Starting phenix.real_space_refine on Mon Nov 20 21:22:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/11_2023/8b41_15836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/11_2023/8b41_15836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/11_2023/8b41_15836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/11_2023/8b41_15836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/11_2023/8b41_15836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/11_2023/8b41_15836.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 155 5.16 5 C 20336 2.51 5 N 5217 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "E TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 31259 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2125 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain breaks: 3 Chain: "F" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1618 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain breaks: 2 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Time building chain proxies: 16.10, per 1000 atoms: 0.52 Number of scatterers: 31259 At special positions: 0 Unit cell: (180.978, 128.898, 207.018, 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 155 16.00 O 5551 8.00 N 5217 7.00 C 20336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " 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: 13.47 Conformation dependent library (CDL) restraints added in 6.2 seconds 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 29 sheets defined 50.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.741A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.606A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.529A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.099A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.835A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 removed outlier: 3.866A pdb=" N THR A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.541A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 4.179A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.592A pdb=" N VAL A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 444 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 445' Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.858A pdb=" N ALA A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.414A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.501A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.611A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.653A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.725A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.921A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.728A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.959A pdb=" N THR B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 141 Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.759A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.658A pdb=" N SER B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.018A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.705A pdb=" N GLY B 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 removed outlier: 4.205A pdb=" N THR B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.887A pdb=" N THR B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.750A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.720A pdb=" N ILE B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.218A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.624A pdb=" N ASN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 535 through 543 removed outlier: 4.047A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.048A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 590 " --> pdb=" O LEU B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.744A pdb=" N ILE B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.543A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.593A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.729A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.658A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 807 Processing helix chain 'C' and resid 16 through 20 removed outlier: 3.600A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.800A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 124 through 141 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.163A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.876A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 256 removed outlier: 4.210A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.913A pdb=" N THR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 removed outlier: 3.829A pdb=" N LEU C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.561A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.509A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 395 removed outlier: 3.621A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 441 through 445 removed outlier: 4.083A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.663A pdb=" N LEU C 515 " --> pdb=" O ILE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 3.908A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 542 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.614A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.043A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.523A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.800A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 707 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 729 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.683A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.628A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 Processing helix chain 'D' and resid 16 through 20 removed outlier: 4.141A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 50 removed outlier: 3.907A pdb=" N THR D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.762A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.053A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 removed outlier: 3.860A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.767A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.981A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 384 through 392 removed outlier: 3.854A pdb=" N LYS D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 390 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 409 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.806A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.747A pdb=" N GLU D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.623A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.582A pdb=" N ILE D 610 " --> pdb=" O PRO D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.635A pdb=" N ILE D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 701 through 707 removed outlier: 3.551A pdb=" N ILE D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 705 " --> pdb=" O ALA D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.964A pdb=" N CYS D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 753 removed outlier: 4.102A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 776 removed outlier: 3.557A pdb=" N GLU D 775 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.773A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 121 through 148 Proline residue: E 128 - end of helix removed outlier: 4.026A pdb=" N TRP E 145 " --> pdb=" O CYS E 141 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 168 removed outlier: 3.887A pdb=" N SER E 168 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 