Starting phenix.real_space_refine on Sat Jul 27 23:45:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5v_13202/07_2024/7p5v_13202.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5v_13202/07_2024/7p5v_13202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5v_13202/07_2024/7p5v_13202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5v_13202/07_2024/7p5v_13202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5v_13202/07_2024/7p5v_13202.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5v_13202/07_2024/7p5v_13202.cif" } resolution = 3.06 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 174 5.16 5 C 26757 2.51 5 N 6957 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 PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 41274 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: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 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: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "K" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Time building chain proxies: 20.64, per 1000 atoms: 0.50 Number of scatterers: 41274 At special positions: 0 Unit cell: (179.676, 169.26, 205.716, 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 6957 7.00 C 26757 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=2.02 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 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 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 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: 15.37 Conformation dependent library (CDL) restraints added in 7.4 seconds 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9642 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 38 sheets defined 47.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.577A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (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: 5.283A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.878A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.942A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.797A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.550A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 4.286A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.628A pdb=" N GLU A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.863A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.407A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.861A 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: 3.601A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.503A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.690A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.985A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.961A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 15 through 20 removed outlier: 4.189A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.754A pdb=" N LEU B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 5.026A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.928A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.724A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.629A pdb=" N GLN B 221 " --> pdb=" O ARG B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' 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 346 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.710A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.851A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 395 removed outlier: 3.935A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.691A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.575A pdb=" N LEU B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.671A pdb=" N LEU B 515 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.970A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.934A 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 609 through 613 Processing helix chain 'B' and resid 629 through 637 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.547A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.509A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.584A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 707 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.570A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.934A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 753 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.505A pdb=" N GLU B 775 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 20 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: 5.298A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.915A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.962A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.562A 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 347 removed outlier: 3.830A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 removed outlier: 3.506A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.537A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 removed outlier: 4.289A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.872A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 495 removed outlier: 3.665A pdb=" N GLU C 493 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.870A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.588A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.871A 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 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.649A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.719A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.839A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.915A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 Processing helix chain 'D' and resid 15 through 20 removed outlier: 4.098A pdb=" N ARG D 18 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 3.609A 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 118 removed outlier: 3.718A pdb=" N LEU D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.894A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.953A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 removed outlier: 3.638A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 removed outlier: 3.528A pdb=" N GLN D 221 " --> pdb=" O ARG D 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 221' 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 347 removed outlier: 4.136A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.674A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.647A pdb=" N LEU D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.905A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 3.758A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.939A pdb=" N PHE D 443 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.728A pdb=" N LEU D 515 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 543 removed outlier: 4.015A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.014A 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 609 through 613 Processing helix chain 'D' and resid 629 through 637 Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.564A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 removed outlier: 3.576A pdb=" N GLY D 705 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 707 " --> pdb=" O ILE D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.585A pdb=" N CYS D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.935A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 removed outlier: 3.519A pdb=" N GLU D 775 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 16 through 20 