Starting phenix.real_space_refine on Sat Mar 23 04:26:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/03_2024/6g9o_4367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/03_2024/6g9o_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_4367/03_2024/6g9o_4367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/03_2024/6g9o_4367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/03_2024/6g9o_4367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g9o_4367/03_2024/6g9o_4367.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 17.12, per 1000 atoms: 0.48 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: 13.53 Conformation dependent library (CDL) restraints added in 6.7 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: 4.59 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: 15.20 Time building geometry restraints manager: 14.70 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 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.900 Check model and map are aligned: 0.630 Set scattering table: 0.270 Process input model: 92.980 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 475 HIS 0.011 0.002 HIS F 694 PHE 0.035 0.003 PHE B 136 TYR 0.014 0.002 TYR A 308 ARG 0.011 0.001 ARG E 781 *********************** 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 : 4.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.8734 (ttm) cc_final: 0.8520 (tmm) REVERT: B 343 MET cc_start: 0.8306 (ttp) cc_final: 0.7352 (ttp) REVERT: B 383 ASP cc_start: 0.8427 (t0) cc_final: 0.7866 (p0) REVERT: B 451 LEU cc_start: 0.9273 (tp) cc_final: 0.8959 (tp) REVERT: B 788 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7896 (pm20) REVERT: C 235 LYS cc_start: 0.9254 (mttt) cc_final: 0.9031 (tppt) REVERT: C 803 TRP cc_start: 0.7425 (t-100) cc_final: 0.6820 (m100) REVERT: D 37 MET cc_start: 0.8654 (ttm) cc_final: 0.8343 (tmm) REVERT: D 134 LEU cc_start: 0.9526 (mt) cc_final: 0.9308 (tt) REVERT: D 343 MET cc_start: 0.8540 (ttp) cc_final: 0.7961 (ttp) REVERT: D 383 ASP cc_start: 0.8475 (t0) cc_final: 0.7973 (p0) REVERT: D 453 LEU cc_start: 0.9489 (mt) cc_final: 0.9266 (mt) REVERT: D 639 HIS cc_start: 0.7816 (m-70) cc_final: 0.7516 (p90) REVERT: E 277 LEU cc_start: 0.9353 (mt) cc_final: 0.9148 (tt) REVERT: E 495 LEU cc_start: 0.8497 (tp) cc_final: 0.7960 (mt) REVERT: E 590 MET cc_start: 0.8504 (mtp) cc_final: 0.7850 (tpt) REVERT: F 331 PHE cc_start: 0.8628 (t80) cc_final: 0.8296 (t80) REVERT: F 332 TYR cc_start: 0.9272 (t80) cc_final: 0.8819 (t80) REVERT: F 383 ASP cc_start: 0.8202 (t0) cc_final: 0.7758 (p0) REVERT: F 451 LEU cc_start: 0.9228 (tp) cc_final: 0.8942 (tp) REVERT: F 550 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8678 (tpp80) REVERT: F 629 ILE cc_start: 0.8680 (pt) cc_final: 0.8301 (mp) REVERT: F 788 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7709 (pm20) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.5260 time to fit residues: 379.8208 Evaluate side-chains 153 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.469 ------------------------------------------------------------------------------- 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: 9.9990 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: 7.9990 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: 3.4026 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 608 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 377 HIS ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 608 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36330 Z= 0.235 Angle : 0.618 7.276 49242 Z= 0.327 Chirality : 0.042 0.154 5682 Planarity : 0.005 0.053 6096 Dihedral : 5.089 23.846 4704 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.03 % Allowed : 1.03 % Favored : 98.95 % 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: -0.96 (0.13), residues: 4272 helix: -0.39 (0.11), residues: 2076 sheet: -0.98 (0.21), residues: 582 loop : -0.58 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 411 HIS 0.008 0.001 HIS C 377 PHE 0.022 0.002 PHE D 136 TYR 0.022 0.001 TYR C 281 ARG 0.005 0.000 ARG D 801 *********************** 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 223 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 4.