Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 17:59:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/05_2023/7p5w_13203.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/05_2023/7p5w_13203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/05_2023/7p5w_13203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/05_2023/7p5w_13203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/05_2023/7p5w_13203.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5w_13203/05_2023/7p5w_13203.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 26730 2.51 5 N 6960 2.21 5 O 7386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 41250 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: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 19.94, per 1000 atoms: 0.48 Number of scatterers: 41250 At special positions: 0 Unit cell: (187.488, 180.978, 188.79, 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 174 16.00 O 7386 8.00 N 6960 7.00 C 26730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, 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 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.19 Conformation dependent library (CDL) restraints added in 6.1 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: 9648 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 40 sheets defined 44.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.285A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) 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: 5.270A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.027A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.506A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 287 removed outlier: 4.563A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 353 through 360 removed outlier: 4.397A 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 391 removed outlier: 4.111A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.696A 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 removed outlier: 3.518A pdb=" N GLU A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 534 through 543 removed outlier: 4.947A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.553A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.503A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.846A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 806 removed outlier: 3.873A pdb=" N LYS A 799 " --> pdb=" O PRO A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.051A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 5.285A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.993A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 233 through 255 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 344 Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.980A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.038A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.006A 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 535 through 543 removed outlier: 3.908A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.723A 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 629 through 636 removed outlier: 3.752A pdb=" N ILE B 632 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.650A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 659' Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.854A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.501A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 removed outlier: 3.617A pdb=" N GLU B 752 " --> pdb=" O ARG B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.639A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.502A pdb=" N GLU B 800 " --> pdb=" O PRO B 796 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 801 " --> pdb=" O GLU B 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.530A 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 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.284A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.098A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 287 removed outlier: 4.623A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 344 Processing helix chain 'C' and resid 353 through 360 removed outlier: 4.358A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.114A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.520A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.621A 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 495 Processing helix chain 'C' and resid 504 through 508 removed outlier: 3.543A pdb=" N GLU C 507 " --> pdb=" O ASP C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 534 through 543 removed outlier: 5.027A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.056A 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 608 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.515A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.510A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.517A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 4.050A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.825A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 806 removed outlier: 3.863A pdb=" N LYS C 799 " --> pdb=" O PRO C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.089A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.502A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.301A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.026A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 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 344 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.904A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.053A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' 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 535 through 542 removed outlier: 3.945A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.727A 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 629 through 636 removed outlier: 3.642A pdb=" N ILE D 632 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.670A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 659 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.862A 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 726 through 730 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.759A pdb=" N VAL D 750 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU D 752 " --> pdb=" O ARG D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 Processing helix chain 'D' and resid 787 through 792 removed outlier: 3.614A pdb=" N SER D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 805 removed outlier: 4.211A pdb=" N LYS D 799 " --> pdb=" O PRO D 795 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 801 " --> pdb=" O GLU D 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.219A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 5.257A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.053A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 