Starting phenix.real_space_refine (version: dev) on Fri Apr 8 17:17:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/04_2022/6g9o_4367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/04_2022/6g9o_4367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/04_2022/6g9o_4367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/04_2022/6g9o_4367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/04_2022/6g9o_4367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/04_2022/6g9o_4367.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B ARG 731": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B ARG 804": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C ARG 731": "NH1" <-> "NH2" Residue "C ARG 734": "NH1" <-> "NH2" Residue "C ARG 804": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "D ARG 496": "NH1" <-> "NH2" Residue "D ARG 666": "NH1" <-> "NH2" Residue "D ARG 719": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 734": "NH1" <-> "NH2" Residue "D ARG 804": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "E ARG 496": "NH1" <-> "NH2" Residue "E ARG 666": "NH1" <-> "NH2" Residue "E ARG 719": "NH1" <-> "NH2" Residue "E ARG 731": "NH1" <-> "NH2" Residue "E ARG 734": "NH1" <-> "NH2" Residue "E ARG 804": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 389": "NH1" <-> "NH2" Residue "F ARG 496": "NH1" <-> "NH2" Residue "F ARG 666": "NH1" <-> "NH2" Residue "F ARG 719": "NH1" <-> "NH2" Residue "F ARG 731": "NH1" <-> "NH2" Residue "F ARG 734": "NH1" <-> "NH2" Residue "F ARG 804": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 35532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Time building chain proxies: 19.12, per 1000 atoms: 0.54 Number of scatterers: 35532 At special positions: 0 Unit cell: (149.425, 146.2, 196.725, 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 150 16.00 O 6282 8.00 N 5982 7.00 C 23118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.04 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=2.04 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=2.04 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: 14.00 Conformation dependent library (CDL) restraints added in 5.3 seconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 18 sheets defined 53.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.635A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 5.141A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.083A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.078A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (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: 3.695A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.849A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.699A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.185A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.739A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.567A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 removed outlier: 4.102A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.552A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.749A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.620A pdb=" N THR A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.995A pdb=" N LYS A 807 " --> pdb=" O TRP A 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.547A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 146 removed outlier: 3.610A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 4.984A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 4.092A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.082A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) 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 347 removed outlier: 3.826A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.945A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.731A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.377A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.590A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.513A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 776 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 removed outlier: 3.841A pdb=" N LYS B 807 " --> pdb=" O TRP B 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.635A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 5.140A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.083A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 removed outlier: 4.077A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (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: 3.696A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.849A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.700A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.185A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 removed outlier: 3.739A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.568A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.101A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.553A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 590 Processing helix chain 'C' and resid 607 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.750A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 678 through 684 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 Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.514A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 removed outlier: 3.619A pdb=" N THR C 793 " --> pdb=" O ASP C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 808 removed outlier: 3.995A pdb=" N LYS C 807 " --> pdb=" O TRP C 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.547A pdb=" N TYR D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.609A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 4.984A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 4.093A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.082A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.825A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.945A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.731A pdb=" N LEU D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.377A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 3.589A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE D 512 " --> pdb=" O PRO D 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 Processing helix chain 'D' and resid 608 through 613 Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 removed outlier: 3.512A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 747 through 753 Processing helix chain 'D' and resid 770 through 776 Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 removed outlier: 3.841A pdb=" N LYS D 807 " --> pdb=" O TRP D 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.636A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 5.141A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.082A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 