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.8777 (tp) cc_final: 0.8132 (mt) REVERT: A 501 LYS cc_start: 0.9348 (tmtt) cc_final: 0.9102 (tptp) REVERT: A 590 MET cc_start: 0.7838 (tpp) cc_final: 0.7633 (tpp) REVERT: A 707 LEU cc_start: 0.7869 (mt) cc_final: 0.7454 (tp) REVERT: B 332 TYR cc_start: 0.9308 (t80) cc_final: 0.9023 (t80) REVERT: B 383 ASP cc_start: 0.8430 (t0) cc_final: 0.7791 (p0) REVERT: B 590 MET cc_start: 0.8298 (mmp) cc_final: 0.7963 (mmp) REVERT: C 590 MET cc_start: 0.6771 (tpt) cc_final: 0.6504 (tpp) REVERT: C 803 TRP cc_start: 0.7517 (t-100) cc_final: 0.6912 (m-10) REVERT: D 37 MET cc_start: 0.8605 (ttm) cc_final: 0.8309 (tmm) REVERT: D 52 MET cc_start: 0.8084 (ttp) cc_final: 0.7844 (ttp) REVERT: D 134 LEU cc_start: 0.9539 (mt) cc_final: 0.9273 (tt) REVERT: D 383 ASP cc_start: 0.8473 (t0) cc_final: 0.7834 (p0) REVERT: D 590 MET cc_start: 0.8202 (mmp) cc_final: 0.7691 (mmp) REVERT: D 803 TRP cc_start: 0.6547 (m-10) cc_final: 0.6154 (m-10) REVERT: E 277 LEU cc_start: 0.9297 (mt) cc_final: 0.9074 (tt) REVERT: E 326 ILE cc_start: 0.9431 (pt) cc_final: 0.9017 (mt) REVERT: E 343 MET cc_start: 0.8142 (ttp) cc_final: 0.7941 (ttp) REVERT: E 495 LEU cc_start: 0.8413 (tp) cc_final: 0.7890 (tp) REVERT: E 501 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9090 (tptp) REVERT: E 590 MET cc_start: 0.8492 (mtp) cc_final: 0.7851 (tpt) REVERT: F 331 PHE cc_start: 0.8642 (t80) cc_final: 0.8404 (t80) REVERT: F 332 TYR cc_start: 0.9266 (t80) cc_final: 0.9026 (t80) REVERT: F 383 ASP cc_start: 0.8347 (t0) cc_final: 0.7755 (p0) REVERT: F 590 MET cc_start: 0.8347 (mmp) cc_final: 0.8042 (mmp) REVERT: F 689 TYR cc_start: 0.8268 (m-80) cc_final: 0.7889 (m-80) REVERT: F 788 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7505 (pm20) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.4685 time to fit residues: 173.6689 Evaluate side-chains 127 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.217 ------------------------------------------------------------------------------- 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: 5.9990 chunk 120 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 387 optimal weight: 1.9990 chunk 418 optimal weight: 0.5980 chunk 345 optimal weight: 6.9990 chunk 384 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 400 ASN A 554 ASN A 617 GLN B 288 ASN ** 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 D 288 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 400 ASN E 554 ASN F 288 ASN F 400 ASN F 758 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36330 Z= 0.198 Angle : 0.547 8.322 49242 Z= 0.291 Chirality : 0.040 0.150 5682 Planarity : 0.004 0.067 6096 Dihedral : 4.739 23.468 4704 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.03 % Allowed : 1.95 % Favored : 98.02 % 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: -0.65 (0.13), residues: 4272 helix: -0.10 (0.12), residues: 2094 sheet: -0.81 (0.21), residues: 585 loop : -0.48 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 803 HIS 0.004 0.001 HIS F 119 PHE 0.023 0.002 PHE D 331 TYR 0.019 0.001 TYR F 281 ARG 0.013 0.000 ARG E 685 *********************** 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 198 