287 removed outlier: 4.612A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 353 through 360 removed outlier: 4.368A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.135A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.571A pdb=" N PHE E 443 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.587A 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 removed outlier: 3.504A pdb=" N GLU E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 534 through 543 removed outlier: 4.979A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.949A 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 608 through 613 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.506A pdb=" N ILE E 632 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 679 through 684 Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.505A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY E 705 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 729 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.938A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 806 removed outlier: 3.835A pdb=" N LYS E 799 " --> pdb=" O PRO E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.039A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (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: 5.299A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.032A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 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 314 through 344 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.943A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.043A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' 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 494 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 535 through 542 removed outlier: 3.821A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 3.584A 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 629 through 636 removed outlier: 3.745A pdb=" N ILE F 632 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE F 633 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 636 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.659A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 655 through 659' Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.878A 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 749 through 753 removed outlier: 3.560A pdb=" N GLU F 752 " --> pdb=" O ARG F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 775 removed outlier: 3.531A pdb=" N GLU F 775 " --> pdb=" O GLU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 removed outlier: 3.582A pdb=" N SER F 792 " --> pdb=" O GLU F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 795 No H-bonds generated for 'chain 'F' and resid 793 through 795' Processing helix chain 'F' and resid 796 through 806 removed outlier: 4.152A pdb=" N ARG F 801 " --> pdb=" O GLU F 797 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.902A pdb=" N LYS K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.632A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.847A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.583A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR J 91 " --> pdb=" O PRO J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.521A pdb=" N LEU A 498 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 5.969A 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 removed outlier: 6.792A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.844A 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: 7.001A 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: 6.610A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 6.251A 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 Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 714 removed outlier: 6.900A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.268A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.744A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.947A 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: 7.055A 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: 6.662A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 6.280A 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 Processing sheet with id=AB9, first strand: chain 'D' and resid 712 through 714 removed outlier: 7.047A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.280A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 459 through 461 removed outlier: 6.738A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.865A 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 712 through 714 removed outlier: 7.227A 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: 6.593A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 459 through 461 Processing sheet with id=AC9, first strand: chain 'F' and resid 712 through 714 removed outlier: 7.038A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.601A pdb=" N VAL K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.660A pdb=" N SER K 120 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.558A pdb=" N VAL L 79 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.602A pdb=" N SER L 120 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.527A pdb=" N VAL G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.634A pdb=" N SER G 120 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.590A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.556A pdb=" N SER H 120 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.556A pdb=" N SER H 120 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 98 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 110 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.579A pdb=" N SER I 120 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.585A pdb=" N VAL J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.622A pdb=" N SER J 120 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) 1753 hydrogen bonds defined for protein. 