Starting phenix.real_space_refine on Wed Dec 13 07:56:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/12_2023/8jns_36450_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/12_2023/8jns_36450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/12_2023/8jns_36450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/12_2023/8jns_36450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/12_2023/8jns_36450_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/12_2023/8jns_36450_updated.pdb" } resolution = 4.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 174 5.16 5 C 15336 2.51 5 N 4041 2.21 5 O 4593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 424": "OE1" <-> "OE2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 448": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 424": "OE1" <-> "OE2" Residue "E ARG 436": "NH1" <-> "NH2" Residue "E ARG 440": "NH1" <-> "NH2" Residue "E ARG 448": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E GLU 486": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F ARG 436": "NH1" <-> "NH2" Residue "F ARG 440": "NH1" <-> "NH2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F GLU 486": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 24168 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "C" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "D" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "E" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "F" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 375} Chain breaks: 2 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "H" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "I" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.14, per 1000 atoms: 0.50 Number of scatterers: 24168 At special positions: 0 Unit cell: (168.96, 171.6, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 174 16.00 P 18 15.00 Mg 6 11.99 O 4593 8.00 N 4041 7.00 C 15336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.18 Conformation dependent library (CDL) restraints added in 4.5 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 8 sheets defined 52.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.418A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.834A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 134 through 147 removed outlier: 3.952A pdb=" N MET A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.022A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 255 through 263 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 removed outlier: 4.886A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 374 through 383 removed outlier: 4.497A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 459 through 465 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 removed outlier: 3.767A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 4.525A pdb=" N LYS A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 4.418A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.833A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.597A pdb=" N ARG B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.953A pdb=" N MET B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.022A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.684A pdb=" N ARG B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.649A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 removed outlier: 4.886A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 374 through 383 removed outlier: 4.497A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.775A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.501A pdb=" N PHE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 removed outlier: 3.767A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 481 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 4.525A pdb=" N LYS B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG C 16 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 4.419A pdb=" N THR C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 50 through 64 removed outlier: 3.834A pdb=" N ARG C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 removed outlier: 3.531A pdb=" N TYR C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.597A pdb=" N ARG C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 147 removed outlier: 3.953A pdb=" N MET C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.541A pdb=" N LEU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 199 through 211 removed outlier: 4.022A pdb=" N PHE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 255 through 263 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 295 through 305 removed outlier: 3.648A pdb=" N TYR C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 326 removed outlier: 4.886A pdb=" N VAL C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 359 through 362 Processing helix chain 'C' and resid 374 through 383 removed outlier: 4.498A pdb=" N ARG C 380 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.738A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 393 " --> pdb=" O ASP C 389 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.767A pdb=" N ALA C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 4.525A pdb=" N LYS C 538 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 134 through 147 removed outlier: 3.953A pdb=" N MET D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 199 through 211 removed outlier: 4.021A pdb=" N PHE D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 removed outlier: 4.915A pdb=" N ASP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.649A pdb=" N TYR D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'D' and resid 330 through 339 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 359 through 362 Processing helix chain 'D' and resid 374 through 383 removed outlier: 4.498A pdb=" N ARG D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 398 removed outlier: 3.738A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 429 through 439 Processing helix chain 'D' and resid 459 through 465 removed outlier: 3.592A pdb=" N PHE D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 484 removed outlier: 