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.8805 (tp) cc_final: 0.8432 (tp) REVERT: B 332 TYR cc_start: 0.9299 (t80) cc_final: 0.9090 (t80) REVERT: B 383 ASP cc_start: 0.8495 (t0) cc_final: 0.7922 (p0) REVERT: B 590 MET cc_start: 0.8285 (mmp) cc_final: 0.7902 (mmp) REVERT: B 737 HIS cc_start: 0.8681 (m-70) cc_final: 0.8405 (m-70) REVERT: C 590 MET cc_start: 0.6776 (tpt) cc_final: 0.6507 (tpp) REVERT: C 803 TRP cc_start: 0.7570 (t-100) cc_final: 0.6905 (m-10) REVERT: D 37 MET cc_start: 0.8614 (ttm) cc_final: 0.8296 (tmm) REVERT: D 52 MET cc_start: 0.8106 (ttp) cc_final: 0.7699 (ttp) REVERT: D 134 LEU cc_start: 0.9556 (mt) cc_final: 0.9263 (tt) REVERT: D 383 ASP cc_start: 0.8464 (t0) cc_final: 0.7949 (p0) REVERT: D 590 MET cc_start: 0.8381 (mmp) cc_final: 0.8035 (mmp) REVERT: D 737 HIS cc_start: 0.8480 (m-70) cc_final: 0.8140 (m-70) REVERT: D 803 TRP cc_start: 0.6618 (m-10) cc_final: 0.6272 (m-10) REVERT: E 265 MET cc_start: 0.8768 (mmm) cc_final: 0.8512 (mmm) REVERT: E 326 ILE cc_start: 0.9434 (pt) cc_final: 0.9102 (mt) REVERT: E 495 LEU cc_start: 0.8397 (tp) cc_final: 0.8109 (tp) REVERT: E 590 MET cc_start: 0.8491 (mtp) cc_final: 0.7853 (tpt) REVERT: F 37 MET cc_start: 0.8647 (tmm) cc_final: 0.8412 (tmm) REVERT: F 331 PHE cc_start: 0.8638 (t80) cc_final: 0.8416 (t80) REVERT: F 383 ASP cc_start: 0.8303 (t0) cc_final: 0.7834 (p0) REVERT: F 590 MET cc_start: 0.8375 (mmp) cc_final: 0.8006 (mmm) REVERT: F 689 TYR cc_start: 0.8265 (m-80) cc_final: 0.7736 (m-80) REVERT: F 788 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7552 (pm20) outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.4525 time to fit residues: 151.3221 Evaluate side-chains 129 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 4.477 ------------------------------------------------------------------------------- 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: 20.0000 chunk 291 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 388 optimal weight: 4.9990 chunk 411 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 368 optimal weight: 0.0270 chunk 110 optimal weight: 6.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- 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** B 116 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN 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 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN ** 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: 0.8224 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 36330 Z= 0.244 Angle : 0.578 8.701 49242 Z= 0.303 Chirality : 0.041 0.203 5682 Planarity : 0.004 0.046 6096 Dihedral : 4.670 21.306 4704 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.42 (0.13), residues: 4272 helix: 0.13 (0.12), residues: 2049 sheet: -0.68 (0.22), residues: 570 loop : -0.45 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 803 HIS 0.006 0.001 HIS F 499 PHE 0.016 0.002 PHE B 331 TYR 0.021 0.001 TYR F 308 ARG 0.008 0.000 ARG A 666 *********************** 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 180 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9177 (mtm) cc_final: 0.8973 (mtm) REVERT: A 265 MET cc_start: 0.8739 (mmm) cc_final: 0.8484 (mmm) REVERT: A 375 MET cc_start: 0.8831 (mpp) cc_final: 0.8359 (mpp) REVERT: A 495 LEU cc_start: 0.8852 (tp) cc_final: 0.8431 (tp) REVERT: B 37 MET cc_start: 0.8642 (tmm) cc_final: 0.8402 (tmm) REVERT: B 383 ASP cc_start: 0.8490 (t0) cc_final: 0.8209 (p0) REVERT: B 590 MET cc_start: 0.8194 (mmp) cc_final: 0.7889 (mmp) REVERT: B 734 ARG cc_start: 0.8674 (mtm180) cc_final: 0.8375 (mtm110) REVERT: B 737 HIS cc_start: 0.8616 (m-70) cc_final: 0.8330 (m-70) REVERT: C 590 MET cc_start: 0.6752 (tpt) cc_final: 0.6517 (tpp) REVERT: C 