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: 5.079A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.901A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.890A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.522A 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 347 removed outlier: 3.793A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.564A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.514A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 395 removed outlier: 4.341A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.854A pdb=" N PHE E 443 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E 444 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.517A 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 removed outlier: 3.616A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 535 through 543 removed outlier: 3.553A pdb=" N ASP E 538 " --> pdb=" O ILE E 535 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.860A 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: 3.592A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 637 removed outlier: 3.538A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 678 through 684 removed outlier: 3.599A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 4.085A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.876A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 15 through 20 removed outlier: 4.231A pdb=" N ARG F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 118 removed outlier: 3.707A pdb=" N LEU F 118 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.853A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.873A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 removed outlier: 3.690A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 221 removed outlier: 3.606A pdb=" N GLN F 221 " --> pdb=" O ARG F 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 221' 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 346 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.731A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.581A pdb=" N LEU F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.957A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 441 through 445 removed outlier: 3.898A pdb=" N LEU F 445 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 485 through 495 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 535 through 543 removed outlier: 4.060A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 3.955A 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 609 through 613 Processing helix chain 'F' and resid 629 through 637 Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.505A pdb=" N LEU F 661 " --> pdb=" O ILE F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.609A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.542A pdb=" N GLY F 705 " --> pdb=" O ALA F 702 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU F 707 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 removed outlier: 3.607A pdb=" N CYS F 730 " --> pdb=" O LEU F 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.966A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.851A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.581A pdb=" N ARG G 31 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.834A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.621A pdb=" N HIS H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.636A pdb=" N ARG I 31 " --> pdb=" O PRO I 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.808A pdb=" N THR I 91 " --> pdb=" O PRO I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.701A pdb=" N HIS J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.676A pdb=" N ARG K 31 " --> pdb=" O PRO K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.530A pdb=" N HIS L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.528A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.645A 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 735 through 737 removed outlier: 6.581A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.697A pdb=" N GLU B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.623A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 596 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 714 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.645A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.579A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.692A pdb=" N GLU D 484 " --> pdb=" O ILE D 461 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.589A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.820A 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: 6.353A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 498 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR D 524 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE D 500 " --> pdb=" O THR D 524 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU D 596 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 714 " --> pdb=" O LEU D 690 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.554A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU E 644 " --> pdb=" O TYR E 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.717A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 735 through 737 removed outlier: 6.549A pdb=" N LEU E 736 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC1, first strand: chain 'F' and resid 223 through 224 removed outlier: 3.643A pdb=" N GLU F 484 " --> pdb=" O ILE F 461 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.693A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 498 " --> pdb=" O HIS F 522 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR F 524 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE F 500 " --> pdb=" O THR F 524 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 596 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 714 " --> pdb=" O LEU F 690 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.544A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 18 " --> pdb=" O MET G 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.952A pdb=" N SER G 114 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.952A pdb=" N SER G 114 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.568A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.528A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 18 " --> pdb=" O MET I 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.714A pdb=" N SER I 114 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.714A pdb=" N SER I 114 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.551A pdb=" N VAL J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.554A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.589A pdb=" N VAL K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU K 18 " --> pdb=" O MET K 83 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.916A pdb=" N SER K 114 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.916A pdb=" N SER K 114 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.503A pdb=" N VAL L 5 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.586A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 11 through 12 1941 hydrogen bonds defined for protein. 4845 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: 18.72 Time building geometry restraints manager: 16.