252 removed outlier: 3.545A pdb=" N LEU E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 284 removed outlier: 4.375A pdb=" N ALA E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 312 through 342 removed outlier: 3.690A pdb=" N LYS E 318 " --> pdb=" O HIS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 381 removed outlier: 3.760A pdb=" N ILE E 377 " --> pdb=" O MET E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 removed outlier: 3.593A pdb=" N ARG E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 392 " --> pdb=" O PHE E 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 50 removed outlier: 3.909A pdb=" N ASP F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.535A pdb=" N LYS F 125 " --> pdb=" O HIS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 148 removed outlier: 4.461A pdb=" N TRP F 145 " --> pdb=" O CYS F 141 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 156 removed outlier: 3.693A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 285 removed outlier: 3.723A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 343 removed outlier: 3.796A pdb=" N PHE F 321 " --> pdb=" O SER F 317 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS F 322 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR F 337 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.819A pdb=" N HIS G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.664A pdb=" N ARG H 31 " --> pdb=" O PRO H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.534A pdb=" N ARG J 31 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.412A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.397A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA8, first strand: chain 'B' and resid 735 through 737 removed outlier: 6.698A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'C' and resid 421 through 422 removed outlier: 4.153A pdb=" N THR C 421 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 498 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 524 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 500 " --> pdb=" O THR C 524 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 521 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LYS C 552 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 523 " --> pdb=" O LYS C 552 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 691 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 56 removed outlier: 8.253A pdb=" N ARG D 306 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 297 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.340A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 498 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR D 524 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 500 " --> pdb=" O THR D 524 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'D' and resid 643 through 645 removed outlier: 7.057A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 759 through 760 removed outlier: 6.716A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AB8, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.883A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AC3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.545A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AC6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.734A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.347A pdb=" N GLY J 10 " --> pdb=" O THR J 112 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.347A pdb=" N GLY J 10 " --> pdb=" O THR J 112 " (cutoff:3.500A) 1504 hydrogen bonds defined for protein. 3882 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: 12.53 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9795 1.34 - 1.46: 7535 1.46 - 1.58: 14443 1.58 - 1.70: 0 1.70 - 1.81: 219 Bond restraints: 31992 Sorted by residual: bond pdb=" CA VAL J 100 " pdb=" CB VAL J 100 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 8.17e-01 bond pdb=" CA ASP E 256 " pdb=" CB ASP E 256 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.72e-01 bond pdb=" CA VAL I 100 " pdb=" CB VAL I 100 " ideal model delta sigma weight residual 1.531 1.540 -0.009 1.11e-02 8.12e+03 6.52e-01 bond pdb=" C LEU B 700 " pdb=" O LEU B 700 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.44e-01 bond pdb=" C ILE C 365 " pdb=" O ILE C 365 " ideal model delta sigma weight residual 1.232 1.239 -0.008 1.01e-02 9.80e+03 5.82e-01 ... (remaining 31987 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.95: 788 106.95 - 113.79: 18096 113.79 - 120.64: 13216 120.64 - 127.49: 10902 127.49 - 134.34: 346 Bond angle restraints: 43348 Sorted by residual: angle pdb=" C GLY E 255 " pdb=" N ASP E 256 " pdb=" CA ASP E 256 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" N LYS C 547 " pdb=" CA LYS C 547 " pdb=" C LYS C 547 " ideal model delta sigma weight residual 114.04 110.41 3.63 1.24e+00 6.50e-01 8.55e+00 angle pdb=" N GLN B 617 " pdb=" CA GLN B 617 " pdb=" C GLN B 617 " ideal model delta sigma weight residual 114.56 111.49 3.07 1.27e+00 6.20e-01 5.86e+00 angle pdb=" N LYS F 304 " pdb=" CA LYS F 304 " pdb=" C LYS F 304 " ideal model delta sigma weight residual 114.56 111.68 2.88 1.27e+00 6.20e-01 5.14e+00 angle pdb=" N VAL A 567 " pdb=" CA VAL A 567 " pdb=" C VAL A 567 " ideal model delta sigma weight residual 112.98 110.20 2.78 1.25e+00 6.40e-01 4.94e+00 ... (remaining 43343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 17692 16.72 - 33.43: 1169 33.43 - 50.15: 255 50.15 - 66.87: 47 66.87 - 83.59: 10 Dihedral angle restraints: 19173 sinusoidal: 7894 harmonic: 11279 Sorted by residual: dihedral pdb=" CA ILE A 278 " pdb=" C ILE A 278 " pdb=" N ILE A 279 " pdb=" CA ILE A 279 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP D 458 " pdb=" CB ASP D 458 " pdb=" CG ASP D 458 " pdb=" OD1 ASP D 458 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA HIS D 253 " pdb=" C HIS D 253 " pdb=" N VAL D 254 " pdb=" CA VAL D 254 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 19170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2819 0.029 - 0.057: 1467 0.057 - 0.086: 395 0.086 - 0.114: 185 0.114 - 0.143: 37 Chirality restraints: 4903 Sorted by residual: chirality pdb=" CA VAL B 786 " pdb=" N VAL B 786 " pdb=" C VAL B 786 " pdb=" CB VAL B 786 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 654 " pdb=" N ILE A 654 " pdb=" C ILE A 654 " pdb=" CB ILE A 654 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE B 508 " pdb=" N ILE B 508 " pdb=" C ILE B 508 " pdb=" CB ILE B 508 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.56e-01 ... (remaining 4900 not shown) Planarity restraints: 5371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 320 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C ILE C 320 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE C 320 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 321 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 383 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO C 384 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 323 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C SER C 323 " 0.027 2.00e-02 2.50e+03 pdb=" O SER C 323 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE C 324 " -0.009 2.00e-02 2.50e+03 ... (remaining 5368 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1022 2.71 - 3.26: 32059 3.26 - 3.81: 51306 3.81 - 4.35: 64126 4.35 - 4.90: 106493 Nonbonded interactions: 255006 Sorted by model distance: nonbonded pdb=" OH TYR C 513 " pdb=" O VAL C 536 " model vdw 2.169 2.440 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR C 679 " pdb=" OD2 ASP C 703 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR D 48 " pdb=" OE1 GLN D 49 " model vdw 2.223 2.440 nonbonded pdb=" NH1 ARG A 419 " pdb=" O HIS A 431 " model vdw 2.228 2.520 ... (remaining 255001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 176 or resid 230 through 808)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 176 or resid 230 through 808)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.800 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: 0.030 Extract box with map and model: 9.340 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 82.860 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 99.