803 TRP cc_start: 0.7559 (t-100) cc_final: 0.6916 (m-10) REVERT: D 37 MET cc_start: 0.8598 (ttm) cc_final: 0.8383 (tmm) REVERT: D 52 MET cc_start: 0.8339 (ttp) cc_final: 0.7870 (ttp) REVERT: D 134 LEU cc_start: 0.9566 (mt) cc_final: 0.9280 (tt) REVERT: D 383 ASP cc_start: 0.8583 (t0) cc_final: 0.8326 (p0) REVERT: D 590 MET cc_start: 0.8331 (mmp) cc_final: 0.8029 (mmp) REVERT: D 737 HIS cc_start: 0.8372 (m-70) cc_final: 0.8031 (m-70) REVERT: E 265 MET cc_start: 0.8760 (mmm) cc_final: 0.8377 (tpp) REVERT: E 326 ILE cc_start: 0.9459 (pt) cc_final: 0.9148 (mt) REVERT: E 375 MET cc_start: 0.8744 (mpp) cc_final: 0.8338 (mpp) REVERT: E 495 LEU cc_start: 0.8512 (tp) cc_final: 0.8059 (tp) REVERT: E 590 MET cc_start: 0.8529 (mtp) cc_final: 0.7827 (tpt) REVERT: F 37 MET cc_start: 0.8593 (tmm) cc_final: 0.8332 (tmm) REVERT: F 383 ASP cc_start: 0.8522 (t0) cc_final: 0.8196 (p0) REVERT: F 590 MET cc_start: 0.8389 (mmp) cc_final: 0.8035 (mmm) REVERT: F 737 HIS cc_start: 0.8741 (m-70) cc_final: 0.8414 (m-70) REVERT: F 788 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7400 (pm20) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4672 time to fit residues: 142.3100 Evaluate side-chains 122 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 4.451 ------------------------------------------------------------------------------- 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: 6.9990 chunk 233 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 351 optimal weight: 0.9990 chunk 284 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 0.0050 chunk 369 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 288 ASN C 400 ASN D 116 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36330 Z= 0.210 Angle : 0.535 7.313 49242 Z= 0.283 Chirality : 0.040 0.147 5682 Planarity : 0.004 0.045 6096 Dihedral : 4.540 22.502 4704 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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 (0.13), residues: 4272 helix: 0.24 (0.12), residues: 2043 sheet: -0.60 (0.22), residues: 570 loop : -0.36 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 803 HIS 0.004 0.001 HIS A 119 PHE 0.018 0.001 PHE D 331 TYR 0.025 0.001 TYR F 308 ARG 0.007 0.000 ARG C 719 *********************** 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 181 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8796 (mmm) cc_final: 0.8492 (mmm) REVERT: A 375 MET cc_start: 0.8821 (mpp) cc_final: 0.8419 (mpp) REVERT: A 495 LEU cc_start: 0.8813 (tp) cc_final: 0.8476 (tp) REVERT: B 37 MET cc_start: 0.8673 (tmm) cc_final: 0.8422 (tmm) REVERT: B 383 ASP cc_start: 0.8614 (t0) cc_final: 0.8235 (p0) REVERT: B 737 HIS cc_start: 0.8602 (m-70) cc_final: 0.8321 (m-70) REVERT: C 590 MET cc_start: 0.6769 (tpt) cc_final: 0.6534 (tpp) REVERT: C 803 TRP cc_start: 0.7613 (t-100) cc_final: 0.6972 (m-10) REVERT: D 37 MET cc_start: 0.8596 (ttm) cc_final: 0.8363 (tmm) REVERT: D 52 MET cc_start: 0.8253 (ttp) cc_final: 0.7711 (ttp) REVERT: D 134 LEU cc_start: 0.9581 (mt) cc_final: 0.9267 (tt) REVERT: D 383 ASP cc_start: 0.8514 (t0) cc_final: 0.8276 (p0) REVERT: D 590 MET cc_start: 0.8306 (mmp) cc_final: 0.8006 (mmp) REVERT: D 737 HIS cc_start: 0.8362 (m-70) cc_final: 0.8017 (m-70) REVERT: E 326 ILE cc_start: 0.9484 (pt) cc_final: 0.9208 (mt) REVERT: E 375 MET cc_start: 0.8735 (mpp) cc_final: 0.8384 (mpp) REVERT: E 495 LEU cc_start: 0.8503 (tp) cc_final: 0.8197 (tp) REVERT: E 590 MET cc_start: 0.8466 (mtp) cc_final: 0.7777 (tpt) REVERT: F 37 MET cc_start: 0.8646 (tmm) cc_final: 0.8364 (tmm) REVERT: F 383 ASP cc_start: 0.8549 (t0) cc_final: 0.8174 (p0) REVERT: F 590 MET cc_start: 0.8312 (mmp) cc_final: 0.7968 (mmm) REVERT: F 737 HIS cc_start: 0.8757 (m-70) cc_final: 