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13071 1.34 - 1.46: 7844 1.46 - 1.58: 21061 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 42216 Sorted by residual: bond pdb=" CB CYS F 295 " pdb=" SG CYS F 295 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.87e+00 bond pdb=" CB CYS D 295 " pdb=" SG CYS D 295 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.82e+00 bond pdb=" CB CYS A 310 " pdb=" SG CYS A 310 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CB CYS D 310 " pdb=" SG CYS D 310 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB CYS A 295 " pdb=" SG CYS A 295 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.77e+00 ... (remaining 42211 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.66: 1049 106.66 - 113.50: 23509 113.50 - 120.34: 15668 120.34 - 127.18: 16496 127.18 - 134.02: 503 Bond angle restraints: 57225 Sorted by residual: angle pdb=" N ILE E 535 " pdb=" CA ILE E 535 " pdb=" C ILE E 535 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N ILE C 535 " pdb=" CA ILE C 535 " pdb=" C ILE C 535 " ideal model delta sigma weight residual 112.96 108.34 4.62 1.00e+00 1.00e+00 2.13e+01 angle pdb=" N ILE A 535 " pdb=" CA ILE A 535 " pdb=" C ILE A 535 " ideal model delta sigma weight residual 111.90 108.92 2.98 8.10e-01 1.52e+00 1.35e+01 angle pdb=" N GLN A 711 " pdb=" CA GLN A 711 " pdb=" C GLN A 711 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.79e+00 angle pdb=" C GLN L 39 " pdb=" N ALA L 40 " pdb=" CA ALA L 40 " ideal model delta sigma weight residual 120.68 116.71 3.97 1.52e+00 4.33e-01 6.81e+00 ... (remaining 57220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 23764 17.92 - 35.83: 1307 35.83 - 53.75: 287 53.75 - 71.67: 33 71.67 - 89.58: 10 Dihedral angle restraints: 25401 sinusoidal: 10497 harmonic: 14904 Sorted by residual: dihedral pdb=" CA LYS F 51 " pdb=" C LYS F 51 " pdb=" N MET F 52 " pdb=" CA MET F 52 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LYS D 51 " pdb=" C LYS D 51 " pdb=" N MET D 52 " pdb=" CA MET D 52 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA LYS A 51 " pdb=" C LYS A 51 " pdb=" N MET A 52 " pdb=" CA MET A 52 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 25398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3755 0.030 - 0.061: 1936 0.061 - 0.091: 489 0.091 - 0.121: 272 0.121 - 0.152: 43 Chirality restraints: 6495 Sorted by residual: chirality pdb=" CA ILE F 299 " pdb=" N ILE F 299 " pdb=" C ILE F 299 " pdb=" CB ILE F 299 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE B 654 " pdb=" N ILE B 654 " pdb=" C ILE B 654 " pdb=" CB ILE B 654 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE F 654 " pdb=" N ILE F 654 " pdb=" C ILE F 654 " pdb=" CB ILE F 654 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 6492 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 22 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 21 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 22 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO F 22 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.018 5.00e-02 4.00e+02 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 615 2.66 - 3.22: 39335 3.22 - 3.78: 64025 3.78 - 4.34: 90708 4.34 - 4.90: 148415 Nonbonded interactions: 343098 Sorted by model distance: nonbonded pdb=" OG SER C 634 " pdb=" OH TYR I 52 " model vdw 2.106 2.440 nonbonded pdb=" OG SER E 634 " pdb=" OH TYR K 52 " model vdw 2.128 2.440 nonbonded pdb=" OG SER A 634 " pdb=" OH TYR G 52 " model vdw 2.134 2.440 nonbonded pdb=" OE2 GLU B 630 " pdb=" OH TYR B 653 " model vdw 2.177 2.440 nonbonded pdb=" OE2 GLU D 630 " pdb=" OH TYR D 653 " model vdw 2.187 2.440 ... (remaining 343093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 176 or resid 230 through 808)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 176 or resid 230 through 808)) selection = chain 'E' selection = (chain 'F' and (resid 15 through 176 or resid 230 through 808)) } 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: 1.930 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: 0.040 Extract box with map and model: 1.790 Check model and map are aligned: 0.330 Set scattering table: 0.430 Process input model: 108.440 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.190 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.004 0.045 42216 Z= 0.237 Angle : 0.514 8.367 57225 Z= 0.282 Chirality : 0.041 0.152 6495 Planarity : 0.003 0.035 7128 Dihedral : 11.638 89.585 15687 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.53 % Allowed : 6.83 % Favored : 89.64 % 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: -0.53 (0.12), residues: 4986 helix: -0.31 (0.11), residues: 2178 sheet: -0.41 (0.18), residues: 921 loop : -0.06 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 342 HIS 0.004 0.001 HIS E 694 PHE 0.014 0.001 PHE A 146 TYR 0.015 0.002 TYR D 106 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 670 time to evaluate : 4.612 Fit side-chains REVERT: A 505 ILE cc_start: 0.6833 (mm) cc_final: 0.6608 (mm) REVERT: A 515 LEU cc_start: 0.5261 (mt) cc_final: 0.4986 (mt) REVERT: B 35 MET cc_start: 0.7599 (mtm) cc_final: 0.7390 (mtt) REVERT: B 153 LEU cc_start: 0.7213 (mt) cc_final: 0.6985 (mt) REVERT: B 220 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6973 (pt0) REVERT: B 279 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7637 (tp) REVERT: B 375 MET cc_start: 0.5686 (mtt) cc_final: 0.5357 (mtt) REVERT: B 385 LEU cc_start: 0.6607 (tp) cc_final: 0.6297 (mp) REVERT: B 647 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7810 (p90) REVERT: C 171 ARG cc_start: 0.4990 (ttt-90) cc_final: 0.4618 (mtp-110) REVERT: C 275 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 504 ASP cc_start: 0.4574 (t0) cc_final: 0.4195 (t0) REVERT: C 755 ASN cc_start: 0.7244 (m110) cc_final: 0.6948 (m-40) REVERT: D 102 ASP cc_start: 0.7947 (m-30) cc_final: 0.7743 (m-30) REVERT: D 148 ARG cc_start: 0.7024 (ttt180) cc_final: 0.6657 (mpt-90) REVERT: D 228 GLU cc_start: 0.6425 (mm-30) cc_final: 0.6016 (tt0) REVERT: D 279 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7512 (tp) REVERT: D 370 ASN cc_start: 0.5408 (OUTLIER) cc_final: 0.5028 (p0) REVERT: D 375 MET cc_start: 0.5841 (mtt) cc_final: 0.5613 (mtt) REVERT: D 385 LEU cc_start: 0.6546 (tp) cc_final: 0.6340 (mp) REVERT: D 647 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.7620 (p90) REVERT: D 770 PRO cc_start: 0.6970 (Cg_endo) cc_final: 0.6474 (Cg_exo) REVERT: E 102 ASP cc_start: 0.7357 (m-30) cc_final: 0.7096 (m-30) REVERT: E 232 LEU cc_start: 0.2296 (OUTLIER) cc_final: 0.1979 (mm) REVERT: E 279 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (tp) REVERT: E 448 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6981 (mp) REVERT: E 505 ILE cc_start: 0.7329 (mm) cc_final: 0.6892 (tp) REVERT: E 623 ASP cc_start: 0.7637 (t0) cc_final: 0.7376 (t70) REVERT: F 15 PRO cc_start: 0.4276 (Cg_endo) cc_final: 0.3975 (Cg_exo) REVERT: F 353 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.4440 (m-80) REVERT: F 385 LEU cc_start: 0.6981 (tp) cc_final: 0.6200 (mp) REVERT: F 493 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6573 (mm-30) REVERT: F 647 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.7936 (p90) REVERT: G 68 PHE cc_start: 0.3010 (m-10) cc_final: 0.2682 (m-10) REVERT: H 97 TYR cc_start: 0.6980 (t80) cc_final: 0.6191 (t80) REVERT: I 34 MET cc_start: 0.6070 (mmm) cc_final: 0.5740 (mmm) REVERT: I 58 THR cc_start: 0.7046 (p) cc_final: 0.6719 (t) REVERT: J 67 ARG cc_start: 0.5226 (mtm110) cc_final: 0.4475 (mtp85) REVERT: J 68 PHE cc_start: 0.7000 (m-10) cc_final: 0.6316 (m-10) REVERT: J 103 GLU cc_start: 0.6178 (mt-10) cc_final: 0.5784 (mt-10) REVERT: K 34 MET cc_start: 0.5809 (mmm) cc_final: 0.5540 (mmm) REVERT: K 58 THR cc_start: 0.7167 (p) cc_final: 0.6763 (p) REVERT: K 72 ARG cc_start: 