4521 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: 17.43 Time building geometry restraints manager: 18.30 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: 13065 1.34 - 1.46: 9636 1.46 - 1.58: 19263 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 42204 Sorted by residual: bond pdb=" C ALA C 485 " pdb=" N PRO C 486 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.71e+00 bond pdb=" C ALA E 485 " pdb=" N PRO E 486 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.52e+00 bond pdb=" C ALA A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.12e+00 bond pdb=" CA VAL B 742 " pdb=" CB VAL B 742 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.05e+00 bond pdb=" C GLN L 39 " pdb=" N ALA L 40 " ideal model delta sigma weight residual 1.331 1.310 0.021 2.07e-02 2.33e+03 1.04e+00 ... (remaining 42199 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.09: 1096 107.09 - 113.83: 24044 113.83 - 120.58: 16443 120.58 - 127.32: 15140 127.32 - 134.06: 517 Bond angle restraints: 57240 Sorted by residual: angle pdb=" N VAL B 591 " pdb=" CA VAL B 591 " pdb=" C VAL B 591 " ideal model delta sigma weight residual 113.71 110.68 3.03 9.50e-01 1.11e+00 1.02e+01 angle pdb=" C THR H 104 " pdb=" N THR H 105 " pdb=" CA THR H 105 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.77e+00 angle pdb=" C THR K 104 " pdb=" N THR K 105 " pdb=" CA THR K 105 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.55e+00 angle pdb=" C THR G 104 " pdb=" N THR G 105 " pdb=" CA THR G 105 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.51e+00 angle pdb=" C THR L 104 " pdb=" N THR L 105 " pdb=" CA THR L 105 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.23e+00 ... (remaining 57235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 23495 16.76 - 33.51: 1391 33.51 - 50.27: 397 50.27 - 67.03: 76 67.03 - 83.79: 3 Dihedral angle restraints: 25362 sinusoidal: 10476 harmonic: 14886 Sorted by residual: dihedral pdb=" CA TRP L 33 " pdb=" C TRP L 33 " pdb=" N MET L 34 " pdb=" CA MET L 34 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP J 33 " pdb=" C TRP J 33 " pdb=" N MET J 34 " pdb=" CA MET J 34 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TRP H 33 " pdb=" C TRP H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 25359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3668 0.027 - 0.054: 1873 0.054 - 0.081: 649 0.081 - 0.108: 222 0.108 - 0.135: 86 Chirality restraints: 6498 Sorted by residual: chirality pdb=" CA ILE F 438 " pdb=" N ILE F 438 " pdb=" C ILE F 438 " pdb=" CB ILE F 438 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL L 93 " pdb=" N VAL L 93 " pdb=" C VAL L 93 " pdb=" CB VAL L 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE F 674 " pdb=" N ILE F 674 " pdb=" C ILE F 674 " pdb=" CB ILE F 674 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 6495 not shown) Planarity restraints: 7122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 795 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 796 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 796 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 796 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 795 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO D 796 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 796 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 796 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 795 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO F 796 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 796 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 796 " 0.017 5.00e-02 4.00e+02 ... (remaining 7119 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 791 2.68 - 3.24: 41445 3.24 - 3.79: 67004 3.79 - 4.35: 90060 4.35 - 4.90: 146018 Nonbonded interactions: 345318 Sorted by model distance: nonbonded pdb=" OH TYR B 513 " pdb=" O VAL B 536 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR H 101 " pdb=" O GLN H 107 " model vdw 2.146 2.440 nonbonded pdb=" OG1 THR L 101 " pdb=" O GLN L 107 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR J 101 " pdb=" O GLN J 107 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR D 513 " pdb=" O VAL D 536 " model vdw 2.153 2.440 ... (remaining 345313 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 10.910 Check model and map are aligned: 0.650 Set scattering table: 0.360 Process input model: 102.390 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.310 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 0.044 42204 Z= 0.150 Angle : 0.487 7.016 57240 Z= 0.276 Chirality : 0.039 0.135 6498 Planarity : 0.003 0.033 7122 Dihedral : 11.731 83.787 15642 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 3.75 % 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: -0.37 (0.12), residues: 4980 helix: 0.24 (0.12), residues: 2007 sheet: -0.64 (0.19), residues: 879 loop : -0.36 (0.14), residues: 2094 *********************** 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 940 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 768 time to evaluate : 4.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 40 residues processed: 919 average time/residue: 0.5741 time to fit residues: 843.3738 Evaluate side-chains 392 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 352 time to evaluate : 4.571 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 1 residues processed: 40 average time/residue: 0.4088 time to fit residues: 37.0132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 5.9990 chunk 377 optimal weight: 0.8980 chunk 209 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 390 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 452 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN B 377 HIS ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN B 650 HIS ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 404 GLN D 617 GLN D 696 ASN E 253 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 649 ASN ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 650 HIS ** F 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN G 74 ASN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS H 106 ASN I 84 ASN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 42204 Z= 0.314 Angle : 0.618 8.491 57240 Z= 0.320 Chirality : 0.044 0.206 6498 Planarity : 0.004 0.042 7122 Dihedral : 4.217 19.066 5502 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 2.60 % 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: -0.75 (0.12), residues: 4980 helix: -0.15 (0.12), residues: 2067 sheet: -0.60 (0.19), residues: 879 loop : -0.61 (0.14), residues: 2034 *********************** 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 502 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 383 time to evaluate : 4.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 65 residues processed: 487 average time/residue: 0.5308 time to fit residues: 431.6675 Evaluate side-chains 338 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 273 time to evaluate : 4.882 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4007 time to fit residues: 55.2415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 7.9990 chunk 140 optimal weight: 0.0570 chunk 376 optimal weight: 0.5980 chunk 307 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 453 optimal weight: 5.9990 chunk 489 optimal weight: 8.9990 chunk 403 optimal weight: 9.9990 chunk 449 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 363 optimal weight: 0.8980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 478 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN E 288 ASN ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 42204 Z= 0.177 Angle : 0.539 9.499 57240 Z= 0.279 Chirality : 0.041 0.197 6498 Planarity : 0.003 0.032 7122 Dihedral : 4.095 20.306 5502 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.96 % 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: -0.56 (0.12), residues: 4980 helix: 0.02 (0.12), residues: 2034 sheet: -0.59 (0.19), residues: 912 loop : -0.47 (0.14), residues: 2034 *********************** 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 415 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 325 time to evaluate : 4.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 26 residues processed: 399 average time/residue: 0.5500 time to fit residues: 376.6082 Evaluate side-chains 293 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 267 time to evaluate : 5.027 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4004 time to fit residues: 26.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 5.9990 chunk 340 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 304 optimal weight: 0.9980 chunk 454 optimal weight: 9.9990 chunk 481 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 430 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 GLN K 74 ASN K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 42204 Z= 0.218 Angle : 0.550 9.870 57240 Z= 0.285 Chirality : 0.041 0.199 6498 Planarity : 0.003 0.034 7122 Dihedral : 4.142 18.408 5502 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.99 % 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: -0.69 (0.12), residues: 4980 helix: -0.11 (0.12), residues: 2073 sheet: -0.60 (0.19), residues: 903 loop : -0.55 (0.14), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 4 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 387 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 296 time to evaluate : 4.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 34 residues processed: 373 average time/residue: 0.5089 time to fit residues: 322.6267 Evaluate side-chains 284 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 4.570 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3782 time to fit residues: 30.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 358 optimal weight: 0.5980 chunk 198 optimal weight: 9.9990 chunk 410 optimal weight: 9.9990 chunk 332 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 432 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 711 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN C 649 ASN C 650 HIS C 729 GLN C 755 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 ASN L 116 GLN ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.102 42204 Z= 0.423 Angle : 0.672 14.006 57240 Z= 0.347 Chirality : 0.045 0.255 6498 Planarity : 0.004 0.042 7122 Dihedral : 4.571 20.424 5502 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 1.81 % 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: -1.14 (0.12), residues: 4980 helix: -0.59 (0.11), residues: 2040 sheet: -0.73 (0.19), residues: 909 loop : -0.73 (0.14), residues: 2031 *********************** REFINEMENT MACRO_CYCLE 5 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 375 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 292 time to evaluate : 5.404 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 outliers start: 83 outliers final: 48 residues processed: 361 average time/residue: 0.5287 time to fit residues: 324.4734 Evaluate side-chains 306 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 5.075 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3982 time to fit residues: 42.9778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 0.7980 chunk 433 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 481 optimal weight: 6.9990 chunk 399 optimal weight: 0.5980 chunk 223 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN C 758 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 42204 Z= 0.185 Angle : 0.544 9.532 57240 Z= 0.282 Chirality : 0.041 0.164 6498 Planarity : 0.003 0.085 7122 Dihedral : 4.293 22.048 5502 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.29 % 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: -0.84 (0.12), residues: 4980 helix: -0.23 (0.12), residues: 2055 sheet: -0.65 (0.19), residues: 909 loop : -0.65 (0.14), residues: 2016 *********************** REFINEMENT MACRO_CYCLE 6 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 353 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 294 time to evaluate : 5.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 21 residues processed: 343 average time/residue: 0.5231 time to fit residues: 306.3707 Evaluate side-chains 276 residues out of total 4584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 4.862 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3823 time to fit residues: 21.9762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 58.6446 > 50: distance: 2 - 76: 11.512 distance: 70 - 76: 12.874 distance: 76 - 77: 27.678 distance: 77 - 78: 5.518 distance: 77 - 80: 22.552 distance: 78 - 79: 4.776 distance: 78 - 85: 19.839 distance: 80 - 81: 13.129 distance: 81 - 82: 12.019 distance: 82 - 83: 7.341 distance: 82 - 84: 15.494 distance: 85 - 86: 35.080 distance: 86 - 87: 30.397 distance: 86 - 89: 16.385 distance: 87 - 88: 30.484 distance: 87 - 93: 28.669 distance: 89 - 90: 15.964 distance: 90 - 91: 43.001 distance: 93 - 94: 40.958 distance: 94 - 95: 37.178 distance: 94 - 97: 17.709 distance: 95 - 104: 8.047 distance: 97 - 98: 8.650 distance: 98 - 99: 23.278 distance: 99 - 100: 20.637 distance: 100 - 101: 17.377 distance: 101 - 102: 7.783 distance: 101 - 103: 13.765 distance: 104 - 105: 51.522 distance: 105 - 106: 35.034 distance: 106 - 107: 19.721 distance: 106 - 108: 17.519 distance: 108 - 109: 12.154 distance: 109 - 110: 24.181 distance: 109 - 112: 26.880 distance: 110 - 111: 23.628 distance: 110 - 116: 27.919 distance: 112 - 113: 25.068 distance: 113 - 114: 33.804 distance: 113 - 115: 4.255 distance: 116 - 117: 8.411 distance: 117 - 118: 36.967 distance: 117 - 120: 23.773 distance: 118 - 119: 41.011 distance: 118 - 127: 18.212 distance: 120 - 121: 22.955 distance: 121 - 122: 7.513 distance: 122 - 123: 31.864 distance: 123 - 124: 17.947 distance: 124 - 125: 8.081 distance: 124 - 126: 9.788 distance: 127 - 128: 12.725 distance: 128 - 129: 46.267 distance: 129 - 130: 8.392 distance: 129 - 135: 44.913 distance: 131 - 132: 31.585 distance: 132 - 133: 56.396 distance: 132 - 134: 13.140 distance: 135 - 136: 22.711 distance: 136 - 137: 38.559 distance: 136 - 139: 28.510 distance: 137 - 138: 54.716 distance: 137 - 144: 3.292 distance: 144 - 145: 10.102 distance: 145 - 146: 22.180 distance: 145 - 148: 12.427 distance: 146 - 147: 19.619 distance: 146 - 150: 16.514 distance: 148 - 149: 32.554 distance: 150 - 151: 21.431 distance: 151 - 152: 31.998 distance: 151 - 154: 37.721 distance: 152 - 153: 25.986 distance: 152 - 158: 27.607 distance: 154 - 155: 16.569 distance: 155 - 156: 12.061 distance: 155 - 157: 37.822