0.8432 (m-70) REVERT: F 788 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7415 (pm20) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.4598 time to fit residues: 141.6257 Evaluate side-chains 127 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.780 ------------------------------------------------------------------------------- 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: 10.0000 chunk 370 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 412 optimal weight: 30.0000 chunk 342 optimal weight: 2.9990 chunk 190 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS C 288 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS D 592 ASN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 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: 0.8241 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36330 Z= 0.218 Angle : 0.543 7.114 49242 Z= 0.287 Chirality : 0.040 0.170 5682 Planarity : 0.004 0.044 6096 Dihedral : 4.474 20.509 4704 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4272 helix: 0.28 (0.12), residues: 2058 sheet: -0.52 (0.23), residues: 570 loop : -0.34 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D 803 HIS 0.004 0.001 HIS A 119 PHE 0.019 0.001 PHE A 353 TYR 0.024 0.001 TYR F 308 ARG 0.008 0.000 ARG D 765 *********************** 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 165 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8830 (mpp) cc_final: 0.8347 (mpp) REVERT: A 495 LEU cc_start: 0.8843 (tp) cc_final: 0.8507 (tp) REVERT: B 37 MET cc_start: 0.8712 (tmm) cc_final: 0.8438 (tmm) REVERT: B 383 ASP cc_start: 0.8488 (t0) cc_final: 0.8110 (p0) REVERT: B 737 HIS cc_start: 0.8574 (m-70) cc_final: 0.8288 (m-70) REVERT: C 52 MET cc_start: 0.8236 (ttp) cc_final: 0.8009 (ttm) REVERT: C 590 MET cc_start: 0.6779 (tpt) cc_final: 0.6578 (tpp) REVERT: C 803 TRP cc_start: 0.7643 (t-100) cc_final: 0.6982 (m-10) REVERT: D 37 MET cc_start: 0.8604 (ttm) cc_final: 0.8393 (tmm) REVERT: D 383 ASP cc_start: 0.8567 (t0) cc_final: 0.8295 (p0) REVERT: D 590 MET cc_start: 0.8274 (mmp) cc_final: 0.7947 (mmp) REVERT: D 737 HIS cc_start: 0.8353 (m-70) cc_final: 0.8046 (m-70) REVERT: D 788 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7417 (pm20) REVERT: E 326 ILE cc_start: 0.9500 (pt) cc_final: 0.9232 (mt) REVERT: E 375 MET cc_start: 0.8750 (mpp) cc_final: 0.8376 (mpp) REVERT: E 495 LEU cc_start: 0.8532 (tp) cc_final: 0.8104 (tp) REVERT: E 590 MET cc_start: 0.8502 (mtp) cc_final: 0.7760 (tpt) REVERT: F 37 MET cc_start: 0.8659 (tmm) cc_final: 0.8358 (tmm) REVERT: F 383 ASP cc_start: 0.8494 (t0) cc_final: 0.8234 (p0) REVERT: F 414 ASP cc_start: 0.8937 (p0) cc_final: 0.8438 (t0) REVERT: F 590 MET cc_start: 0.8341 (mmp) cc_final: 0.7911 (mmm) REVERT: F 737 HIS cc_start: 0.8735 (m-70) cc_final: 0.8404 (m-70) REVERT: F 788 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7414 (pm20) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4394 time to fit residues: 123.5000 Evaluate side-chains 125 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 4.394 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 410 optimal weight: 30.0000 chunk 256 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 189 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3826 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= 0.201 Angle : 0.530 11.155 49242 Z= 0.282 Chirality : 0.040 0.150 5682 Planarity : 0.004 0.045 6096 Dihedral : 4.419 28.639 4704 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -0.16 (0.13), residues: 4272 helix: 0.29 (0.12), residues: 2058 sheet: -0.45 (0.23), residues: 573 loop : -0.27 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 803 HIS 0.004 0.001 HIS A 119 PHE 0.014 0.001 PHE A 