pt) REVERT: B 772 VAL cc_start: 0.8624 (m) cc_final: 0.8403 (p) REVERT: B 776 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8221 (tptp) REVERT: B 868 GLU cc_start: 0.8351 (mp0) cc_final: 0.7945 (mm-30) REVERT: B 869 MET cc_start: 0.8371 (mtp) cc_final: 0.7956 (mtp) REVERT: B 896 ILE cc_start: 0.7059 (mm) cc_final: 0.6746 (tp) REVERT: B 921 LYS cc_start: 0.8199 (mttt) cc_final: 0.7716 (tptt) REVERT: B 925 ASN cc_start: 0.7714 (m-40) cc_final: 0.7453 (m-40) REVERT: B 931 ILE cc_start: 0.7997 (mm) cc_final: 0.7626 (mm) REVERT: B 964 LYS cc_start: 0.8709 (ptpp) cc_final: 0.8478 (mtmm) REVERT: B 1001 LEU cc_start: 0.9342 (mt) cc_final: 0.9073 (tt) REVERT: B 1009 THR cc_start: 0.9129 (p) cc_final: 0.8863 (t) REVERT: B 1013 ILE cc_start: 0.8813 (pt) cc_final: 0.8587 (mt) REVERT: B 1038 LYS cc_start: 0.8283 (mttt) cc_final: 0.7974 (mtpp) REVERT: B 1050 MET cc_start: 0.6496 (ptp) cc_final: 0.6229 (ptp) REVERT: B 1103 PHE cc_start: 0.6579 (m-80) cc_final: 0.6164 (m-80) REVERT: C 293 LEU cc_start: 0.8333 (tp) cc_final: 0.7333 (tp) REVERT: C 298 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: C 314 GLN cc_start: 0.8187 (tt0) cc_final: 0.7886 (mm-40) REVERT: C 458 LYS cc_start: 0.4085 (mttt) cc_final: 0.3766 (mmtm) REVERT: C 462 LYS cc_start: 0.8156 (mttt) cc_final: 0.7896 (mmtm) REVERT: C 695 TYR cc_start: 0.7120 (p90) cc_final: 0.6520 (p90) REVERT: C 712 ILE cc_start: 0.6556 (tt) cc_final: 0.6325 (tt) REVERT: C 732 THR cc_start: 0.8622 (m) cc_final: 0.8331 (p) REVERT: C 814 LYS cc_start: 0.7793 (mttt) cc_final: 0.7092 (mmmt) REVERT: C 864 LEU cc_start: 0.7846 (tp) cc_final: 0.7589 (tt) REVERT: C 902 MET cc_start: 0.7461 (ttp) cc_final: 0.6937 (ttm) REVERT: C 933 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8457 (tptp) REVERT: C 962 LEU cc_start: 0.8973 (tp) cc_final: 0.8695 (tp) REVERT: C 1014 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8162 (mmm160) REVERT: C 1043 CYS cc_start: 0.1639 (m) cc_final: 0.1127 (m) REVERT: C 1071 GLN cc_start: 0.7327 (mt0) cc_final: 0.6974 (mp10) REVERT: C 1139 ASP cc_start: 0.6697 (t0) cc_final: 0.6138 (m-30) REVERT: D 40 ASP cc_start: 0.6422 (p0) cc_final: 0.6175 (t70) REVERT: D 287 ASP cc_start: 0.8149 (t0) cc_final: 0.7676 (t0) REVERT: D 310 LYS cc_start: 0.7937 (tttt) cc_final: 0.7391 (tppt) REVERT: D 503 VAL cc_start: 0.2409 (OUTLIER) cc_final: 0.2000 (p) REVERT: D 660 TYR cc_start: 0.7114 (m-80) cc_final: 0.6768 (m-10) REVERT: D 725 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6195 (tm-30) REVERT: D 790 LYS cc_start: 0.8349 (mttt) cc_final: 0.7854 (mmmt) REVERT: D 887 THR cc_start: 0.7089 (p) cc_final: 0.6852 (p) REVERT: D 888 PHE cc_start: 0.6255 (p90) cc_final: 0.6012 (p90) REVERT: D 978 ASN cc_start: 0.8628 (m-40) cc_final: 0.8348 (m110) outliers start: 9 outliers final: 2 residues processed: 749 average time/residue: 0.4360 time to fit residues: 504.4531 Evaluate side-chains 421 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 417 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 217 optimal weight: 0.9990 chunk 337 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 63 ASN A 81 GLN A 98 GLN A 159 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 378 HIS A 522 GLN A 546 ASN A 572 ASN