removed outlier: 4.077A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (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: 3.696A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.849A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.700A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.184A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 removed outlier: 3.740A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP E 411 " --> pdb=" O LEU E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.568A pdb=" N ILE E 512 " --> pdb=" O PRO E 509 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.102A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.553A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 590 Processing helix chain 'E' and resid 607 through 613 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 678 through 684 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 Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 removed outlier: 3.619A pdb=" N THR E 793 " --> pdb=" O ASP E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 808 removed outlier: 3.995A pdb=" N LYS E 807 " --> pdb=" O TRP E 803 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.547A pdb=" N TYR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.609A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.983A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.092A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 4.082A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.826A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.945A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.731A pdb=" N LEU F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.377A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 411 removed outlier: 3.589A pdb=" N GLU F 399 " --> pdb=" O SER F 395 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 494 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 removed outlier: 3.635A pdb=" N THR F 563 " --> pdb=" O PRO F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 590 Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.512A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 Processing helix chain 'F' and resid 770 through 776 Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 removed outlier: 3.840A pdb=" N LYS F 807 " --> pdb=" O TRP F 803 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.456A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 474 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 550 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 523 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 552 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN A 575 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 551 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.912A 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 'B' and resid 53 through 56 removed outlier: 8.816A pdb=" N ARG B 306 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 297 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU B 432 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 596 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 598 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 690 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.456A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 474 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 550 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 523 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 552 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN C 575 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 551 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 667 " --> pdb=" O ASP C 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 690 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.911A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 removed outlier: 8.816A pdb=" N ARG D 306 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 297 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU D 432 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 521 " --> pdb=" O ARG D 550 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS D 552 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU D 523 " --> pdb=" O LYS D 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 598 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU D 667 " --> pdb=" O ASP D 691 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 690 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.457A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 474 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E 550 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 523 " --> pdb=" O ARG E 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS E 552 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN E 575 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU E 551 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 644 " --> pdb=" O TYR E 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU E 667 " --> pdb=" O ASP E 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU E 736 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.911A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 56 removed outlier: 8.816A pdb=" N ARG F 306 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 297 " --> pdb=" O ARG F 306 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU F 432 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 521 " --> pdb=" O ARG F 550 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS F 552 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 523 " --> pdb=" O LYS F 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 596 " --> pdb=" O GLU F 618 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 598 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU F 667 " --> pdb=" O ASP F 691 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 459 through 461 1632 hydrogen bonds defined for protein. 