728 TYR 0.025 0.001 TYR F 308 ARG 0.005 0.000 ARG F 262 *********************** 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 175 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8809 (mpp) cc_final: 0.8323 (mpp) REVERT: A 495 LEU cc_start: 0.8835 (tp) cc_final: 0.8503 (tp) REVERT: B 37 MET cc_start: 0.8806 (tmm) cc_final: 0.8494 (tmm) REVERT: B 737 HIS cc_start: 0.8575 (m-70) cc_final: 0.8278 (m-70) REVERT: C 52 MET cc_start: 0.8221 (ttp) cc_final: 0.7951 (ttm) REVERT: C 803 TRP cc_start: 0.7621 (t-100) cc_final: 0.6973 (m-10) REVERT: D 37 MET cc_start: 0.8593 (ttm) cc_final: 0.8314 (tmm) REVERT: D 590 MET cc_start: 0.8300 (mmp) cc_final: 0.8021 (mmp) REVERT: D 737 HIS cc_start: 0.8366 (m-70) cc_final: 0.8047 (m-70) REVERT: D 788 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7447 (pm20) REVERT: E 326 ILE cc_start: 0.9504 (pt) cc_final: 0.9249 (mt) REVERT: E 375 MET cc_start: 0.8737 (mpp) cc_final: 0.8356 (mpp) REVERT: E 495 LEU cc_start: 0.8559 (tp) cc_final: 0.8132 (tp) REVERT: E 590 MET cc_start: 0.8511 (mtp) cc_final: 0.7926 (mmm) REVERT: F 37 MET cc_start: 0.8738 (tmm) cc_final: 0.8389 (tmm) REVERT: F 590 MET cc_start: 0.8298 (mmp) cc_final: 0.7893 (mmm) REVERT: F 737 HIS cc_start: 0.8741 (m-70) cc_final: 0.8403 (m-70) REVERT: F 788 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7383 (pm20) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.4606 time to fit residues: 136.4517 Evaluate side-chains 129 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 4.531 ------------------------------------------------------------------------------- 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: 8.9990 chunk 163 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.0670 chunk 261 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 203 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN C 288 ASN D 288 ASN E 288 ASN F 288 ASN F 592 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 36330 Z= 0.136 Angle : 0.498 8.921 49242 Z= 0.263 Chirality : 0.039 0.148 5682 Planarity : 0.003 0.046 6096 Dihedral : 4.251 19.346 4704 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.07 (0.14), residues: 4272 helix: 0.33 (0.12), residues: 2070 sheet: -0.41 (0.23), residues: 576 loop : -0.19 (0.17), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 803 HIS 0.003 0.001 HIS F 478 PHE 0.029 0.001 PHE C 275 TYR 0.027 0.001 TYR F 308 ARG 0.004 0.000 ARG D 171 *********************** 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 188 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8773 (mpp) cc_final: 0.8297 (mpp) REVERT: A 495 LEU cc_start: 0.8896 (tp) cc_final: 0.8577 (tp) REVERT: B 37 MET cc_start: 0.8743 (tmm) cc_final: 0.8485 (tmm) REVERT: B 629 ILE cc_start: 0.8664 (pt) cc_final: 0.8344 (mp) REVERT: B 737 HIS cc_start: 0.8584 (m-70) cc_final: 0.8291 (m-70) REVERT: C 803 TRP cc_start: 0.7615 (t-100) cc_final: 0.6945 (m-10) REVERT: D 37 MET cc_start: 0.8614 (ttm) cc_final: 0.8309 (tmm) REVERT: D 737 HIS cc_start: 0.8381 (m-70) cc_final: 0.8092 (m-70) REVERT: D 788 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7411 (pm20) REVERT: E 37 MET cc_start: 0.8816 (ptp) cc_final: 0.8380 (ptp) REVERT: E 326 ILE cc_start: 0.9482 (pt) cc_final: 0.9252 (mt) REVERT: E 375 MET cc_start: 0.8797 (mpp) cc_final: 0.8406 (mpp) REVERT: E 430 LEU cc_start: 0.8773 (tp) cc_final: 0.8563 (tp) REVERT: E 495 LEU cc_start: 0.8564 (tp) cc_final: 0.8275 (tp) REVERT: E 590 MET cc_start: 0.8499 (mtp) cc_final: 0.7733 (tpt) REVERT: F 37 MET cc_start: 0.8721 (tmm) cc_final: 0.8404 (tmm) REVERT: F 277 LEU cc_start: 0.9480 (mt) cc_final: 0.9245 (tt) REVERT: F 414 ASP cc_start: 0.8854 (p0) cc_final: 0.8342 (t0) REVERT: F 590 MET cc_start: 0.8222 (mmp) cc_final: 0.7793 (mmm) REVERT: F 629 ILE cc_start: 0.8676 (pt) cc_final: 0.8319 (mp) REVERT: F 737 HIS cc_start: 0.8755 (m-70) cc_final: 0.8429 (m-70) REVERT: F 788 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7403 (pm20) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.4372 time to fit residues: 140.0077 Evaluate side-chains 133 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.231 ------------------------------------------------------------------------------- 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: 5.9990 chunk 382 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 117 optimal weight: 0.0670 chunk 345 optimal weight: 7.9990 chunk 361 optimal weight: 0.5980 chunk 381 optimal weight: 7.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN C 288 ASN D 288 ASN E 288 ASN F 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4043 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= 0.129 Angle : 0.480 7.464 49242 Z= 0.256 Chirality : 0.039 0.148 5682 Planarity : 0.003 0.046 6096 Dihedral : 4.147 18.702 4704 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 4272 helix: 0.40 (0.12), residues: 2070 sheet: -0.38 (0.23), residues: 576 loop : -0.16 (0.17), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 803 HIS 0.003 0.001 HIS B 522 PHE 0.024 0.001 PHE B 331 TYR 0.023 0.001 TYR F 308 ARG 0.004 0.000 ARG D 266 *********************** 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 187 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8885 (ptp) cc_final: 0.8489 (ptp) REVERT: A 375 MET cc_start: 0.8757 (mpp) cc_final: 0.8274 (mpp) REVERT: A 495 LEU cc_start: 0.8879 (tp) cc_final: 0.8552 (tp) REVERT: B 37 MET cc_start: 0.8654 (tmm) cc_final: 0.8370 (tmm) REVERT: B 629 ILE cc_start: 0.8696 (pt) cc_final: 0.8378 (mp) REVERT: B 737 HIS cc_start: 0.8638 (m-70) cc_final: 0.8339 (m-70) REVERT: C 803 TRP cc_start: 0.7598 (t-100) cc_final: 0.6924 (m-10) REVERT: D 28 THR cc_start: 0.9070 (m) cc_final: 0.8867 (m) REVERT: D 37 MET cc_start: 0.8623 (ttm) cc_final: 0.8327 (tmm) REVERT: D 737 HIS cc_start: 0.8396 (m-70) cc_final: 0.8107 (m-70) REVERT: D 788 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7336 (pm20) REVERT: E 37 MET cc_start: 0.8724 (ptp) cc_final: 0.8249 (ptp) REVERT: E 326 ILE cc_start: 0.9471 (pt) cc_final: 0.9238 (mt) REVERT: E 375 MET cc_start: 0.8823 (mpp) cc_final: 0.8476 (mpp) REVERT: E 430 LEU cc_start: 0.8788 (tp) cc_final: 0.8516 (tp) REVERT: E 495 LEU cc_start: 0.8632 (tp) cc_final: 0.8344 (tp) REVERT: E 590 MET cc_start: 0.8494 (mtp) cc_final: 0.7723 (tpt) REVERT: F 37 MET cc_start: 0.8719 (tmm) cc_final: 0.8393 (tmm) REVERT: F 277 LEU cc_start: 0.9450 (mt) cc_final: 0.9219 (tt) REVERT: F 326 ILE cc_start: 0.9510 (pt) cc_final: 0.9304 (mt) REVERT: F 414 ASP cc_start: 0.8898 (p0) cc_final: 0.8371 (t0) REVERT: F 590 MET cc_start: 0.8206 (mmp) cc_final: 0.7985 (mmp) REVERT: F 629 ILE cc_start: 0.8668 (pt) cc_final: 0.8317 (mp) REVERT: F 737 HIS cc_start: 0.8757 (m-70) cc_final: 0.8431 (m-70) REVERT: F 788 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7420 (pm20) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.4366 time to fit residues: 141.0443 Evaluate side-chains 137 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 4.470 ------------------------------------------------------------------------------- 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: 9.9990 chunk 246 optimal weight: 0.0980 chunk 191 optimal weight: 7.9990 chunk 281 optimal weight: 3.9990 chunk 424 optimal weight: 5.9990 chunk 390 optimal weight: 3.9990 chunk 337 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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** B 107 