0.5351 (ptt180) cc_final: 0.4696 (ptt90) REVERT: L 84 ASN cc_start: 0.5091 (m110) cc_final: 0.4341 (t0) REVERT: L 86 LEU cc_start: 0.3072 (mp) cc_final: 0.2653 (mt) outliers start: 162 outliers final: 67 residues processed: 818 average time/residue: 0.5478 time to fit residues: 720.6304 Evaluate side-chains 433 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 354 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 670 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 107 GLN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 2.9990 chunk 377 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 390 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 452 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN B 253 HIS B 418 GLN B 526 ASN B 585 ASN C 239 GLN C 560 GLN C 709 ASN D 253 HIS D 418 GLN D 526 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN F 253 HIS H 82 GLN H 84 ASN H 110 GLN J 77 ASN J 102 ASN K 77 ASN L 77 ASN L 110 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42216 Z= 0.205 Angle : 0.545 10.716 57225 Z= 0.288 Chirality : 0.042 0.168 6495 Planarity : 0.004 0.039 7128 Dihedral : 6.056 57.834 5675 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.36 % Allowed : 10.01 % Favored : 86.63 % 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: -0.38 (0.12), residues: 4986 helix: -0.12 (0.11), residues: 2151 sheet: -0.31 (0.18), residues: 915 loop : -0.10 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 342 HIS 0.009 0.001 HIS K 32 PHE 0.012 0.001 PHE A 146 TYR 0.016 0.001 TYR J 104 ARG 0.007 0.000 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 389 time to evaluate : 4.875 Fit side-chains revert: symmetry clash REVERT: A 515 LEU cc_start: 0.5295 (mt) cc_final: 0.5085 (mt) REVERT: A 689 TYR cc_start: 0.7355 (m-80) cc_final: 0.7062 (m-80) REVERT: B 220 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6866 (pt0) REVERT: B 279 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7556 (tp) REVERT: B 353 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6029 (m-80) REVERT: B 375 MET cc_start: 0.5755 (mtt) cc_final: 0.5406 (mtt) REVERT: B 385 LEU cc_start: 0.6536 (tp) cc_final: 0.6232 (mp) REVERT: B 647 TRP cc_start: 0.8410 (OUTLIER) cc_final: 0.7769 (p90) REVERT: C 104 HIS cc_start: 0.8913 (OUTLIER) cc_final: 0.7685 (t70) REVERT: C 171 ARG cc_start: 0.5053 (ttt-90) cc_final: 0.4603 (mtp-110) REVERT: C 250 PHE cc_start: 0.6891 (t80) cc_final: 0.6668 (t80) REVERT: C 504 ASP cc_start: 0.4563 (t0) cc_final: 0.4263 (t0) REVERT: C 755 ASN cc_start: 0.7204 (m110) cc_final: 0.6969 (m-40) REVERT: D 375 MET cc_start: 0.5787 (mtt) cc_final: 0.5520 (mtt) REVERT: D 513 TYR cc_start: 0.5682 (m-10) cc_final: 0.5469 (m-10) REVERT: D 570 GLN cc_start: 0.6636 (pp30) cc_final: 0.6196 (pp30) REVERT: D 647 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7422 (p90) REVERT: E 448 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7197 (mp) REVERT: E 623 ASP cc_start: 0.7618 (t0) cc_final: 0.7349 (t70) REVERT: F 279 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7615 (tp) REVERT: F 353 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.4186 (m-80) REVERT: F 385 LEU cc_start: 0.6929 (tp) cc_final: 0.6182 (mp) REVERT: F 493 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6467 (mm-30) REVERT: F 647 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.8048 (p90) REVERT: F 689 TYR cc_start: 0.6942 (m-80) cc_final: 0.6603 (m-80) REVERT: G 58 THR cc_start: 0.7135 (p) cc_final: 0.6834 (t) REVERT: G 68 PHE cc_start: 0.3242 (m-10) cc_final: 0.2784 (m-10) REVERT: G 83 MET cc_start: 0.3728 (mpp) cc_final: 0.2951 (mpp) REVERT: H 3 GLN cc_start: 0.6319 (tp40) cc_final: 0.5907 (tp40) REVERT: I 3 GLN cc_start: 0.3225 (pm20) cc_final: 0.2750 (pm20) REVERT: J 59 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6529 (mp0) REVERT: J 67 ARG cc_start: 0.5495 (mtm110) cc_final: 0.4797 (mtp85) REVERT: K 34 MET cc_start: 0.5827 (mmm) cc_final: 0.5603 (mmm) REVERT: K 58 THR cc_start: 0.6959 (p) cc_final: 0.6694 (t) REVERT: K 68 PHE cc_start: 0.2786 (m-10) cc_final: 0.2373 (m-10) REVERT: K 72 ARG cc_start: 0.5600 (ptt180) cc_final: 0.4974 (ptt90) REVERT: L 83 MET cc_start: 0.5097 (mtm) cc_final: 0.4646 (mtm) REVERT: L 84 ASN cc_start: 0.5422 (m110) cc_final: 0.4773 (t0) REVERT: L 86 LEU cc_start: 0.3116 (mp) cc_final: 0.2745 (mt) REVERT: L 104 TYR cc_start: 0.5521 (m-80) cc_final: 0.5168 (m-10) outliers start: 154 outliers final: 90 residues processed: 523 average time/residue: 0.5087 time to fit residues: 440.2274 Evaluate side-chains 421 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 321 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU 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 670 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 376 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 453 optimal weight: 7.9990 chunk 489 optimal weight: 10.0000 chunk 403 optimal weight: 0.9980 chunk 449 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 363 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 568 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 42216 Z= 0.357 Angle : 0.600 12.147 57225 Z= 0.315 Chirality : 0.045 0.221 6495 Planarity : 0.004 0.043 7128 Dihedral : 5.955 56.976 5638 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.41 % Allowed : 10.91 % Favored : 84.69 % 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: -0.72 (0.12), residues: 4986 helix: -0.38 (0.11), residues: 2166 sheet: -0.57 (0.17), residues: 921 loop : -0.25 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 342 HIS 0.005 0.001 HIS D 312 PHE 0.018 0.002 PHE A 146 TYR 0.020 0.002 TYR B 106 ARG 0.007 0.001 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 347 time to evaluate : 4.812 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7297 (mp) REVERT: A 527 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5558 (pp) REVERT: A 689 TYR cc_start: 0.7443 (m-80) cc_final: 0.7160 (m-80) REVERT: B 220 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6807 (pt0) REVERT: B 375 MET cc_start: 0.5959 (mtt) cc_final: 0.5605 (mtt) REVERT: B 385 LEU cc_start: 0.6538 (tp) cc_final: 0.6324 (mp) REVERT: B 647 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.7669 (p90) REVERT: C 104 HIS cc_start: 0.8985 (OUTLIER) cc_final: 0.7870 (t70) REVERT: C 171 ARG cc_start: 0.5163 (ttt-90) cc_final: 0.4728 (mtp-110) REVERT: C 275 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8055 (t80) REVERT: C 504 ASP cc_start: 0.4532 (t0) cc_final: 0.4304 (t0) REVERT: C 527 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5482 (pp) REVERT: D 370 ASN cc_start: 0.6051 (OUTLIER) cc_final: 0.5313 (p0) REVERT: D 375 MET cc_start: 0.5994 (mtt) cc_final: 0.5642 (mtt) REVERT: D 570 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6161 (pp30) REVERT: D 647 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7617 (p90) REVERT: E 102 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: E 275 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7897 (t80) REVERT: E 448 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7271 (mp) REVERT: E 623 ASP cc_start: 0.7609 (t0) cc_final: 0.7333 (t70) REVERT: F 15 PRO cc_start: 0.4242 (Cg_endo) cc_final: 0.3942 (Cg_exo) REVERT: F 353 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.4220 (m-80) REVERT: F 385 LEU cc_start: 0.7257 (tp) cc_final: 0.6396 (mp) REVERT: F 647 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.8021 (p90) REVERT: F 689 TYR cc_start: 0.6798 (m-80) cc_final: 0.6502 (m-10) REVERT: G 58 THR cc_start: 0.7023 (p) cc_final: 0.6761 (t) REVERT: G 68 PHE cc_start: 0.3166 (m-10) cc_final: 0.2449 (m-10) REVERT: G 73 ASP cc_start: 0.4499 (p0) cc_final: 0.3934 (p0) REVERT: G 83 MET cc_start: 0.3911 (mpp) cc_final: 0.3457 (mpp) REVERT: H 3 GLN cc_start: 0.5936 (tp40) cc_final: 0.5611 (tp40) REVERT: I 3 GLN cc_start: 0.3247 (pm20) cc_final: 0.2906 (pm20) REVERT: I 83 MET cc_start: 0.3858 (mpp) cc_final: 0.3111 (mpt) REVERT: J 59 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6355 (mp0) REVERT: J 67 ARG cc_start: 0.5603 (mtm110) cc_final: 0.4723 (mtp85) REVERT: J 74 ASN cc_start: 0.6018 (OUTLIER) cc_final: 0.5268 (t0) REVERT: K 58 THR cc_start: 0.6832 (p) cc_final: 0.6577 (t) REVERT: K 68 PHE cc_start: 0.3196 (m-10) cc_final: 0.2619 (m-10) REVERT: K 72 ARG cc_start: 0.5712 (ptt180) cc_final: 0.4950 (ptt90) REVERT: K 105 TRP cc_start: 0.6478 (m100) cc_final: 0.6198 (m100) REVERT: L 83 MET cc_start: 0.5070 (mtm) cc_final: 0.4686 (mtm) REVERT: L 84 ASN cc_start: 0.5610 (m110) cc_final: 0.4606 (t0) REVERT: L 86 LEU cc_start: 0.2979 (mp) cc_final: 0.2605 (mt) REVERT: L 104 TYR cc_start: 0.5670 (m-80) cc_final: 0.5126 (m-10) outliers start: 202 outliers final: 139 residues processed: 521 average time/residue: 0.5066 time to fit residues: 440.3640 Evaluate side-chains 466 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 311 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 SER Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR 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: 3.9990 chunk 235 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 chunk 481 optimal weight: 6.9990 chunk 237 optimal weight: 0.7980 chunk 430 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS D 253 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN G 77 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 42216 Z= 0.245 Angle : 0.541 9.893 57225 Z= 0.286 Chirality : 0.043 0.197 6495 Planarity : 0.004 0.039 7128 Dihedral : 5.773 56.326 5631 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.10 % Allowed : 12.19 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 4986 helix: -0.27 (0.11), residues: 2166 sheet: -0.59 (0.17), residues: 921 loop : -0.23 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 342 HIS 0.005 0.001 HIS A 104 PHE 0.015 0.002 PHE D 393 TYR 0.021 0.001 TYR J 104 ARG 0.004 0.000 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 340 time to evaluate : 4.835 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 689 TYR cc_start: 0.7421 (m-80) cc_final: 0.7107 (m-80) REVERT: B 220 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: B 375 MET cc_start: 0.5877 (mtt) cc_final: 0.5674 (mtt) REVERT: B 385 LEU cc_start: 0.6621 (tp) cc_final: 0.6324 (mp) REVERT: B 647 TRP cc_start: 0.8360 (OUTLIER) cc_final: 0.7550 (p90) REVERT: C 104 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.7704 (t70) REVERT: C 171 ARG cc_start: 0.5123 (ttt-90) cc_final: 0.4746 (mtp-110) REVERT: C 504 ASP cc_start: 0.4503 (t0) cc_final: 0.4262 (t0) REVERT: D 234 LYS cc_start: 0.6772 (tppt) cc_final: 0.6360 (tppt) REVERT: D 370 ASN cc_start: 0.5965 (OUTLIER) cc_final: 0.5221 (p0) REVERT: D 375 MET cc_start: 0.5804 (mtt) cc_final: 0.5475 (mtt) REVERT: D 570 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6128 (pp30) REVERT: D 591 VAL cc_start: 0.7752 (t) cc_final: 0.7293 (p) REVERT: D 647 TRP cc_start: 0.8579 (OUTLIER) cc_final: 0.7533 (p90) REVERT: E 102 ASP cc_start: 0.7190 (m-30) cc_final: 0.6889 (m-30) REVERT: E 275 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7961 (t80) REVERT: E 448 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7263 (mp) REVERT: E 623 ASP cc_start: 0.7569 (t0) cc_final: 0.7288 (t70) REVERT: F 15 PRO cc_start: 0.4220 (Cg_endo) cc_final: 0.3918 (Cg_exo) REVERT: F 353 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.4245 (m-80) REVERT: F 385 LEU cc_start: 0.7173 (tp) cc_final: 0.6332 (mp) REVERT: F 647 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.7974 (p90) REVERT: F 689 TYR cc_start: 0.6918 (m-80) cc_final: 0.6554 (m-10) REVERT: G 58 THR cc_start: 0.6875 (p) cc_final: 0.6637 (t) REVERT: G 68 PHE cc_start: 0.3462 (m-10) cc_final: 0.2774 (m-10) REVERT: G 73 ASP cc_start: 0.4419 (p0) cc_final: 0.3890 (p0) REVERT: G 83 MET cc_start: 0.3843 (mpp) cc_final: 0.3477 (mpp) REVERT: H 3 GLN cc_start: 0.5859 (tp40) cc_final: 0.5613 (tp40) REVERT: H 36 TRP cc_start: 0.5044 (m100) cc_final: 0.4085 (m100) REVERT: I 83 MET cc_start: 0.4102 (mpp) cc_final: 0.3769 (mpt) REVERT: J 59 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6349 (mp0) REVERT: J 67 ARG cc_start: 0.5630 (mtm110) cc_final: 0.4828 (mtp85) REVERT: J 74 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5259 (t0) REVERT: J 83 MET cc_start: 0.3750 (mtm) cc_final: 0.3532 (ptt) REVERT: K 34 MET cc_start: 0.6220 (mmm) cc_final: 0.5934 (mmm) REVERT: K 58 THR cc_start: 0.6823 (p) cc_final: 0.6601 (t) REVERT: K 68 PHE cc_start: 0.3176 (m-10) cc_final: 0.2600 (m-10) REVERT: K 72 ARG cc_start: 0.5731 (ptt180) cc_final: 0.4925 (ptt90) REVERT: L 83 MET cc_start: 0.4962 (mtm) cc_final: 0.4738 (mtm) REVERT: L 84 ASN cc_start: 0.5523 (m110) cc_final: 0.4792 (t0) REVERT: L 86 LEU cc_start: 0.3090 (mp) cc_final: 0.2748 (mt) outliers start: 188 outliers final: 136 residues processed: 508 average time/residue: 0.4959 time to fit residues: 421.8165 Evaluate side-chains 461 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 313 time to evaluate : 4.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 SER Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 358 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 410 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 245 optimal weight: 0.0470 chunk 432 optimal weight: 20.0000 chunk 121 optimal weight: 0.6980 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN F 253 HIS F 570 GLN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 42216 Z= 0.191 Angle : 0.515 10.973 57225 Z= 0.271 Chirality : 0.042 0.240 6495 Planarity : 0.003 0.039 7128 Dihedral : 5.586 57.242 5631 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.99 % Allowed : 12.63 % Favored : 83.38 % 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: -0.50 (0.12), residues: 4986 helix: -0.15 (0.11), residues: 2169 sheet: -0.52 (0.17), residues: 915 loop : -0.17 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 342 HIS 0.004 0.001 HIS A 104 PHE 0.016 0.001 PHE I 68 TYR 0.019 0.001 TYR H 104 ARG 0.005 0.000 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 339 time to evaluate : 5.291 Fit side-chains revert: symmetry clash REVERT: A 527 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5486 (pp) REVERT: A 689 TYR cc_start: 0.7401 (m-80) cc_final: 0.7101 (m-80) REVERT: B 220 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6826 (pt0) REVERT: B 375 MET cc_start: 0.5845 (mtt) cc_final: 0.5531 (mtt) REVERT: B 385 LEU cc_start: 0.6504 (tp) cc_final: 0.6221 (mp) REVERT: B 599 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 647 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.7548 (p90) REVERT: B 767 GLU cc_start: 0.3845 (OUTLIER) cc_final: 0.2714 (mp0) REVERT: C 48 THR cc_start: 0.7888 (m) cc_final: 0.7520 (m) REVERT: C 104 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.7787 (t70) REVERT: C 171 ARG cc_start: 0.5140 (ttt-90) cc_final: 0.4790 (mtp-110) REVERT: C 527 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5437 (pp) REVERT: C 723 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7030 (mt) REVERT: D 234 LYS cc_start: 0.6595 (tppt) cc_final: 0.6315 (tppt) REVERT: D 370 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.5110 (p0) REVERT: D 375 MET cc_start: 0.5721 (mtt) cc_final: 0.5410 (mtt) REVERT: D 570 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6116 (pp30) REVERT: D 591 VAL cc_start: 0.7671 (t) cc_final: 0.7268 (p) REVERT: D 647 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7503 (p90) REVERT: E 623 ASP cc_start: 0.7535 (t0) cc_final: 0.7265 (t70) REVERT: F 353 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.4123 (m-80) REVERT: F 385 LEU cc_start: 0.6908 (tp) cc_final: 0.6150 (mp) REVERT: F 647 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.8076 (p90) REVERT: F 726 GLU cc_start: 0.5699 (mp0) cc_final: 0.5408 (pm20) REVERT: G 34 MET cc_start: 0.5682 (mmm) cc_final: 0.5451 (mmp) REVERT: G 58 THR cc_start: 0.7007 (p) cc_final: 0.6691 (t) REVERT: G 68 PHE cc_start: 0.3407 (m-10) cc_final: 0.2772 (m-10) REVERT: G 73 ASP cc_start: 0.4428 (p0) cc_final: 0.3886 (p0) REVERT: G 83 MET cc_start: 0.3892 (mpp) cc_final: 0.3323 (mpp) REVERT: H 36 TRP cc_start: 0.4836 (m100) cc_final: 0.3941 (m100) REVERT: I 83 MET cc_start: 0.4025 (mpp) cc_final: 0.3360 (mpt) REVERT: J 67 ARG cc_start: 0.5619 (mtm110) cc_final: 0.4836 (mtp85) REVERT: J 74 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5233 (t0) REVERT: K 34 MET cc_start: 0.6131 (mmm) cc_final: 0.5835 (mmm) REVERT: K 58 THR cc_start: 0.7100 (p) cc_final: 0.6823 (t) REVERT: K 68 PHE cc_start: 0.3195 (m-10) cc_final: 0.2627 (m-10) REVERT: L 84 ASN cc_start: 0.5485 (m110) cc_final: 0.4787 (t0) REVERT: L 86 LEU cc_start: 0.3068 (mp) cc_final: 0.2740 (mt) outliers start: 183 outliers final: 130 residues processed: 500 average time/residue: 0.4913 time to fit residues: 413.4191 Evaluate side-chains 451 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 307 time to evaluate : 4.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 SER Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 109 THR 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: 0.2980 chunk 95 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 312 HIS D 253 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 42216 Z= 0.333 Angle : 0.584 9.330 57225 Z= 0.306 Chirality : 0.044 0.227 6495 Planarity : 0.004 0.039 7128 Dihedral : 5.757 56.995 5621 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.32 % Allowed : 12.81 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4986 helix: -0.29 (0.11), residues: 2145 sheet: -0.65 (0.17), residues: 918 loop : -0.27 (0.15), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 342 HIS 0.005 0.001 HIS D 253 PHE 0.022 0.002 PHE D 353 TYR 0.017 0.002 TYR C 264 ARG 0.006 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 317 time to evaluate : 4.857 Fit side-chains REVERT: A 263 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7413 (mp) REVERT: A 527 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5296 (pp) REVERT: A 689 TYR cc_start: 0.7473 (m-80) cc_final: 0.7162 (m-80) REVERT: B 162 LYS cc_start: 0.6677 (ptpt) cc_final: 0.6272 (mtpp) REVERT: B 220 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: B 341 TRP cc_start: 0.4589 (OUTLIER) cc_final: 0.3739 (t60) REVERT: B 375 MET cc_start: 0.5999 (mtt) cc_final: 0.5602 (mtt) REVERT: B 385 LEU cc_start: 0.6567 (tp) cc_final: 0.6305 (mp) REVERT: B 647 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7612 (p90) REVERT: B 767 GLU cc_start: 0.3923 (OUTLIER) cc_final: 0.2779 (mp0) REVERT: C 104 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.7818 (t70) REVERT: C 171 ARG cc_start: 0.5197 (ttt-90) cc_final: 0.4792 (mtp-110) REVERT: C 429 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5948 (pp20) REVERT: C 527 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5497 (pp) REVERT: C 723 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7238 (mt) REVERT: D 234 LYS cc_start: 0.6590 (tppt) cc_final: 0.6341 (tppt) REVERT: D 370 ASN cc_start: 0.6022 (OUTLIER) cc_final: 0.5274 (p0) REVERT: D 375 MET cc_start: 0.5745 (mtt) cc_final: 0.5340 (mtt) REVERT: D 570 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6156 (pp30) REVERT: D 591 VAL cc_start: 0.7814 (t) cc_final: 0.7386 (p) REVERT: D 647 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.7628 (p90) REVERT: D 648 TYR cc_start: 0.7942 (m-80) cc_final: 0.7677 (m-80) REVERT: D 749 ARG cc_start: 0.6348 (mtp180) cc_final: 0.5744 (mtp180) REVERT: D 767 GLU cc_start: 0.4858 (OUTLIER) cc_final: 0.3734 (mp0) REVERT: E 102 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: F 353 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.4078 (m-80) REVERT: F 385 LEU cc_start: 0.7186 (tp) cc_final: 0.6306 (mp) REVERT: F 647 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.8029 (p90) REVERT: F 689 TYR cc_start: 0.6781 (m-80) cc_final: 0.6473 (m-10) REVERT: F 726 GLU cc_start: 0.5720 (mp0) cc_final: 0.5412 (pm20) REVERT: G 58 THR cc_start: 0.6900 (p) cc_final: 0.6669 (t) REVERT: G 68 PHE cc_start: 0.3422 (m-10) cc_final: 0.2766 (m-10) REVERT: G 83 MET cc_start: 0.3612 (mpp) cc_final: 0.2975 (mpp) REVERT: H 36 TRP cc_start: 0.4984 (m100) cc_final: 0.4023 (m100) REVERT: J 38 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.4975 (ptp-110) REVERT: J 67 ARG cc_start: 0.5745 (mtm110) cc_final: 0.4731 (mtp85) REVERT: J 74 ASN cc_start: 0.6020 (OUTLIER) cc_final: 0.5205 (t0) REVERT: K 34 MET cc_start: 0.6182 (mmm) cc_final: 0.5975 (mmm) REVERT: K 58 THR cc_start: 0.6942 (p) cc_final: 0.6676 (t) REVERT: K 68 PHE cc_start: 0.3236 (m-10) cc_final: 0.2658 (m-10) REVERT: L 28 PRO cc_start: 0.5490 (Cg_endo) cc_final: 0.5276 (Cg_exo) REVERT: L 38 ARG cc_start: 0.5979 (ptp-170) cc_final: 0.5634 (ptp-110) REVERT: L 83 MET cc_start: 0.4975 (mtm) cc_final: 0.4597 (mtt) REVERT: L 84 ASN cc_start: 0.5556 (m110) cc_final: 0.4773 (t0) REVERT: L 86 LEU cc_start: 0.3061 (mp) cc_final: 0.2706 (mt) REVERT: L 104 TYR cc_start: 0.5407 (m-80) cc_final: 0.5111 (m-10) outliers start: 198 outliers final: 154 residues processed: 490 average time/residue: 0.5075 time to fit residues: 422.8838 Evaluate side-chains 477 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 304 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 341 TRP Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 SER Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 274 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 405 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 479 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 chunk 221 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 660 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42216 Z= 0.175 Angle : 0.511 10.477 57225 Z= 0.268 Chirality : 0.042 0.235 6495 Planarity : 0.003 0.040 7128 Dihedral : 5.456 57.651 5619 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.51 % Allowed : 13.79 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4986 helix: -0.03 (0.11), residues: 2127 sheet: -0.55 (0.17), residues: 912 loop : -0.14 (0.15), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 342 HIS 0.005 0.001 HIS A 104 PHE 0.015 0.001 PHE D 353 TYR 0.018 0.001 TYR L 97 ARG 0.004 0.000 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 336 time to evaluate : 5.223 Fit side-chains REVERT: A 263 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 527 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5477 (pp) REVERT: A 689 TYR cc_start: 0.7379 (m-80) cc_final: 0.7077 (m-80) REVERT: B 162 LYS cc_start: 0.6574 (ptpt) cc_final: 0.6311 (mttt) REVERT: B 375 MET cc_start: 0.5618 (mtt) cc_final: 0.5389 (mtt) REVERT: B 599 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 647 TRP cc_start: 0.8296 (OUTLIER) cc_final: 0.7488 (p90) REVERT: B 767 GLU cc_start: 0.3933 (OUTLIER) cc_final: 0.2820 (mp0) REVERT: C 48 THR cc_start: 0.7845 (m) cc_final: 0.7460 (m) REVERT: C 104 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.7792 (t70) REVERT: C 527 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5445 (pp) REVERT: D 162 LYS cc_start: 0.6912 (ptpt) cc_final: 0.6514 (mtpp) REVERT: D 375 MET cc_start: 0.5362 (mtt) cc_final: 0.5045 (mtt) REVERT: D 570 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6147 (pp30) REVERT: D 591 VAL cc_start: 0.7638 (t) cc_final: 0.7285 (p) REVERT: D 647 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.7595 (p90) REVERT: D 749 ARG cc_start: 0.6680 (mtp180) cc_final: 0.6070 (mtp85) REVERT: D 767 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.3682 (mp0) REVERT: F 153 LEU cc_start: 0.7451 (mt) cc_final: 0.7193 (mp) REVERT: F 353 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.4038 (m-10) REVERT: F 385 LEU cc_start: 0.7139 (tp) cc_final: 0.6311 (mp) REVERT: F 647 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.8078 (p90) REVERT: F 726 GLU cc_start: 0.5673 (mp0) cc_final: 0.5383 (pm20) REVERT: G 34 MET cc_start: 0.5346 (mmm) cc_final: 0.4787 (mmp) REVERT: G 58 THR cc_start: 0.6878 (p) cc_final: 0.6660 (t) REVERT: G 68 PHE cc_start: 0.3391 (m-10) cc_final: 0.2767 (m-10) REVERT: G 83 MET cc_start: 0.3823 (mpp) cc_final: 0.3191 (mpp) REVERT: H 36 TRP cc_start: 0.4867 (m100) cc_final: 0.4105 (m100) REVERT: J 38 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.4701 (ptp-110) REVERT: J 67 ARG cc_start: 0.5745 (mtm110) cc_final: 0.4893 (mtp85) REVERT: J 74 ASN cc_start: 0.5920 (OUTLIER) cc_final: 0.5181 (t0) REVERT: K 68 PHE cc_start: 0.3277 (m-10) cc_final: 0.2776 (m-10) REVERT: L 38 ARG cc_start: 0.5918 (ptp-170) cc_final: 0.5568 (ptp-110) REVERT: L 56 GLU cc_start: 0.6195 (mm-30) cc_final: 0.5896 (mm-30) REVERT: L 84 ASN cc_start: 0.5384 (m110) cc_final: 0.4720 (t0) REVERT: L 86 LEU cc_start: 0.3142 (mp) cc_final: 0.2804 (mt) outliers start: 161 outliers final: 126 residues processed: 479 average time/residue: 0.5073 time to fit residues: 407.8443 Evaluate side-chains 448 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 308 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 SER Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 286 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 377 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN D 253 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 ASN F 253 HIS ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 42216 Z= 0.154 Angle : 0.507 12.898 57225 Z= 0.266 Chirality : 0.041 0.261 6495 Planarity : 0.003 0.040 7128 Dihedral : 5.247 55.335 5612 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.49 % Allowed : 14.20 % Favored : 82.31 % 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: -0.33 (0.12), residues: 4986 helix: 0.04 (0.11), residues: 2154 sheet: -0.48 (0.18), residues: 912 loop : -0.13 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 342 HIS 0.006 0.001 HIS D 253 PHE 0.025 0.001 PHE C 250 TYR 0.021 0.001 TYR J 104 ARG 0.004 0.000 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 323 time to evaluate : 5.032 Fit side-chains revert: symmetry clash REVERT: A 527 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.5211 (pp) REVERT: A 689 TYR cc_start: 0.7372 (m-80) cc_final: 0.7092 (m-80) REVERT: B 162 LYS cc_start: 0.6532 (ptpt) cc_final: 0.6281 (mttt) REVERT: B 375 MET cc_start: 0.5745 (mtt) cc_final: 0.5427 (mtt) REVERT: B 599 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7983 (mt) REVERT: B 647 TRP cc_start: 0.8340 (OUTLIER) cc_final: 0.7682 (p90) REVERT: B 767 GLU cc_start: 0.3893 (OUTLIER) cc_final: 0.2779 (mp0) REVERT: C 48 THR cc_start: 0.7807 (m) cc_final: 0.7424 (m) REVERT: C 104 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.7786 (t70) REVERT: C 527 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5411 (pp) REVERT: C 723 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7138 (mt) REVERT: D 162 LYS cc_start: 0.6935 (ptpt) cc_final: 0.6520 (mtpp) REVERT: D 375 MET cc_start: 0.5513 (mtt) cc_final: 0.5219 (mtt) REVERT: D 570 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.6113 (pp30) REVERT: D 591 VAL cc_start: 0.7594 (t) cc_final: 0.7279 (p) REVERT: D 647 TRP cc_start: 0.8484 (OUTLIER) cc_final: 0.7485 (p90) REVERT: D 648 TYR cc_start: 0.7825 (m-80) cc_final: 0.7462 (m-80) REVERT: E 275 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7823 (t80) REVERT: E 587 LEU cc_start: 0.7195 (tp) cc_final: 0.6920 (tp) REVERT: F 353 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.4044 (m-10) REVERT: F 385 LEU cc_start: 0.6832 (tp) cc_final: 0.6089 (mp) REVERT: F 647 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.8029 (p90) REVERT: F 726 GLU cc_start: 0.5693 (mp0) cc_final: 0.5396 (pm20) REVERT: G 34 MET cc_start: 0.5380 (mmm) cc_final: 0.4930 (mmp) REVERT: G 58 THR cc_start: 0.6831 (p) cc_final: 0.6606 (t) REVERT: G 68 PHE cc_start: 0.3248 (m-10) cc_final: 0.2775 (m-10) REVERT: G 83 MET cc_start: 0.4144 (mpp) cc_final: 0.3457 (mpp) REVERT: H 34 MET cc_start: 0.6226 (mmm) cc_final: 0.5853 (mmp) REVERT: H 36 TRP cc_start: 0.4893 (m100) cc_final: 0.4163 (m100) REVERT: J 38 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.4655 (ptp-110) REVERT: J 67 ARG cc_start: 0.5694 (mtm110) cc_final: 0.4836 (mtp85) REVERT: J 74 ASN cc_start: 0.5838 (OUTLIER) cc_final: 0.5142 (t0) REVERT: J 83 MET cc_start: 0.4512 (ptt) cc_final: 0.4300 (mtm) REVERT: K 34 MET cc_start: 0.5349 (mmm) cc_final: 0.5037 (mmp) REVERT: K 68 PHE cc_start: 0.3086 (m-10) cc_final: 0.2645 (m-10) REVERT: L 36 TRP cc_start: 0.5028 (m100) cc_final: 0.4636 (m100) REVERT: L 38 ARG cc_start: 0.5938 (ptp-170) cc_final: 0.5615 (ptp-110) REVERT: L 84 ASN cc_start: 0.5348 (m110) cc_final: 0.4741 (t0) REVERT: L 86 LEU cc_start: 0.3412 (mp) cc_final: 0.2991 (mt) REVERT: L 102 ASN cc_start: 0.6231 (p0) cc_final: 0.5640 (m-40) outliers start: 160 outliers final: 124 residues processed: 462 average time/residue: 0.5190 time to fit residues: 402.8295 Evaluate side-chains 441 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 303 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 SER Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 5.9990 chunk 459 optimal weight: 0.8980 chunk 419 optimal weight: 5.9990 chunk 447 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 351 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 404 optimal weight: 0.0170 chunk 423 optimal weight: 0.8980 chunk 445 optimal weight: 0.0040 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 431 HIS B 624 ASN D 253 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 ASN F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 42216 Z= 0.144 Angle : 0.504 10.524 57225 Z= 0.263 Chirality : 0.041 0.235 6495 Planarity : 0.003 0.042 7128 Dihedral : 4.944 55.146 5599 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.21 % Allowed : 14.44 % Favored : 82.35 % 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: -0.28 (0.12), residues: 4986 helix: 0.08 (0.11), residues: 2175 sheet: -0.41 (0.18), residues: 906 loop : -0.13 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 342 HIS 0.006 0.001 HIS D 253 PHE 0.021 0.001 PHE D 353 TYR 0.026 0.001 TYR L 97 ARG 0.007 0.000 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 313 time to evaluate : 4.858 Fit side-chains revert: symmetry clash REVERT: A 527 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5299 (pp) REVERT: A 689 TYR cc_start: 0.7362 (m-80) cc_final: 0.7096 (m-80) REVERT: B 375 