3942 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: 14.74 Time building geometry restraints manager: 15.22 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: 11173 1.34 - 1.46: 7715 1.46 - 1.58: 17238 1.58 - 1.70: 0 1.70 - 1.81: 204 Bond restraints: 36330 Sorted by residual: bond pdb=" CG ASN F 695 " pdb=" OD1 ASN F 695 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.34e+01 bond pdb=" CG ASN B 695 " pdb=" OD1 ASN B 695 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.33e+01 bond pdb=" CG ASN D 695 " pdb=" OD1 ASN D 695 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.32e+01 bond pdb=" CD GLN F 467 " pdb=" NE2 GLN F 467 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.27e+01 bond pdb=" CD GLN B 467 " pdb=" NE2 GLN B 467 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.25e+01 ... (remaining 36325 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.47: 609 105.47 - 112.69: 19402 112.69 - 119.92: 13193 119.92 - 127.15: 15581 127.15 - 134.37: 457 Bond angle restraints: 49242 Sorted by residual: angle pdb=" N ASN C 585 " pdb=" CA ASN C 585 " pdb=" CB ASN C 585 " ideal model delta sigma weight residual 114.17 108.98 5.19 1.14e+00 7.69e-01 2.07e+01 angle pdb=" N ASN A 585 " pdb=" CA ASN A 585 " pdb=" CB ASN A 585 " ideal model delta sigma weight residual 114.17 108.99 5.18 1.14e+00 7.69e-01 2.06e+01 angle pdb=" N ASN E 585 " pdb=" CA ASN E 585 " pdb=" CB ASN E 585 " ideal model delta sigma weight residual 114.17 109.02 5.15 1.14e+00 7.69e-01 2.04e+01 angle pdb=" CB ARG C 765 " pdb=" CG ARG C 765 " pdb=" CD ARG C 765 " ideal model delta sigma weight residual 111.30 103.21 8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CB ARG A 765 " pdb=" CG ARG A 765 " pdb=" CD ARG A 765 " ideal model delta sigma weight residual 111.30 103.22 8.08 2.30e+00 1.89e-01 1.24e+01 ... (remaining 49237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 21098 15.46 - 30.92: 749 30.92 - 46.38: 155 46.38 - 61.84: 0 61.84 - 77.30: 12 Dihedral angle restraints: 22014 sinusoidal: 9192 harmonic: 12822 Sorted by residual: dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual 93.00 170.30 -77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS F 57 " pdb=" SG CYS F 57 " pdb=" SG CYS F 65 " pdb=" CB CYS F 65 " ideal model delta sinusoidal sigma weight residual 93.00 170.29 -77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual 93.00 170.28 -77.28 1 1.00e+01 1.00e-02 7.49e+01 ... (remaining 22011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3475 0.036 - 0.071: 1572 0.071 - 0.107: 466 0.107 - 0.143: 135 0.143 - 0.179: 34 Chirality restraints: 5682 Sorted by residual: chirality pdb=" CA ILE E 508 " pdb=" N ILE E 508 " pdb=" C ILE E 508 " pdb=" CB ILE E 508 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ILE A 508 " pdb=" N ILE A 508 " pdb=" C ILE A 508 " pdb=" CB ILE A 508 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE C 508 " pdb=" N ILE C 508 " pdb=" C ILE C 508 " pdb=" CB ILE C 508 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 5679 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO D 22 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 21 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO B 22 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO F 22 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.032 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6087 2.77 - 3.30: 34426 3.30 - 3.83: 55085 3.83 - 4.37: 66335 4.37 - 4.90: 112007 Nonbonded interactions: 273940 Sorted by model distance: nonbonded pdb=" O CYS F 139 " pdb=" OE1 GLN F 267 " model vdw 2.233 3.040 nonbonded pdb=" O CYS D 139 " pdb=" OE1 GLN D 267 " model vdw 2.234 3.040 nonbonded pdb=" O CYS B 139 " pdb=" OE1 GLN B 267 " model vdw 2.234 3.040 nonbonded pdb=" O ASP A 25 " pdb=" OG1 THR A 28 " model vdw 2.257 2.440 nonbonded pdb=" O ASP E 25 " pdb=" OG1 THR E 28 " model vdw 2.258 2.440 ... (remaining 273935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 23118 2.51 5 N 5982 2.21 5 O 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 9.410 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.290 Process input model: 88.220 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.007 0.100 36330 Z= 0.471 Angle : 0.836 8.089 49242 Z= 0.465 Chirality : 0.045 0.179 5682 Planarity : 0.005 0.057 6096 Dihedral : 8.429 69.017 13608 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.00 % 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: -2.09 (0.12), residues: 4272 helix: -1.58 (0.10), residues: 2088 sheet: -1.15 (0.20), residues: 579 loop : -0.87 (0.15), residues: 1605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.5180 time to fit residues: 377.2246 Evaluate side-chains 136 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 4.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 217 optimal weight: 0.0170 chunk 172 optimal weight: 1.9990 chunk 333 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 386 optimal weight: 6.9990 overall best weight: 2.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 377 HIS ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN B 288 ASN B 404 GLN B 608 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 377 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 288 ASN D 404 GLN D 608 HIS D 758 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 377 HIS ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 718 ASN F 288 ASN F 404 GLN F 608 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 36330 Z= 0.191 Angle : 0.598 7.074 49242 Z= 0.318 Chirality : 0.041 0.162 5682 Planarity : 0.005 0.053 6096 Dihedral : 5.053 23.771 4704 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4272 helix: -0.36 (0.11), residues: 2076 sheet: -0.97 (0.21), residues: 582 loop : -0.55 (0.16), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.4773 time to fit residues: 178.2486 Evaluate side-chains 113 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 4.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 387 optimal weight: 7.9990 chunk 418 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 384 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 310 optimal weight: 0.6980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 617 GLN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN C 617 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 ASN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 ASN F 758 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 36330 Z= 0.239 Angle : 0.581 8.647 49242 Z= 0.306 Chirality : 0.041 0.158 5682 Planarity : 0.004 0.069 6096 Dihedral : 4.771 23.476 4704 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4272 helix: -0.02 (0.12), residues: 2058 sheet: -0.79 (0.21), residues: 582 loop : -0.44 (0.16), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.4377 time to fit residues: 129.5325 Evaluate side-chains 112 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 4.336 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3017 time to fit residues: 6.4630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 6.9990 chunk 291 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 260 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 411 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 368 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 36330 Z= 0.291 Angle : 0.603 7.052 49242 Z= 0.316 Chirality : 0.042 0.160 5682 Planarity : 0.004 0.047 6096 Dihedral : 4.735 21.356 4704 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4272 helix: -0.01 (0.12), residues: 2076 sheet: -0.83 (0.21), residues: 597 loop : -0.43 (0.16), residues: 1599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.4711 time to fit residues: 131.8431 Evaluate side-chains 114 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 4.