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** C 288 ASN ** 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** ** F 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 36330 Z= 0.237 Angle : 0.550 8.132 49242 Z= 0.290 Chirality : 0.040 0.149 5682 Planarity : 0.004 0.043 6096 Dihedral : 4.305 25.137 4704 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.10 (0.14), residues: 4272 helix: 0.33 (0.12), residues: 2079 sheet: -0.39 (0.23), residues: 576 loop : -0.24 (0.17), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 803 HIS 0.005 0.001 HIS F 499 PHE 0.029 0.002 PHE C 275 TYR 0.035 0.001 TYR D 281 ARG 0.005 0.000 ARG D 171 ********************** 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 169 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8831 (mpp) cc_final: 0.8345 (mpp) REVERT: A 495 LEU cc_start: 0.8825 (tp) cc_final: 0.8417 (tp) REVERT: B 37 MET cc_start: 0.8679 (tmm) cc_final: 0.8403 (tmm) REVERT: B 737 HIS cc_start: 0.8572 (m-70) cc_final: 0.8279 (m-70) REVERT: C 803 TRP cc_start: 0.7549 (t-100) cc_final: 0.6917 (m-10) REVERT: D 37 MET cc_start: 0.8622 (ttm) cc_final: 0.8332 (tmm) REVERT: D 128 LEU cc_start: 0.9401 (mm) cc_final: 0.9042 (tp) REVERT: D 343 MET cc_start: 0.8856 (ttp) cc_final: 0.8631 (ttt) REVERT: D 737 HIS cc_start: 0.8357 (m-70) cc_final: 0.8047 (m-70) REVERT: D 788 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7438 (pm20) REVERT: E 35 MET cc_start: 0.8946 (mtm) cc_final: 0.8723 (mtm) REVERT: E 37 MET cc_start: 0.8799 (ptp) cc_final: 0.8323 (ptp) REVERT: E 326 ILE cc_start: 0.9474 (pt) cc_final: 0.9209 (mt) REVERT: E 375 MET cc_start: 0.8806 (mpp) cc_final: 0.8513 (mpp) REVERT: E 495 LEU cc_start: 0.8611 (tp) cc_final: 0.8186 (tp) REVERT: E 590 MET cc_start: 0.8528 (mtp) cc_final: 0.7899 (mmm) REVERT: F 37 MET cc_start: 0.8747 (tmm) cc_final: 0.8236 (tmm) REVERT: F 590 MET cc_start: 0.8255 (mmp) cc_final: 0.7838 (mmm) REVERT: F 737 HIS cc_start: 0.8698 (m-70) cc_final: 0.8389 (m-70) REVERT: F 788 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7404 (pm20) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.4482 time to fit residues: 130.0369 Evaluate side-chains 125 residues out of total 3996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 4.385 ------------------------------------------------------------------------------- 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: 20.0000 chunk 360 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 338 optimal weight: 30.0000 chunk 141 optimal weight: 4.9990 chunk 347 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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** ** 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** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 288 ASN F 467 GLN ** F 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.071800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048665 restraints weight = 191276.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050067 restraints weight = 106942.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050417 restraints weight = 67569.325| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36330 Z= 0.217 Angle : 0.536 7.552 49242 Z= 0.285 Chirality : 0.040 0.159 5682 Planarity : 0.004 0.044 6096 Dihedral : 4.341 24.316 4704 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 4272 helix: 0.22 (0.12), residues: 2124 sheet: -0.32 (0.24), residues: 558 loop : -0.34 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 803 HIS 0.005 0.001 HIS C 104 PHE 0.030 0.002 PHE E 275 TYR 0.025 0.001 TYR F 308 ARG 0.005 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5248.02 seconds wall clock time: 97 minutes 53.27 seconds (5873.27 seconds total)