3.767A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 4.525A pdb=" N LYS D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 134 through 147 removed outlier: 3.952A pdb=" N MET E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 199 through 211 removed outlier: 4.038A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 241 removed outlier: 4.657A pdb=" N ASP E 241 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 295 through 305 removed outlier: 3.648A pdb=" N TYR E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'E' and resid 330 through 339 Processing helix chain 'E' and resid 345 through 354 Processing helix chain 'E' and resid 359 through 362 Processing helix chain 'E' and resid 374 through 383 removed outlier: 4.497A pdb=" N ARG E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 396 Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 429 through 439 Processing helix chain 'E' and resid 458 through 467 Processing helix chain 'E' and resid 470 through 483 removed outlier: 3.768A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 541 removed outlier: 4.525A pdb=" N LYS E 538 " --> pdb=" O LEU E 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 121 Processing helix chain 'F' and resid 134 through 147 removed outlier: 3.953A pdb=" N MET F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 172 Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.959A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.830A pdb=" N ILE F 240 " --> pdb=" O CYS F 236 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 275 through 280 Processing helix chain 'F' and resid 295 through 305 removed outlier: 3.648A pdb=" N TYR F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 326 removed outlier: 4.886A pdb=" N VAL F 318 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 Processing helix chain 'F' and resid 345 through 354 Processing helix chain 'F' and resid 359 through 362 Processing helix chain 'F' and resid 374 through 383 removed outlier: 4.497A pdb=" N ARG F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 398 removed outlier: 3.711A pdb=" N SER F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 429 through 439 Processing helix chain 'F' and resid 458 through 467 Processing helix chain 'F' and resid 470 through 485 removed outlier: 3.768A pdb=" N ALA F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 541 removed outlier: 4.525A pdb=" N LYS F 538 " --> pdb=" O LEU F 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU G 10 " --> pdb=" O GLU G 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG G 16 " --> pdb=" O THR G 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 50 through 64 removed outlier: 3.542A pdb=" N ARG G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 77 Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.837A pdb=" N PHE G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 94 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 50 through 64 removed outlier: 3.542A pdb=" N ARG H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 75 No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.837A pdb=" N PHE H 86 " --> pdb=" O HIS H 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG I 16 " --> pdb=" O THR I 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR I 28 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 50 through 64 removed outlier: 3.541A pdb=" N ARG I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.836A pdb=" N PHE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA I 94 " --> pdb=" O TYR I 90 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 272 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 186 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 248 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 188 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A 250 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 190 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 252 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 285 through 290 removed outlier: 6.569A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 186 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL B 248 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 188 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP B 250 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 190 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 252 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.675A pdb=" N THR C 272 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 245 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU C 269 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE C 247 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR C 271 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 249 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER C 186 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 248 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL C 188 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP C 250 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 190 " --> pdb=" O ASP C 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 252 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 285 through 290 removed outlier: 6.561A pdb=" N PHE D 154 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 288 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE D 156 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 290 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS D 158 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 272 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG D 267 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER D 186 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL D 248 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL D 188 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP D 250 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU D 190 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL D 252 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 445 through 447 Processing sheet with id= F, first strand: chain 'E' and resid 285 