MET cc_start: 0.5713 (mtt) cc_final: 0.5384 (mtt) REVERT: B 599 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 647 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7724 (p90) REVERT: B 767 GLU cc_start: 0.4122 (OUTLIER) cc_final: 0.2967 (mp0) REVERT: C 48 THR cc_start: 0.7763 (m) cc_final: 0.7401 (m) REVERT: C 104 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.7825 (t70) REVERT: C 527 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5612 (pp) REVERT: D 162 LYS cc_start: 0.6938 (ptpt) cc_final: 0.6510 (mtpp) REVERT: D 375 MET cc_start: 0.5453 (mtt) cc_final: 0.5186 (mtt) REVERT: D 591 VAL cc_start: 0.7466 (t) cc_final: 0.7192 (p) REVERT: D 647 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7509 (p90) REVERT: D 648 TYR cc_start: 0.7870 (m-80) cc_final: 0.7504 (m-80) REVERT: F 153 LEU cc_start: 0.7551 (mt) cc_final: 0.7310 (mp) REVERT: F 279 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7618 (tp) REVERT: F 353 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.4057 (m-10) REVERT: F 385 LEU cc_start: 0.6838 (tp) cc_final: 0.6083 (mp) REVERT: F 647 TRP cc_start: 0.8481 (OUTLIER) cc_final: 0.8177 (p90) REVERT: F 726 GLU cc_start: 0.5671 (mp0) cc_final: 0.5384 (pm20) REVERT: F 767 GLU cc_start: 0.3779 (OUTLIER) cc_final: 0.2833 (mp0) REVERT: G 34 MET cc_start: 0.5424 (mmm) cc_final: 0.5022 (mmp) REVERT: G 68 PHE cc_start: 0.3311 (m-10) cc_final: 0.2786 (m-10) REVERT: G 83 MET cc_start: 0.4139 (mpp) cc_final: 0.3490 (mpp) REVERT: H 36 TRP cc_start: 0.4850 (m100) cc_final: 0.4135 (m100) REVERT: H 84 ASN cc_start: 0.5728 (t0) cc_final: 0.5382 (t0) REVERT: K 68 PHE cc_start: 0.3382 (m-10) cc_final: 0.2953 (m-10) REVERT: L 84 ASN cc_start: 0.5301 (m110) cc_final: 0.4771 (t0) REVERT: L 86 LEU cc_start: 0.3463 (mp) cc_final: 0.3086 (mt) REVERT: L 102 ASN cc_start: 0.6448 (p0) cc_final: 0.5741 (m-40) outliers start: 147 outliers final: 117 residues processed: 440 average time/residue: 0.5306 time to fit residues: 395.8554 Evaluate side-chains 429 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 301 time to evaluate : 4.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 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 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain F residue 767 GLU Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 0.1980 chunk 472 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 chunk 224 optimal weight: 0.7980 chunk 328 optimal weight: 0.9990 chunk 496 optimal weight: 8.9990 chunk 456 optimal weight: 2.9990 chunk 395 optimal weight: 0.7980 chunk 41 optimal weight: 0.0040 chunk 305 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 42216 Z= 0.141 Angle : 0.502 12.701 57225 Z= 0.261 Chirality : 0.041 0.267 6495 Planarity : 0.003 0.042 7128 Dihedral : 4.764 55.214 5592 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.95 % Allowed : 14.83 % Favored : 82.22 % 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: -0.23 (0.12), residues: 4986 helix: 0.13 (0.12), residues: 2175 sheet: -0.39 (0.18), residues: 906 loop : -0.12 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 342 HIS 0.006 0.001 HIS D 253 PHE 0.020 0.001 PHE D 353 TYR 0.022 0.001 TYR L 97 ARG 0.006 0.000 ARG E 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 323 time to evaluate : 4.817 Fit side-chains REVERT: A 516 LYS cc_start: 0.5559 (mmmt) cc_final: 0.5311 (ttmt) REVERT: A 527 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5289 (pp) REVERT: A 689 TYR cc_start: 0.7303 (m-80) cc_final: 0.7057 (m-80) REVERT: B 155 HIS cc_start: 0.6827 (t-170) cc_final: 0.6545 (t-170) REVERT: B 343 MET cc_start: 0.5730 (ttm) cc_final: 0.5436 (ttp) REVERT: B 375 MET cc_start: 0.5709 (mtt) cc_final: 0.5387 (mtt) REVERT: B 599 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7946 (mp) REVERT: B 647 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7706 (p90) REVERT: B 767 GLU cc_start: 0.4105 (OUTLIER) cc_final: 0.2948 (mp0) REVERT: C 48 THR cc_start: 0.7746 (m) cc_final: 0.7383 (m) REVERT: C 104 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.7816 (t70) REVERT: C 527 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5577 (pp) REVERT: C 723 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7236 (mt) REVERT: D 162 LYS cc_start: 0.6921 (ptpt) cc_final: 0.6496 (mtpp) REVERT: D 341 TRP cc_start: 0.5119 (t60) cc_final: 0.4653 (t60) REVERT: D 375 MET cc_start: 0.5435 (mtt) cc_final: 0.5219 (mtt) REVERT: D 591 VAL cc_start: 0.7455 (t) cc_final: 0.7202 (p) REVERT: D 648 TYR cc_start: 0.7869 (m-80) cc_final: 0.7631 (m-80) REVERT: D 749 ARG cc_start: 0.6733 (mtp180) cc_final: 0.6193 (mtp85) REVERT: E 587 LEU cc_start: 0.7119 (tp) cc_final: 0.6857 (tp) REVERT: F 153 LEU cc_start: 0.7590 (mt) cc_final: 0.7351 (mp) REVERT: F 279 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7621 (tp) REVERT: F 353 PHE cc_start: 0.5854 (OUTLIER) cc_final: 0.4000 (m-10) REVERT: F 385 LEU cc_start: 0.6730 (tp) cc_final: 0.5981 (mp) REVERT: F 647 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.8165 (p90) REVERT: F 767 GLU cc_start: 0.3774 (OUTLIER) cc_final: 0.2828 (mp0) REVERT: G 34 MET cc_start: 0.5384 (mmm) cc_final: 0.5026 (mmp) REVERT: G 68 PHE cc_start: 0.3397 (m-10) cc_final: 0.2854 (m-10) REVERT: G 83 MET cc_start: 0.4140 (mpp) cc_final: 0.3428 (mpp) REVERT: H 36 TRP cc_start: 0.4831 (m100) cc_final: 0.4114 (m100) REVERT: H 84 ASN cc_start: 0.6179 (t0) cc_final: 0.5940 (t0) REVERT: K 34 MET cc_start: 0.5555 (mmm) cc_final: 0.5219 (mmm) REVERT: L 36 TRP cc_start: 0.4814 (m100) cc_final: 0.4613 (m100) REVERT: L 84 ASN cc_start: 0.5385 (m110) cc_final: 0.4848 (t0) REVERT: L 86 LEU cc_start: 0.3473 (mp) cc_final: 0.3081 (mt) REVERT: L 102 ASN cc_start: 0.6436 (p0) cc_final: 0.5734 (m-40) outliers start: 135 outliers final: 117 residues processed: 440 average time/residue: 0.5024 time to fit residues: 371.0700 Evaluate side-chains 429 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 301 time to evaluate : 4.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 789 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 670 ASN Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain F residue 767 GLU Chi-restraints excluded: chain F residue 771 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 789 ASP Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 2.9990 chunk 420 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 364 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 109 optimal weight: 0.0270 chunk 395 optimal weight: 0.0470 chunk 165 optimal weight: 0.3980 chunk 406 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 418 GLN F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.168364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.141455 restraints weight = 74797.214| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.45 r_work: 0.3642 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 42216 Z= 0.132 Angle : 0.501 11.600 57225 Z= 0.259 Chirality : 0.041 0.271 6495 Planarity : 0.003 0.042 7128 Dihedral : 4.670 55.645 5586 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.68 % Allowed : 15.42 % Favored : 81.89 % 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: -0.13 (0.12), residues: 4986 helix: 0.25 (0.12), residues: 2151 sheet: -0.37 (0.18), residues: 909 loop : -0.08 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 342 HIS 0.006 0.001 HIS D 253 PHE 0.021 0.001 PHE B 433 TYR 0.024 0.001 TYR L 97 ARG 0.007 0.000 ARG J 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9283.34 seconds wall clock time: 166 minutes 28.56 seconds (9988.56 seconds total)