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.002 0.030 31992 Z= 0.157 Angle : 0.482 7.151 43348 Z= 0.272 Chirality : 0.039 0.143 4903 Planarity : 0.003 0.040 5371 Dihedral : 11.826 83.587 11817 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.69 % Allowed : 7.60 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3759 helix: 0.13 (0.13), residues: 1674 sheet: -0.45 (0.21), residues: 626 loop : -0.60 (0.16), residues: 1459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 610 time to evaluate : 3.787 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 outliers start: 163 outliers final: 69 residues processed: 751 average time/residue: 0.4632 time to fit residues: 545.5017 Evaluate side-chains 399 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 330 time to evaluate : 3.574 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.2871 time to fit residues: 41.5486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 2.9990 chunk 284 optimal weight: 0.0270 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 294 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 341 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 570 GLN B 592 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 696 ASN C 105 GLN C 408 ASN C 431 HIS C 670 ASN D 116 ASN D 418 GLN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN E 106 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN H 32 HIS H 74 ASN H 110 GLN I 3 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31992 Z= 0.194 Angle : 0.564 10.062 43348 Z= 0.295 Chirality : 0.041 0.187 4903 Planarity : 0.004 0.036 5371 Dihedral : 4.158 19.712 4179 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.94 % Allowed : 13.82 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3759 helix: 0.31 (0.13), residues: 1679 sheet: -0.33 (0.21), residues: 626 loop : -0.59 (0.16), residues: 1454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 389 time to evaluate : 3.767 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 outliers start: 102 outliers final: 44 residues processed: 476 average time/residue: 0.4142 time to fit residues: 320.8076 Evaluate side-chains 357 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 313 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2820 time to fit residues: 27.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 342 optimal weight: 10.0000 chunk 369 optimal weight: 0.0010 chunk 304 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31992 Z= 0.283 Angle : 0.580 9.087 43348 Z= 0.304 Chirality : 0.042 0.161 4903 Planarity : 0.004 0.045 5371 Dihedral : 4.302 20.891 4179 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.17 % Allowed : 14.95 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3759 helix: 0.27 (0.13), residues: 1679 sheet: -0.42 (0.22), residues: 622 loop : -0.66 (0.16), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 337 time to evaluate : 2.946 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 outliers start: 110 outliers final: 69 residues processed: 418 average time/residue: 0.4053 time to fit residues: 277.9185 Evaluate side-chains 359 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 290 time to evaluate : 3.373 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.2874 time to fit residues: 42.3598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 0.0870 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 0.1980 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 325 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 431 HIS ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31992 Z= 0.186 Angle : 0.525 11.260 43348 Z= 0.274 Chirality : 0.040 0.162 4903 Planarity : 0.003 0.044 5371 Dihedral : 4.175 19.343 4179 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.90 % Allowed : 16.07 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3759 helix: 0.28 (0.13), residues: 1711 sheet: -0.52 (0.22), residues: 602 loop : -0.64 (0.16), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 328 time to evaluate : 3.466 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 outliers start: 66 outliers final: 23 residues processed: 381 average time/residue: 0.3139 time to fit residues: 196.3594 Evaluate side-chains 299 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 276 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2015 time to fit residues: 11.8692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 8.9990 chunk 206 optimal weight: 0.0370 chunk 5 optimal weight: 9.9990 chunk 270 optimal weight: 0.6980 chunk 149 optimal weight: 0.0010 chunk 310 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 326 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 106 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS F 113 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31992 Z= 0.173 Angle : 0.514 11.414 43348 Z= 0.268 Chirality : 0.040 0.153 4903 Planarity : 0.003 0.043 5371 Dihedral : 4.093 20.040 4179 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.41 % Allowed : 17.71 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3759 helix: 0.33 (0.13), residues: 1710 sheet: -0.34 (0.22), residues: 622 loop : -0.69 (0.17), residues: 1427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 312 time to evaluate : 3.851 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 outliers start: 49 outliers final: 27 residues processed: 344 average time/residue: 0.3882 time to fit residues: 221.6988 Evaluate side-chains 311 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 284 time to evaluate : 3.111 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2604 time to fit residues: 18.0479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 190 optimal weight: 9.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS I 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31992 Z= 0.199 Angle : 0.527 10.631 43348 Z= 0.274 Chirality : 0.041 0.202 4903 Planarity : 0.003 0.057 5371 Dihedral : 4.115 20.497 4179 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.73 % Allowed : 18.12 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3759 helix: 0.37 (0.13), residues: 1694 sheet: -0.35 (0.21), residues: 622 loop : -0.67 (0.17), residues: 1443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 304 time to evaluate : 3.950 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 outliers start: 60 outliers final: 24 residues processed: 350 average time/residue: 0.4158 time to fit residues: 241.8554 Evaluate side-chains 305 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 281 time to evaluate : 3.571 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2889 time to fit residues: 17.8573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 265 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2911 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: