Starting phenix.real_space_refine on Sat Feb 24 03:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5y_13208/02_2024/7p5y_13208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5y_13208/02_2024/7p5y_13208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5y_13208/02_2024/7p5y_13208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5y_13208/02_2024/7p5y_13208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5y_13208/02_2024/7p5y_13208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5y_13208/02_2024/7p5y_13208.pdb" } resolution = 3.29 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= 0.004 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 180 5.16 5 C 26616 2.51 5 N 6930 2.21 5 O 7380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41106 Number of models: 1 Model: "" Number of chains: 12 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: 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: "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: 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: "E" 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: "F" 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: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 929 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "H" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 929 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 929 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 929 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 929 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 929 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Time building chain proxies: 20.04, per 1000 atoms: 0.49 Number of scatterers: 41106 At special positions: 0 Unit cell: (196.602, 187.488, 187.488, 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 180 16.00 O 7380 8.00 N 6930 7.00 C 26616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, 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=2.03 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=2.03 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=2.03 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 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " 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: 15.23 Conformation dependent library (CDL) restraints added in 7.0 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9636 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 52 sheets defined 44.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 5.189A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.091A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.920A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.058A 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 287 removed outlier: 4.619A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 343 Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.507A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.097A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.546A pdb=" N ASN A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.817A pdb=" N GLN A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.732A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 534 through 543 removed outlier: 5.395A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.397A 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 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.607A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 611 " --> pdb=" O HIS A 608 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 removed outlier: 5.034A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.523A pdb=" N GLY A 659 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.600A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.628A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.635A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 removed outlier: 3.653A pdb=" N SER A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 805 removed outlier: 3.602A pdb=" N LYS A 799 " --> pdb=" O PRO A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 5.235A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 4.045A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.568A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.505A pdb=" N GLY B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 286 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 314 through 343 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.311A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 420 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 494 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 534 through 543 removed outlier: 4.664A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.053A 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 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.066A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.644A pdb=" N ILE B 610 " --> pdb=" O PRO B 607 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 611 " --> pdb=" O HIS B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 611' Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.546A pdb=" N ILE B 632 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.591A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.719A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.551A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 805 removed outlier: 4.036A pdb=" N LYS B 799 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 801 " --> pdb=" O GLU B 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.504A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 118 removed outlier: 3.779A pdb=" N LEU C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.144A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.193A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.916A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 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 314 through 343 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.540A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.108A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 removed outlier: 3.639A pdb=" N ASN C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 removed outlier: 3.605A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.734A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.828A 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 494 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 534 through 543 removed outlier: 3.528A pdb=" N ILE C 537 " --> pdb=" O TYR C 534 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.579A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 611 " --> pdb=" O HIS C 608 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 612 " --> pdb=" O SER C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 635 Processing helix chain 'C' and resid 655 through 660 removed outlier: 3.904A pdb=" N GLY C 659 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.513A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.933A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 3.615A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.762A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 752 " --> pdb=" O ARG C 749 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 747 through 753' Processing helix chain 'C' and resid 795 through 806 removed outlier: 3.686A pdb=" N LYS C 799 " --> pdb=" O PRO C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 21 Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 5.085A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 4.055A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.540A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 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 343 Processing helix chain 'D' and resid 354 through 360 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.332A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 534 through 543 removed outlier: 4.704A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.282A 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 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 607 through 611 removed outlier: 3.636A pdb=" N ILE D 610 " --> pdb=" O PRO D 607 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE D 611 " --> pdb=" O HIS D 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 607 through 611' Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.562A pdb=" N ILE D 632 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.545A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 659 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.551A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 729 removed outlier: 3.815A pdb=" N PHE D 728 " --> pdb=" O PRO D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.608A pdb=" N VAL D 750 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 Processing helix chain 'D' and resid 787 through 792 removed outlier: 3.530A pdb=" N SER D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 806 removed outlier: 3.918A pdb=" N LYS D 799 " --> pdb=" O PRO D 795 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 801 " --> pdb=" O GLU D 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 5.070A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.196A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.919A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 343 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.557A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.144A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 412 through 418 removed outlier: 3.576A pdb=" N GLN E 418 " --> pdb=" O ASP E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.786A pdb=" N PHE E 443 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 495 Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 534 through 543 removed outlier: 5.364A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.625A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 611 " --> pdb=" O HIS E 608 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 612 " --> pdb=" O SER E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 638 removed outlier: 5.021A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 660 removed outlier: 3.645A pdb=" N GLY E 659 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.572A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY E 705 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.670A pdb=" N CYS E 730 " --> pdb=" O LEU E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.823A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 removed outlier: 3.731A pdb=" N SER E 792 " --> pdb=" O GLU E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 805 removed outlier: 3.564A pdb=" N LYS E 799 " --> pdb=" O PRO E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 removed outlier: 3.581A pdb=" N LEU F 20 " --> pdb=" O TYR F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 5.123A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.033A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 removed outlier: 3.540A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 299 through 304 removed outlier: 3.877A pdb=" N THR F 303 " --> pdb=" O ILE F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 343 Processing helix chain 'F' and resid 354 through 360 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.299A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 441 through 445 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 495 Processing helix chain 'F' and resid 504 through 508 removed outlier: 3.655A pdb=" N ILE F 508 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 534 through 543 removed outlier: 4.722A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 567 through 569 No H-bonds generated for 'chain 'F' and resid 567 through 569' Processing helix chain 'F' and resid 586 through 590 removed outlier: 4.008A pdb=" N LYS F 589 " --> pdb=" O SER F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 removed outlier: 3.586A pdb=" N ILE F 610 " --> pdb=" O PRO F 607 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE F 611 " --> pdb=" O HIS F 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 607 through 611' Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.594A pdb=" N ILE F 632 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE F 633 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN F 636 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.621A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 726 through 730 Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.644A pdb=" N VAL F 750 " --> pdb=" O PRO F 747 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 775 Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 805 removed outlier: 3.848A pdb=" N LYS F 799 " --> pdb=" O PRO F 795 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 801 " --> pdb=" O GLU F 797 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.542A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 4.017A pdb=" N LYS J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'L' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 removed outlier: 3.597A pdb=" N VAL A 293 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.732A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 498 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (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 'A' and resid 618 through 620 removed outlier: 6.019A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 712 through 714 removed outlier: 7.495A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.715A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 459 through 461 removed outlier: 6.858A pdb=" N VAL B 459 " --> pdb=" O LYS B 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 714 removed outlier: 6.377A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.566A pdb=" N VAL C 293 " --> pdb=" O CYS C 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.727A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 498 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AB4, first strand: chain 'C' and resid 618 through 620 removed outlier: 6.158A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 712 through 714 removed outlier: 7.573A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.775A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 459 through 461 removed outlier: 6.919A pdb=" N VAL D 459 " --> pdb=" O LYS D 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 712 through 714 removed outlier: 6.538A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.738A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 523 " --> pdb=" O ARG E 550 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 460 through 461 Processing sheet with id=AC4, first strand: chain 'E' and resid 618 through 620 removed outlier: 6.071A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 689 through 691 removed outlier: 7.942A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC7, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.728A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 459 through 461 removed outlier: 6.869A pdb=" N VAL F 459 " --> pdb=" O LYS F 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 595 through 597 removed outlier: 3.746A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 712 through 714 removed outlier: 6.543A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.522A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 12 through 13 removed outlier: 7.277A pdb=" N VAL G 12 " --> pdb=" O SER G 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.811A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY G 33 " --> pdb=" O LYS G 99 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS G 99 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 98 " --> pdb=" O TYR G 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.811A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY G 33 " --> pdb=" O LYS G 99 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS G 99 " --> pdb=" O GLY G 33 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.803A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 57 through 60 removed outlier: 3.669A pdb=" N SER H 57 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA H 40 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY H 33 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS H 99 " --> pdb=" O GLY H 33 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 57 through 60 removed outlier: 3.669A pdb=" N SER H 57 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA H 40 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY H 33 " --> pdb=" O LYS H 99 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS H 99 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 69 through 73 Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.511A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.816A pdb=" N VAL I 12 " --> pdb=" O SER I 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.523A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY I 33 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I 99 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL I 98 " --> pdb=" O TYR I 110 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR I 110 " --> pdb=" O VAL I 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.523A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.826A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.513A pdb=" N ARG J 45 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA J 40 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.513A pdb=" N ARG J 45 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA J 40 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 69 through 73 Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.747A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 12 through 13 removed outlier: 7.429A pdb=" N VAL K 12 " --> pdb=" O SER K 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.408A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS K 99 " --> pdb=" O GLY K 33 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 98 " --> pdb=" O TYR K 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.408A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS K 99 " --> pdb=" O GLY K 33 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 3 through 4 removed outlier: 3.852A pdb=" N GLN L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 57 through 60 removed outlier: 3.639A pdb=" N SER L 57 " --> pdb=" O GLU L 52 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA L 40 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 57 through 60 removed outlier: 3.639A pdb=" N SER L 57 " --> pdb=" O GLU L 52 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA L 40 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 92 " --> pdb=" O VAL L 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 115 " --> pdb=" O TYR L 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 69 through 73 1726 hydrogen bonds defined for protein. 4422 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: 19.10 Time building geometry restraints manager: 16.50 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: 13053 1.34 - 1.46: 9520 1.46 - 1.58: 19211 1.58 - 1.70: 0 1.70 - 1.82: 252 Bond restraints: 42036 Sorted by residual: bond pdb=" C ALA E 485 " pdb=" N PRO E 486 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.56e+00 bond pdb=" C ALA A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.27e+00 bond pdb=" N PRO C 795 " pdb=" CA PRO C 795 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.16e+00 bond pdb=" C ALA C 485 " pdb=" N PRO C 486 " ideal model delta sigma weight residual 1.336 1.348 -0.012 1.20e-02 6.94e+03 1.07e+00 bond pdb=" CA ILE D 654 " pdb=" CB ILE D 654 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.05e+00 ... (remaining 42031 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.61: 1089 106.61 - 113.47: 23278 113.47 - 120.33: 15271 120.33 - 127.19: 16843 127.19 - 134.05: 507 Bond angle restraints: 56988 Sorted by residual: angle pdb=" C ASN D 370 " pdb=" N ASP D 371 " pdb=" CA ASP D 371 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 angle pdb=" CA TRP F 647 " pdb=" CB TRP F 647 " pdb=" CG TRP F 647 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.12e+00 angle pdb=" CA TRP D 647 " pdb=" CB TRP D 647 " pdb=" CG TRP D 647 " ideal model delta sigma weight residual 113.60 118.68 -5.08 1.90e+00 2.77e-01 7.14e+00 angle pdb=" N PRO C 457 " pdb=" CA PRO C 457 " pdb=" C PRO C 457 " ideal model delta sigma weight residual 110.21 114.33 -4.12 1.64e+00 3.72e-01 6.30e+00 angle pdb=" N PRO E 457 " pdb=" CA PRO E 457 " pdb=" C PRO E 457 " ideal model delta sigma weight residual 110.21 114.26 -4.05 1.64e+00 3.72e-01 6.10e+00 ... (remaining 56983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 23689 17.76 - 35.53: 1337 35.53 - 53.29: 246 53.29 - 71.06: 28 71.06 - 88.82: 14 Dihedral angle restraints: 25314 sinusoidal: 10440 harmonic: 14874 Sorted by residual: dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 65 " pdb=" CB CYS C 65 " ideal model delta sinusoidal sigma weight residual -86.00 -35.62 -50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 65 " pdb=" CB CYS E 65 " ideal model delta sinusoidal sigma weight residual -86.00 -36.82 -49.18 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 65 " pdb=" CB CYS A 65 " ideal model delta sinusoidal sigma weight residual -86.00 -38.04 -47.96 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 25311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3619 0.027 - 0.054: 1930 0.054 - 0.081: 583 0.081 - 0.109: 273 0.109 - 0.136: 81 Chirality restraints: 6486 Sorted by residual: chirality pdb=" CA ILE E 677 " pdb=" N ILE E 677 " pdb=" C ILE E 677 " pdb=" CB ILE E 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 677 " pdb=" N ILE A 677 " pdb=" C ILE A 677 " pdb=" CB ILE A 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE C 677 " pdb=" N ILE C 677 " pdb=" C ILE C 677 " pdb=" CB ILE C 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 6483 not shown) Planarity restraints: 7110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 795 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 796 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 796 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 796 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 795 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO D 796 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 796 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 796 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 647 " 0.011 2.00e-02 2.50e+03 8.05e-03 1.62e+00 pdb=" CG TRP D 647 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP D 647 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 647 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 647 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 647 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 647 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 647 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 647 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 647 " 0.000 2.00e-02 2.50e+03 ... (remaining 7107 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1068 2.71 - 3.26: 42127 3.26 - 3.80: 66676 3.80 - 4.35: 87191 4.35 - 4.90: 144443 Nonbonded interactions: 341505 Sorted by model distance: nonbonded pdb=" OG1 THR C 303 " pdb=" OH TYR C 308 " model vdw 2.158 2.440 nonbonded pdb=" OG1 THR E 303 " pdb=" OH TYR E 308 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR B 303 " pdb=" OH TYR B 308 " model vdw 2.173 2.440 nonbonded pdb=" OH TYR B 513 " pdb=" O VAL B 536 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR F 513 " pdb=" O VAL F 536 " model vdw 2.192 2.440 ... (remaining 341500 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 10.000 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 104.670 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.360 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 0.042 42036 Z= 0.161 Angle : 0.491 6.143 56988 Z= 0.267 Chirality : 0.039 0.136 6486 Planarity : 0.003 0.039 7110 Dihedral : 11.334 88.821 15624 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.64 % Allowed : 7.71 % Favored : 89.65 % 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: -0.32 (0.12), residues: 4980 helix: 0.19 (0.12), residues: 2046 sheet: -0.73 (0.19), residues: 855 loop : -0.17 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 647 HIS 0.003 0.001 HIS F 522 PHE 0.010 0.001 PHE F 41 TYR 0.012 0.001 TYR F 106 ARG 0.002 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 494 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7744 (t80) REVERT: A 715 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7730 (t) REVERT: A 761 LEU cc_start: 0.7062 (mm) cc_final: 0.6658 (mt) REVERT: B 104 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8596 (t70) REVERT: B 794 LEU cc_start: 0.0388 (OUTLIER) cc_final: -0.0339 (tt) REVERT: C 29 ASP cc_start: 0.6593 (m-30) cc_final: 0.6209 (m-30) REVERT: C 104 HIS cc_start: 0.8913 (OUTLIER) cc_final: 0.8521 (t70) REVERT: C 275 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7614 (t80) REVERT: C 601 CYS cc_start: 0.7321 (m) cc_final: 0.6988 (m) REVERT: D 416 LEU cc_start: 0.6071 (mm) cc_final: 0.5730 (mt) REVERT: D 582 ILE cc_start: 0.6141 (pt) cc_final: 0.5830 (pt) REVERT: D 794 LEU cc_start: 0.0437 (OUTLIER) cc_final: -0.0279 (tp) REVERT: E 29 ASP cc_start: 0.6623 (m-30) cc_final: 0.6047 (m-30) REVERT: E 104 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8497 (t70) REVERT: E 635 PHE cc_start: 0.6033 (m-10) cc_final: 0.5779 (m-10) REVERT: E 787 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.5175 (mp0) REVERT: F 104 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8229 (t70) REVERT: F 265 MET cc_start: 0.7267 (tpp) cc_final: 0.6610 (tpt) REVERT: F 343 MET cc_start: 0.7257 (ptm) cc_final: 0.6787 (ptm) REVERT: F 416 LEU cc_start: 0.6212 (mm) cc_final: 0.5804 (mt) REVERT: F 513 TYR cc_start: 0.6500 (m-80) cc_final: 0.6284 (m-80) REVERT: F 618 GLU cc_start: 0.5033 (mp0) cc_final: 0.3923 (tp30) REVERT: F 794 LEU cc_start: 0.0713 (OUTLIER) cc_final: 0.0183 (tp) REVERT: H 83 MET cc_start: 0.2892 (mpp) cc_final: 0.2476 (mpp) REVERT: I 38 ARG cc_start: 0.6089 (ttm-80) cc_final: 0.5654 (ttp80) REVERT: J 83 MET cc_start: 0.1389 (OUTLIER) cc_final: 0.0223 (ptp) REVERT: L 34 MET cc_start: 0.5137 (mmm) cc_final: 0.4854 (mmm) REVERT: L 83 MET cc_start: 0.3403 (mpp) cc_final: 0.2188 (mpp) outliers start: 121 outliers final: 47 residues processed: 607 average time/residue: 0.5309 time to fit residues: 525.6038 Evaluate side-chains 369 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 310 time to evaluate : 4.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 787 GLU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 716 THR Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 7.9990 chunk 377 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 254 optimal weight: 0.1980 chunk 201 optimal weight: 6.9990 chunk 390 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 290 optimal weight: 0.1980 chunk 452 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 657 GLN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 GLN ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN K 39 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42036 Z= 0.167 Angle : 0.525 10.054 56988 Z= 0.270 Chirality : 0.041 0.185 6486 Planarity : 0.003 0.033 7110 Dihedral : 5.601 57.119 5599 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.75 % Allowed : 10.92 % Favored : 86.33 % 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: -0.20 (0.12), residues: 4980 helix: 0.30 (0.12), residues: 2022 sheet: -0.53 (0.19), residues: 843 loop : -0.18 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 647 HIS 0.006 0.001 HIS B 499 PHE 0.017 0.001 PHE J 106 TYR 0.017 0.001 TYR B 281 ARG 0.004 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 331 time to evaluate : 4.558 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: A 275 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 715 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7706 (t) REVERT: A 761 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6557 (mt) REVERT: B 104 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.8599 (t70) REVERT: B 794 LEU cc_start: 0.0561 (OUTLIER) cc_final: -0.0241 (tt) REVERT: C 104 HIS cc_start: 0.8914 (OUTLIER) cc_final: 0.8578 (t70) REVERT: C 275 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 293 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8794 (m) REVERT: C 537 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6506 (tp) REVERT: C 601 CYS cc_start: 0.7282 (m) cc_final: 0.7014 (m) REVERT: D 416 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5818 (mt) REVERT: D 513 TYR cc_start: 0.6259 (m-80) cc_final: 0.5894 (m-80) REVERT: D 582 ILE cc_start: 0.6043 (pt) cc_final: 0.5785 (pt) REVERT: D 618 GLU cc_start: 0.4440 (OUTLIER) cc_final: 0.4092 (tp30) REVERT: D 657 GLN cc_start: 0.2821 (mp-120) cc_final: 0.2431 (mp10) REVERT: D 794 LEU cc_start: 0.0554 (OUTLIER) cc_final: -0.0128 (tp) REVERT: E 29 ASP cc_start: 0.6568 (m-30) cc_final: 0.6107 (m-30) REVERT: E 104 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8512 (t70) REVERT: F 104 HIS cc_start: 0.8913 (OUTLIER) cc_final: 0.8328 (t70) REVERT: F 265 MET cc_start: 0.7256 (tpp) cc_final: 0.6663 (tpt) REVERT: F 343 MET cc_start: 0.7219 (ptm) cc_final: 0.6799 (ptm) REVERT: F 416 LEU cc_start: 0.6399 (mm) cc_final: 0.5850 (mt) REVERT: F 513 TYR cc_start: 0.6452 (m-80) cc_final: 0.6134 (m-80) REVERT: F 794 LEU cc_start: 0.0578 (OUTLIER) cc_final: 0.0199 (tp) REVERT: G 30 MET cc_start: 0.6351 (mmt) cc_final: 0.6126 (tpp) REVERT: H 83 MET cc_start: 0.2943 (mpp) cc_final: 0.2573 (mpp) REVERT: I 95 TYR cc_start: 0.7638 (m-10) cc_final: 0.7237 (m-80) REVERT: J 83 MET cc_start: 0.0430 (OUTLIER) cc_final: -0.0368 (ptp) REVERT: K 46 GLU cc_start: 0.6453 (mp0) cc_final: 0.6013 (mp0) REVERT: L 34 MET cc_start: 0.5123 (mmm) cc_final: 0.4723 (mmm) outliers start: 126 outliers final: 73 residues processed: 432 average time/residue: 0.4845 time to fit residues: 356.2901 Evaluate side-chains 384 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 295 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 716 THR Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 376 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 453 optimal weight: 9.9990 chunk 489 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 449 optimal weight: 8.9990 chunk 154 optimal weight: 0.6980 chunk 363 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 614 HIS ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 614 HIS ** F 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 42036 Z= 0.370 Angle : 0.624 13.124 56988 Z= 0.320 Chirality : 0.044 0.186 6486 Planarity : 0.004 0.031 7110 Dihedral : 5.981 58.504 5587 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.60 % Allowed : 11.73 % Favored : 84.67 % 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: -0.68 (0.12), residues: 4980 helix: -0.21 (0.12), residues: 2061 sheet: -0.70 (0.19), residues: 858 loop : -0.36 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 647 HIS 0.007 0.001 HIS B 132 PHE 0.028 0.002 PHE E 443 TYR 0.031 0.002 TYR A 513 ARG 0.004 0.001 ARG C 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 318 time to evaluate : 5.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7928 (t) REVERT: A 761 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6561 (mt) REVERT: B 104 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8773 (t70) REVERT: B 243 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8750 (tt) REVERT: B 274 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8150 (tttp) REVERT: B 275 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (t80) REVERT: B 794 LEU cc_start: 0.0395 (OUTLIER) cc_final: -0.0462 (tp) REVERT: C 104 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8651 (t70) REVERT: C 265 MET cc_start: 0.6886 (ttt) cc_final: 0.6462 (ttt) REVERT: C 353 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7189 (m-80) REVERT: D 316 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8610 (m) REVERT: D 416 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6050 (mt) REVERT: D 582 ILE cc_start: 0.6036 (pt) cc_final: 0.5690 (pt) REVERT: D 618 GLU cc_start: 0.4809 (OUTLIER) cc_final: 0.4201 (tp30) REVERT: D 794 LEU cc_start: 0.0530 (OUTLIER) cc_final: -0.0267 (tp) REVERT: E 29 ASP cc_start: 0.6750 (m-30) cc_final: 0.6274 (m-30) REVERT: E 102 ASP cc_start: 0.7337 (m-30) cc_final: 0.6956 (m-30) REVERT: E 104 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8621 (t70) REVERT: E 353 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: E 706 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6906 (mt) REVERT: E 780 LYS cc_start: 0.4650 (mtpp) cc_final: 0.4387 (mmtp) REVERT: F 104 HIS cc_start: 0.9040 (OUTLIER) cc_final: 0.8228 (t70) REVERT: F 416 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6086 (mt) REVERT: F 604 GLU cc_start: 0.3805 (OUTLIER) cc_final: 0.3409 (pt0) REVERT: F 794 LEU cc_start: 0.0255 (OUTLIER) cc_final: -0.0115 (tp) REVERT: G 46 GLU cc_start: 0.6389 (mp0) cc_final: 0.6179 (pp20) REVERT: I 30 MET cc_start: 0.7028 (tpp) cc_final: 0.6826 (tpp) REVERT: I 46 GLU cc_start: 0.6924 (mp0) cc_final: 0.6712 (mp0) REVERT: L 34 MET cc_start: 0.5040 (mmm) cc_final: 0.4776 (mmm) outliers start: 165 outliers final: 104 residues processed: 454 average time/residue: 0.4872 time to fit residues: 376.7587 Evaluate side-chains 402 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 278 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 706 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 590 MET Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 716 THR Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 794 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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-5238/modules/cctbx_project/iotbx/cli_parser.py", line 939, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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-5238/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-5238/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-5238/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-5238/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-5238/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-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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-5238/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-5238/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-5238/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-5238/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: 70.5471 > 50: distance: 49 - 144: 34.830 distance: 52 - 141: 32.635 distance: 60 - 140: 33.173 distance: 111 - 138: 32.909 distance: 114 - 135: 27.128 distance: 129 - 135: 29.437 distance: 135 - 136: 41.806 distance: 136 - 137: 31.319 distance: 136 - 139: 39.299 distance: 137 - 138: 5.747 distance: 137 - 141: 27.631 distance: 139 - 140: 46.596 distance: 141 - 142: 9.337 distance: 142 - 143: 3.246 distance: 142 - 145: 20.431 distance: 143 - 144: 55.608 distance: 143 - 146: 47.196 distance: 146 - 147: 15.519 distance: 147 - 148: 14.521 distance: 147 - 150: 14.288 distance: 148 - 149: 39.637 distance: 148 - 156: 38.539 distance: 150 - 151: 30.291 distance: 151 - 153: 39.650 distance: 152 - 154: 20.328 distance: 153 - 155: 9.481 distance: 154 - 155: 20.894 distance: 156 - 162: 38.448 distance: 157 - 160: 27.166 distance: 158 - 163: 39.719 distance: 160 - 161: 11.659 distance: 161 - 162: 56.414 distance: 163 - 164: 57.123 distance: 165 - 166: 12.220 distance: 165 - 171: 27.941 distance: 166 - 191: 40.068 distance: 167 - 168: 40.458 distance: 168 - 169: 40.026 distance: 168 - 170: 57.404 distance: 171 - 172: 41.438 distance: 172 - 173: 40.952 distance: 173 - 174: 41.702 distance: 173 - 176: 49.675 distance: 174 - 202: 7.455 distance: 176 - 177: 6.094 distance: 177 - 178: 42.021 distance: 177 - 180: 50.682 distance: 178 - 179: 56.282 distance: 178 - 183: 41.122 distance: 179 - 211: 34.909 distance: 180 - 181: 22.607 distance: 180 - 182: 54.402 distance: 183 - 184: 40.502 distance: 184 - 185: 29.466 distance: 184 - 187: 9.146 distance: 185 - 186: 50.028 distance: 185 - 191: 43.556 distance: 186 - 219: 33.935 distance: 187 - 188: 18.739 distance: 188 - 189: 26.795 distance: 188 - 190: 26.985 distance: 191 - 192: 18.129 distance: 192 - 193: 19.222 distance: 192 - 195: 9.724 distance: 193 - 194: 36.498 distance: 193 - 202: 18.780 distance: 194 - 227: 20.491 distance: 195 - 196: 16.844 distance: 196 - 197: 6.706 distance: 196 - 198: 43.932 distance: 197 - 199: 41.721 distance: 198 - 200: 42.906 distance: 199 - 201: 6.767 distance: 200 - 201: 27.428 distance: 202 - 203: 39.940 distance: 203 - 204: 22.518 distance: 203 - 206: 33.848 distance: 204 - 205: 31.562 distance: 204 - 211: 32.422 distance: 205 - 232: 33.389 distance: 206 - 207: 10.073 distance: 207 - 208: 23.602 distance: 208 - 209: 19.494 distance: 209 - 210: 27.231