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 306 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 351 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 0.0980 chunk 369 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 288 ASN A 400 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 288 ASN C 267 GLN C 288 ASN C 400 ASN C 709 ASN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN E 267 GLN E 288 ASN E 400 ASN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 288 ASN F 377 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 36330 Z= 0.150 Angle : 0.509 7.326 49242 Z= 0.270 Chirality : 0.040 0.147 5682 Planarity : 0.004 0.046 6096 Dihedral : 4.480 21.139 4704 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.00 % 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: -0.22 (0.13), residues: 4272 helix: 0.30 (0.12), residues: 2040 sheet: -0.60 (0.22), residues: 567 loop : -0.35 (0.16), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4454 time to fit residues: 141.6888 Evaluate side-chains 116 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 4.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 0.7980 chunk 370 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 190 optimal weight: 30.0000 chunk 34 optimal weight: 0.0050 chunk 136 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 overall best weight: 3.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS C 288 ASN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 36330 Z= 0.221 Angle : 0.545 7.566 49242 Z= 0.286 Chirality : 0.040 0.171 5682 Planarity : 0.004 0.044 6096 Dihedral : 4.441 20.144 4704 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % 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: -0.18 (0.13), residues: 4272 helix: 0.33 (0.12), residues: 2043 sheet: -0.51 (0.23), residues: 567 loop : -0.35 (0.16), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.4557 time to fit residues: 126.1126 Evaluate side-chains 112 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 7.9990 chunk 46 optimal weight: 40.0000 chunk 234 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 346 optimal weight: 30.0000 chunk 230 optimal weight: 1.9990 chunk 410 optimal weight: 30.0000 chunk 256 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 ASN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 36330 Z= 0.237 Angle : 0.557 7.751 49242 Z= 0.295 Chirality : 0.041 0.194 5682 Planarity : 0.004 0.042 6096 Dihedral : 4.478 20.023 4704 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4272 helix: 0.30 (0.12), residues: 2052 sheet: -0.47 (0.23), residues: 573 loop : -0.36 (0.16), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.4384 time to fit residues: 120.0094 Evaluate side-chains 111 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 4.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 279 optimal weight: 0.4980 chunk 203 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 322 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 718 ASN B 288 ASN B 592 ASN C 288 ASN C 718 ASN D 288 ASN E 288 ASN E 718 ASN F 288 ASN F 592 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 36330 Z= 0.156 Angle : 0.506 7.330 49242 Z= 0.268 Chirality : 0.040 0.167 5682 Planarity : 0.003 0.044 6096 Dihedral : 4.307 19.613 4704 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % 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: -0.03 (0.14), residues: 4272 helix: 0.41 (0.12), residues: 2046 sheet: -0.41 (0.23), residues: 576 loop : -0.22 (0.16), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 4.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.4715 time to fit residues: 136.6741 Evaluate side-chains 116 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 4.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 2.9990 chunk 393 optimal weight: 20.0000 chunk 358 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 300 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 chunk 345 optimal weight: 8.9990 chunk 361 optimal weight: 0.3980 chunk 381 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN C 288 ASN D 288 ASN E 288 ASN F 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 36330 Z= 0.126 Angle : 0.490 8.121 49242 Z= 0.259 Chirality : 0.039 0.182 5682 Planarity : 0.003 0.044 6096 Dihedral : 4.162 19.675 4704 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.00 % 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: 0.00 (0.14), residues: 4272 helix: 0.41 (0.12), residues: 2070 sheet: -0.36 (0.23), residues: 579 loop : -0.18 (0.17), residues: 1623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4474 time to fit residues: 138.1983 Evaluate side-chains 120 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 4.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 8.9990 chunk 404 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 337 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 36330 Z= 0.319 Angle : 0.631 8.657 49242 Z= 0.327 Chirality : 0.041 0.177 5682 Planarity : 0.004 0.042 6096 Dihedral : 4.459 20.581 4704 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.00 % 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: -0.27 (0.14), residues: 4272 helix: 0.22 (0.12), residues: 2082 sheet: -0.45 (0.23), residues: 579 loop : -0.38 (0.16), residues: 1611 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.5060 time to fit residues: 133.4626 Evaluate side-chains 113 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 4.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.2980 chunk 360 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 311 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 338 optimal weight: 0.0770 chunk 141 optimal weight: 8.9990 chunk 347 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN C 288 ASN D 288 ASN ** D 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.073104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050301 restraints weight = 194268.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051466 restraints weight = 109061.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051999 restraints weight = 64776.163| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 36330 Z= 0.138 Angle : 0.512 7.719 49242 Z= 0.272 Chirality : 0.040 0.183 5682 Planarity : 0.003 0.043 6096 Dihedral : 4.250 19.591 4704 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % 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: -0.12 (0.14), residues: 4272 helix: 0.29 (0.12), residues: 2112 sheet: -0.38 (0.23), residues: 579 loop : -0.23 (0.17), residues: 1581 =============================================================================== Job complete usr+sys time: 4849.58 seconds wall clock time: 91 minutes 56.89 seconds (5516.89 seconds total)