A 578 ASN A 586 ASN A 598 GLN B 234 ASN B 536 ASN B 564 GLN B 606 ASN B 613 GLN B 955 ASN B 965 GLN B 992 GLN B1023 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 519 HIS C 606 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 955 ASN C1023 ASN C1101 HIS D 87 ASN D 121 ASN D 334 ASN D 477 ASN D 751 ASN D 787 GLN D 895 GLN D 949 GLN D 953 ASN D 954 HIS D1088 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30314 Z= 0.213 Angle : 0.642 12.752 41213 Z= 0.333 Chirality : 0.045 0.241 4603 Planarity : 0.006 0.082 5332 Dihedral : 4.568 59.187 4029 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 11.95 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.21 (0.11), residues: 3700 helix: -2.92 (0.12), residues: 789 sheet: -1.00 (0.20), residues: 597 loop : -2.24 (0.11), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 566 HIS 0.008 0.001 HIS D1048 PHE 0.026 0.002 PHE D 970 TYR 0.018 0.001 TYR C 707 ARG 0.008 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 436 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2579 (tpt) cc_final: -0.3589 (ptp) REVERT: A 171 GLU cc_start: 0.5606 (tt0) cc_final: 0.5006 (mm-30) REVERT: A 190 MET cc_start: -0.0469 (ppp) cc_final: -0.0820 (ptt) REVERT: A 249 MET cc_start: 0.1574 (mmt) cc_final: 0.0190 (ttm) REVERT: A 408 MET cc_start: 0.1772 (mtm) cc_final: 0.1359 (mpp) REVERT: A 431 ASP cc_start: 0.4128 (p0) cc_final: 0.3677 (p0) REVERT: A 455 MET cc_start: -0.1808 (ppp) cc_final: -0.2290 (ppp) REVERT: A 480 MET cc_start: 0.2096 (mtt) cc_final: 0.1638 (mtp) REVERT: A 554 LEU cc_start: -0.0879 (mt) cc_final: -0.1423 (pp) REVERT: A 566 TRP cc_start: -0.0771 (p-90) cc_final: -0.1597 (p-90) REVERT: A 579 MET cc_start: 0.1396 (OUTLIER) cc_final: 0.0664 (mmt) REVERT: A 586 ASN cc_start: 0.5489 (p0) cc_final: 0.4522 (m-40) REVERT: A 589 GLU cc_start: 0.6948 (pm20) cc_final: 0.6724 (mm-30) REVERT: B 54 LEU cc_start: 0.8136 (tp) cc_final: 0.7479 (pp) REVERT: B 313 TYR cc_start: 0.7122 (m-80) cc_final: 0.6728 (m-80) REVERT: B 654 GLU cc_start: 0.6773 (tt0) cc_final: 0.6522 (mt-10) REVERT: B 731 MET cc_start: 0.8326 (mtp) cc_final: 0.7962 (mtt) REVERT: B 740 MET cc_start: 0.7728 (tpp) cc_final: 0.6986 (ttm) REVERT: B 755 GLN cc_start: 0.8116 (mt0) cc_final: 0.7765 (mp10) REVERT: B 759 PHE cc_start: 0.7831 (m-80) cc_final: 0.7279 (m-80) REVERT: B 776 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8161 (tptp) REVERT: B 868 GLU cc_start: 0.8565 (mp0) cc_final: 0.8088 (mm-30) REVERT: B 869 MET cc_start: 0.8579 (mtp) cc_final: 0.8292 (mtp) REVERT: B 872 GLN cc_start: 0.8145 (mt0) cc_final: 0.7734 (tp-100) REVERT: B 921 LYS cc_start: 0.8457 (mttt) cc_final: 0.8039 (tppt) REVERT: B 964 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8558 (mtmm) REVERT: B 990 GLU cc_start: 0.9113 (pp20) cc_final: 0.8830 (pp20) REVERT: B 1038 LYS cc_start: 0.8340 (mttt) cc_final: 0.8105 (mtpp) REVERT: B 1071 GLN cc_start: 0.7082 (mt0) cc_final: 0.6466 (tm-30) REVERT: C 293 LEU cc_start: 0.8850 (tp) cc_final: 0.8590 (tp) REVERT: C 458 LYS cc_start: 0.3929 (mttt) cc_final: 0.3632 (mmtm) REVERT: C 462 LYS cc_start: 0.8061 (mttt) cc_final: 0.7813 (mmtt) REVERT: C 518 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5730 (tp) REVERT: C 754 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8548 (tp) REVERT: C 765 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8391 (tmm-80) REVERT: C 814 LYS cc_start: 0.7846 (mttt) cc_final: 0.6909 (mmmt) REVERT: C 933 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8596 (tptp) REVERT: C 935 GLN cc_start: 0.8609 (mt0) cc_final: 0.8326 (tm-30) REVERT: C 953 ASN cc_start: 0.8808 (m-40) cc_final: 0.8552 (m110) REVERT: C 955 ASN cc_start: 0.8427 (m110) cc_final: 0.8088 (m110) REVERT: C 1014 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8157 (mmm160) REVERT: C 1071 GLN cc_start: 0.7499 (mt0) cc_final: 0.7257 (mp10) REVERT: C 1139 ASP cc_start: 0.6983 (t0) cc_final: 0.6220 (m-30) REVERT: D 52 GLN cc_start: 0.8668 (tt0) cc_final: 0.8234 (tp40) REVERT: D 177 MET cc_start: -0.0911 (mmp) cc_final: -0.2760 (mtt) REVERT: D 287 ASP cc_start: 0.8401 (t0) cc_final: 0.7889 (t70) REVERT: D 697 MET cc_start: 0.7503 (tmm) cc_final: 0.7219 (tmm) REVERT: D 764 LYS cc_start: 0.8799 (mttt) cc_final: 0.8504 (mptt) REVERT: D 814 LYS cc_start: 0.6983 (mmpt) cc_final: 0.6509 (mmmt) REVERT: D 949 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7681 (tp40) REVERT: D 965 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8139 (tp40) REVERT: D 978 ASN cc_start: 0.8861 (m-40) cc_final: 0.8532 (p0) outliers start: 83 outliers final: 47 residues processed: 490 average time/residue: 0.3999 time to fit residues: 314.2852 Evaluate side-chains 405 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 354 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 chunk 301 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 221 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 321 GLN B 606 ASN B1101 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 717 ASN C 787 GLN C 907 ASN C 955 ASN C1023 ASN D 606 ASN D 658 ASN D 953 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30314 Z= 0.240 Angle : 0.633 12.900 41213 Z= 0.323 Chirality : 0.045 0.203 4603 Planarity : 0.005 0.058 5332 Dihedral : 4.430 57.340 4025 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 14.59 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.36 (0.12), residues: 3700 helix: -1.41 (0.16), residues: 826 sheet: -0.68 (0.20), residues: 598 loop : -1.95 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.008 0.001 HIS D1048 PHE 0.019 0.002 PHE D 970 TYR 0.021 0.002 TYR C 365 ARG 0.012 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 378 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: -0.0941 (OUTLIER) cc_final: -0.1296 (m110) REVERT: A 190 MET cc_start: -0.1258 (ppp) cc_final: -0.1586 (ptt) REVERT: A 249 MET cc_start: 0.1349 (mmt) cc_final: -0.0212 (ttm) REVERT: A 288 LYS cc_start: 0.2294 (ptpp) cc_final: 0.1757 (tppp) REVERT: A 408 MET cc_start: 0.1460 (mtm) cc_final: 0.1062 (mpp) REVERT: A 480 MET cc_start: 0.2317 (mtt) cc_final: 0.1787 (mtp) REVERT: A 554 LEU cc_start: -0.0792 (mt) cc_final: -0.1313 (pp) REVERT: A 566 TRP cc_start: -0.0872 (p-90) cc_final: -0.1834 (p-90) REVERT: A 579 MET cc_start: 0.1012 (mmt) cc_final: 0.0373 (mmt) REVERT: A 586 ASN cc_start: 0.5135 (p0) cc_final: 0.3939 (t0) REVERT: B 298 GLU cc_start: 0.7973 (tp30) cc_final: 0.7585 (mt-10) REVERT: B 577 ARG cc_start: 0.4540 (mpt180) cc_final: 0.4321 (mpt180) REVERT: B 654 GLU cc_start: 0.6962 (tt0) cc_final: 0.6692 (mt-10) REVERT: B 751 ASN cc_start: 0.8903 (m110) cc_final: 0.8539 (p0) REVERT: B 755 GLN cc_start: 0.8024 (mt0) cc_final: 0.7568 (mp10) REVERT: B 773 GLU cc_start: 0.8629 (tt0) cc_final: 0.8304 (tt0) REVERT: B 776 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8261 (tptp) REVERT: B 869 MET cc_start: 0.8553 (mtp) cc_final: 0.8345 (mtp) REVERT: B 872 GLN cc_start: 0.8326 (mt0) cc_final: 0.8081 (mm-40) REVERT: B 949 GLN cc_start: 0.8308 (mt0) cc_final: 0.7909 (tp-100) REVERT: B 964 LYS cc_start: 0.9060 (ptpp) cc_final: 0.8775 (mtmm) REVERT: B 1017 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8183 (tm-30) REVERT: B 1050 MET cc_start: 0.5820 (ptp) cc_final: 0.5612 (ptp) REVERT: B 1088 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6506 (m90) REVERT: C 340 GLU cc_start: 0.7096 (pp20) cc_final: 0.6578 (tp30) REVERT: C 458 LYS cc_start: 0.3972 (mttt) cc_final: 0.3695 (mmtm) REVERT: C 462 LYS cc_start: 0.8027 (mttt) cc_final: 0.7759 (mmtm) REVERT: C 518 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6146 (tp) REVERT: C 754 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 759 PHE cc_start: 0.8289 (t80) cc_final: 0.7826 (t80) REVERT: C 935 GLN cc_start: 0.8626 (mt0) cc_final: 0.8395 (tm-30) REVERT: C 953 ASN cc_start: 0.8811 (m-40) cc_final: 0.8606 (m-40) REVERT: C 983 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8451 (ttm110) REVERT: C 1014 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8107 (mmm160) REVERT: C 1071 GLN cc_start: 0.7467 (mt0) cc_final: 0.7264 (mp10) REVERT: C 1139 ASP cc_start: 0.6945 (t0) cc_final: 0.6262 (m-30) REVERT: D 52 GLN cc_start: 0.8842 (tt0) cc_final: 0.8427 (tp40) REVERT: D 177 MET cc_start: -0.1222 (mmp) cc_final: -0.2994 (mtt) REVERT: D 287 ASP cc_start: 0.8463 (t0) cc_final: 0.8151 (t0) REVERT: D 334 ASN cc_start: 0.8193 (t0) cc_final: 0.7641 (m110) REVERT: D 697 MET cc_start: 0.7568 (tmm) cc_final: 0.7253 (tmm) REVERT: D 737 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7866 (p0) REVERT: D 814 LYS cc_start: 0.6987 (mmpt) cc_final: 0.6735 (mmpt) REVERT: D 964 LYS cc_start: 0.9266 (ttpp) cc_final: 0.9054 (ttpt) REVERT: D 965 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8454 (tp40) REVERT: D 978 ASN cc_start: 0.8816 (m-40) cc_final: 0.8609 (p0) REVERT: D 1002 GLN cc_start: 0.8785 (tp40) cc_final: 0.8273 (tp40) REVERT: D 1107 ARG cc_start: 0.6657 (mtm180) cc_final: 0.6379 (ptp90) REVERT: D 1109 PHE cc_start: 0.8492 (t80) cc_final: 0.8127 (t80) outliers start: 99 outliers final: 63 residues processed: 446 average time/residue: 0.3909 time to fit residues: 282.9924 Evaluate side-chains 392 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 324 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.6980 chunk 254 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 0.4980 chunk 339 optimal weight: 8.9990 chunk 359 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 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 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN A 221 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B1135 ASN C 394 ASN C 606 ASN C 955 ASN C1023 ASN D 606 ASN D 953 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30314 Z= 0.151 Angle : 0.558 11.496 41213 Z= 0.277 Chirality : 0.043 0.175 4603 Planarity : 0.004 0.065 5332 Dihedral : 4.142 55.311 4025 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.40 % Allowed : 16.14 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.95 (0.13), residues: 3700 helix: -0.78 (0.17), residues: 832 sheet: -0.50 (0.21), residues: 567 loop : -1.78 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.018 0.001 PHE B 888 TYR 0.020 0.001 TYR B 91 ARG 0.004 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 370 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: -0.2913 (tpt) cc_final: -0.4335 (ptm) REVERT: A 171 GLU cc_start: 0.5247 (tt0) cc_final: 0.4454 (mm-30) REVERT: A 190 MET cc_start: -0.1355 (ppp) cc_final: -0.1703 (ptt) REVERT: A 249 MET cc_start: 0.0949 (mmt) cc_final: -0.0551 (ttm) REVERT: A 288 LYS cc_start: 0.2490 (ptpp) cc_final: 0.1807 (tppp) REVERT: A 408 MET cc_start: 0.1621 (mtm) cc_final: 0.1301 (mpp) REVERT: A 480 MET cc_start: 0.1960 (mtt) cc_final: 0.1526 (mtp) REVERT: A 554 LEU cc_start: -0.0818 (mt) cc_final: -0.1356 (pp) REVERT: A 566 TRP cc_start: -0.0877 (p-90) cc_final: -0.1776 (p-90) REVERT: A 579 MET cc_start: 0.0864 (mmt) cc_final: 0.0071 (mmt) REVERT: B 298 GLU cc_start: 0.7902 (tp30) cc_final: 0.7509 (mt-10) REVERT: B 654 GLU cc_start: 0.6829 (tt0) cc_final: 0.6584 (mt-10) REVERT: B 751 ASN cc_start: 0.8929 (m110) cc_final: 0.8552 (p0) REVERT: B 755 GLN cc_start: 0.7960 (mt0) cc_final: 0.7568 (mp10) REVERT: B 773 GLU cc_start: 0.8655 (tt0) cc_final: 0.8207 (tt0) REVERT: B 776 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8207 (tptp) REVERT: B 868 GLU cc_start: 0.8590 (mp0) cc_final: 0.8050 (mm-30) REVERT: B 869 MET cc_start: 0.8542 (mtp) cc_final: 0.8327 (mtp) REVERT: B 872 GLN cc_start: 0.8311 (mt0) cc_final: 0.8043 (mm-40) REVERT: B 935 GLN cc_start: 0.7841 (tt0) cc_final: 0.7350 (tp-100) REVERT: B 964 LYS cc_start: 0.8985 (ptpp) cc_final: 0.8342 (mtmm) REVERT: B 990 GLU cc_start: 0.9182 (pp20) cc_final: 0.8918 (pp20) REVERT: B 1017 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8260 (tm-30) REVERT: B 1088 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6412 (m90) REVERT: C 141 LEU cc_start: 0.7862 (tp) cc_final: 0.7599 (tp) REVERT: C 293 LEU cc_start: 0.9020 (tp) cc_final: 0.8810 (mp) REVERT: C 340 GLU cc_start: 0.7091 (pp20) cc_final: 0.6542 (tp30) REVERT: C 458 LYS cc_start: 0.4074 (mttt) cc_final: 0.3792 (mmtm) REVERT: C 462 LYS cc_start: 0.7938 (mttt) cc_final: 0.7668 (mmtm) REVERT: C 754 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8777 (tp) REVERT: C 814 LYS cc_start: 0.8020 (mttt) cc_final: 0.6921 (mmmt) REVERT: C 935 GLN cc_start: 0.8679 (mt0) cc_final: 0.8378 (tm-30) REVERT: C 953 ASN cc_start: 0.8826 (m-40) cc_final: 0.8619 (m-40) REVERT: C 983 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8420 (ttm110) REVERT: C 1014 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8088 (mmm160) REVERT: C 1071 GLN cc_start: 0.7444 (mt0) cc_final: 0.7230 (mp10) REVERT: C 1139 ASP cc_start: 0.6947 (t0) cc_final: 0.6266 (m-30) REVERT: D 52 GLN cc_start: 0.8914 (tt0) cc_final: 0.8620 (tp40) REVERT: D 177 MET cc_start: -0.1005 (mmp) cc_final: -0.2677 (mtt) REVERT: D 287 ASP cc_start: 0.8426 (t0) cc_final: 0.8077 (t0) REVERT: D 334 ASN cc_start: 0.8189 (t0) cc_final: 0.7672 (m110) REVERT: D 697 MET cc_start: 0.7605 (tmm) cc_final: 0.7333 (tmm) REVERT: D 737 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7875 (p0) REVERT: D 965 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8391 (tp40) REVERT: D 1107 ARG cc_start: 0.6642 (mtm180) cc_final: 0.6255 (ptp90) outliers start: 79 outliers final: 58 residues processed: 416 average time/residue: 0.3914 time to fit residues: 265.3316 Evaluate side-chains 394 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 333 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 166 CYS Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 811 LYS Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1088 HIS Chi-restraints excluded: chain D residue 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 55.445 > 50: distance: 27 - 203: 11.434 distance: 88 - 217: 11.637 distance: 91 - 214: 12.602 distance: 109 - 192: 10.569 distance: 172 - 177: 4.436 distance: 177 - 178: 5.673 distance: 178 - 179: 21.145 distance: 178 - 181: 8.538 distance: 179 - 180: 6.547 distance: 179 - 185: 18.500 distance: 181 - 182: 8.884 distance: 181 - 183: 3.800 distance: 182 - 184: 10.323 distance: 185 - 186: 15.155 distance: 186 - 187: 11.625 distance: 186 - 189: 19.110 distance: 187 - 188: 6.263 distance: 187 - 192: 13.857 distance: 189 - 190: 5.117 distance: 189 - 191: 6.483 distance: 192 - 193: 5.181 distance: 193 - 194: 9.116 distance: 193 - 196: 5.340 distance: 194 - 195: 15.195 distance: 194 - 203: 7.384 distance: 196 - 197: 6.968 distance: 197 - 198: 3.779 distance: 198 - 199: 6.765 distance: 199 - 200: 3.047 distance: 200 - 201: 6.799 distance: 200 - 202: 4.312 distance: 204 - 205: 6.154 distance: 204 - 207: 3.745 distance: 205 - 206: 13.484 distance: 207 - 208: 10.034 distance: 208 - 209: 5.929 distance: 208 - 210: 9.874 distance: 209 - 211: 3.779 distance: 210 - 212: 6.533 distance: 211 - 213: 7.007 distance: 212 - 213: 7.698 distance: 214 - 215: 4.749 distance: 215 - 218: 7.244 distance: 216 - 223: 3.878 distance: 218 - 219: 12.228 distance: 219 - 220: 16.096 distance: 220 - 221: 7.675 distance: 220 - 222: 17.295 distance: 224 - 225: 3.590 distance: 224 - 227: 8.911 distance: 225 - 226: 4.037 distance: 225 - 230: 5.444 distance: 227 - 228: 25.651 distance: 227 - 229: 18.699 distance: 230 - 231: 6.855 distance: 231 - 232: 10.186 distance: 231 - 234: 10.526 distance: 232 - 233: 12.078 distance: 232 - 238: 8.180 distance: 234 - 235: 5.032 distance: 235 - 236: 13.475 distance: 235 - 237: 11.920 distance: 238 - 239: 11.745 distance: 239 - 240: 14.688 distance: 239 - 242: 12.988 distance: 240 - 241: 8.891 distance: 240 - 246: 7.975 distance: 242 - 243: 6.756 distance: 243 - 244: 23.119 distance: 243 - 245: 32.330 distance: 246 - 247: 3.766 distance: 247 - 248: 6.582 distance: 247 - 250: 3.192 distance: 248 - 249: 7.552 distance: 248 - 251: 3.324 distance: 251 - 252: 3.243 distance: 252 - 253: 6.732 distance: 252 - 255: 4.287 distance: 253 - 254: 16.410 distance: 253 - 259: 3.892 distance: 255 - 256: 4.214 distance: 256 - 257: 3.683 distance: 256 - 258: 5.567