through 290 removed outlier: 6.776A pdb=" N PHE E 154 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE E 288 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE E 156 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 290 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS E 158 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR E 272 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR E 245 " --> pdb=" O ARG E 267 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU E 269 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE E 247 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR E 271 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE E 249 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER E 186 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 248 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL E 188 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP E 250 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 190 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 252 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 445 through 447 Processing sheet with id= H, first strand: chain 'F' and resid 285 through 290 removed outlier: 6.943A pdb=" N PHE F 154 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE F 288 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE F 156 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL F 290 " --> pdb=" O PHE F 156 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS F 158 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 272 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG F 267 " --> pdb=" O THR F 245 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER F 186 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL F 248 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL F 188 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP F 250 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU F 190 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL F 252 " --> pdb=" O LEU F 190 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2370 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: 6.85 Time building geometry restraints manager: 9.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7711 1.34 - 1.47: 4970 1.47 - 1.59: 11631 1.59 - 1.72: 18 1.72 - 1.85: 276 Bond restraints: 24606 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.23e+01 bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.12e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.10e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.06e+01 bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.05e+01 ... (remaining 24601 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.43: 444 104.43 - 112.09: 11141 112.09 - 119.76: 9717 119.76 - 127.42: 11813 127.42 - 135.09: 167 Bond angle restraints: 33282 Sorted by residual: angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 114.11 25.76 1.00e+00 1.00e+00 6.64e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 114.13 25.74 1.00e+00 1.00e+00 6.63e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.15 25.72 1.00e+00 1.00e+00 6.61e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 114.16 25.71 1.00e+00 1.00e+00 6.61e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 114.17 25.70 1.00e+00 1.00e+00 6.61e+02 ... (remaining 33277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 12914 16.90 - 33.79: 1461 33.79 - 50.69: 537 50.69 - 67.59: 267 67.59 - 84.48: 40 Dihedral angle restraints: 15219 sinusoidal: 6417 harmonic: 8802 Sorted by residual: dihedral pdb=" CA ASP F 216 " pdb=" C ASP F 216 " pdb=" N LEU F 217 " pdb=" CA LEU F 217 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ASP C 216 " pdb=" C ASP C 216 " pdb=" N LEU C 217 " pdb=" CA LEU C 217 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASP D 216 " pdb=" C ASP D 216 " pdb=" N LEU D 217 " pdb=" CA LEU D 217 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 15216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2558 0.070 - 0.140: 953 0.140 - 0.210: 235 0.210 - 0.280: 57 0.280 - 0.350: 16 Chirality restraints: 3819 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PHE E 532 " pdb=" N PHE E 532 " pdb=" C PHE E 532 " pdb=" CB PHE E 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 3816 not shown) Planarity restraints: 4233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 116 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP E 116 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP E 116 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 220 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO F 221 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 220 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 221 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.032 5.00e-02 4.00e+02 ... (remaining 4230 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 6 2.09 - 2.79: 6420 2.79 - 3.50: 34967 3.50 - 4.20: 59950 4.20 - 4.90: 100654 Nonbonded interactions: 201997 Sorted by model distance: nonbonded pdb=" CD GLU A 97 " pdb=" CD1 LEU H 51 " model vdw 1.390 3.690 nonbonded pdb=" CD GLU B 97 " pdb=" CD1 LEU I 51 " model vdw 1.745 3.690 nonbonded pdb=" OE1 GLU A 97 " pdb=" CD1 LEU H 51 " model vdw 1.773 3.460 nonbonded pdb=" CD GLU C 97 " pdb=" CD1 LEU G 51 " model vdw 1.799 3.690 nonbonded pdb=" CG GLU A 97 " pdb=" CD1 LEU H 51 " model vdw 1.969 3.860 ... (remaining 201992 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.380 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: 0.010 Extract box with map and model: 4.890 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 60.320 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.170 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.010 0.096 24606 Z= 0.623 Angle : 1.516 25.759 33282 Z= 1.048 Chirality : 0.078 0.350 3819 Planarity : 0.005 0.059 4233 Dihedral : 18.702 84.482 9453 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 39.59 Ramachandran Plot: Outliers : 0.82 % Allowed : 12.81 % Favored : 86.37 % Rotamer: Outliers : 17.81 % Allowed : 13.94 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -4.88 (0.13), residues: 2943 helix: -3.31 (0.09), residues: 1650 sheet: -2.70 (0.34), residues: 195 loop : -2.90 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 189 HIS 0.005 0.001 HIS A 466 PHE 0.018 0.003 PHE F 532 TYR 0.022 0.004 TYR A 371 ARG 0.004 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 484 poor density : 354 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 484 outliers final: 101 residues processed: 759 average time/residue: 0.3677 time to fit residues: 426.3198 Evaluate side-chains 306 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 205 time to evaluate : 3.091 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 0.2385 time to fit residues: 46.8963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 123 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 283 GLN A 482 GLN B 34 ASN B 40 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN C 19 HIS C 34 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 GLN C 482 GLN C 536 HIS D 123 ASN D 136 HIS D 237 ASN D 244 ASN D 262 GLN D 283 GLN E 123 ASN E 244 ASN E 482 GLN E 536 HIS F 123 ASN F 244 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 HIS F 536 HIS G 34 ASN H 14 HIS I 34 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24606 Z= 0.205 Angle : 0.706 8.602 33282 Z= 0.352 Chirality : 0.042 0.223 3819 Planarity : 0.006 0.069 4233 Dihedral : 10.678 80.268 3411 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.29 % Allowed : 4.93 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.49 (0.14), residues: 2943 helix: -1.20 (0.12), residues: 1626 sheet: -2.33 (0.31), residues: 213 loop : -1.99 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP F 189 HIS 0.005 0.001 HIS A 225 PHE 0.015 0.002 PHE F 249 TYR 0.021 0.002 TYR B 90 ARG 0.006 0.001 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 255 average time/residue: 0.3687 time to fit residues: 147.8945 Evaluate side-chains 180 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2298 time to fit residues: 5.2892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 267 optimal weight: 30.0000 chunk 92 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 96 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN F 237 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24606 Z= 0.257 Angle : 0.657 9.689 33282 Z= 0.329 Chirality : 0.040 0.175 3819 Planarity : 0.005 0.064 4233 Dihedral : 10.379 86.117 3411 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 2943 helix: -0.20 (0.12), residues: 1671 sheet: -1.87 (0.30), residues: 219 loop : -1.38 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP D 410 HIS 0.005 0.001 HIS F 158 PHE 0.018 0.002 PHE H 75 TYR 0.019 0.002 TYR B 90 ARG 0.005 0.001 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 2.753 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 outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.3564 time to fit residues: 120.5919 Evaluate side-chains 158 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.980 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2181 time to fit residues: 4.4384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 287 optimal weight: 50.0000 chunk 141 optimal weight: 9.9990 chunk 256 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 123 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 254 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN G 56 ASN H 40 HIS H 64 GLN I 19 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24606 Z= 0.181 Angle : 0.587 10.231 33282 Z= 0.290 Chirality : 0.039 0.297 3819 Planarity : 0.005 0.055 4233 Dihedral : 10.057 89.050 3411 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.46 (0.16), residues: 2943 helix: 0.43 (0.13), residues: 1665 sheet: -1.62 (0.31), residues: 219 loop : -1.05 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 410 HIS 0.003 0.001 HIS B 158 PHE 0.015 0.001 PHE E 301 TYR 0.014 0.001 TYR D 540 ARG 0.006 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3384 time to fit residues: 105.2672 Evaluate side-chains 155 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 257 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN B 96 ASN B 158 HIS B 244 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN I 14 HIS I 40 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24606 Z= 0.247 Angle : 0.649 11.305 33282 Z= 0.317 Chirality : 0.039 0.173 3819 Planarity : 0.005 0.050 4233 Dihedral : 9.647 89.962 3411 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.30 (0.16), residues: 2943 helix: 0.56 (0.13), residues: 1722 sheet: -1.46 (0.33), residues: 219 loop : -1.09 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP D 410 HIS 0.008 0.001 HIS F 158 PHE 0.015 0.002 PHE A 532 TYR 0.016 0.002 TYR D 540 ARG 0.006 0.001 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3544 time to fit residues: 105.6685 Evaluate side-chains 145 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.3980 chunk 258 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 287 optimal weight: 50.0000 chunk 238 optimal weight: 0.0670 chunk 133 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 262 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 536 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.7571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24606 Z= 0.144 Angle : 0.577 9.878 33282 Z= 0.278 Chirality : 0.038 0.160 3819 Planarity : 0.004 0.052 4233 Dihedral : 9.254 86.601 3411 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.16), residues: 2943 helix: 0.90 (0.13), residues: 1683 sheet: -1.29 (0.33), residues: 219 loop : -0.89 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 410 HIS 0.004 0.001 HIS H 19 PHE 0.016 0.001 PHE E 301 TYR 0.014 0.001 TYR A 77 ARG 0.003 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3509 time to fit residues: 106.5132 Evaluate side-chains 149 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS E 219 ASN E 537 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 19 HIS I 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24606 Z= 0.275 Angle : 0.664 14.956 33282 Z= 0.324 Chirality : 0.039 0.154 3819 Planarity : 0.005 0.065 4233 Dihedral : 9.315 89.269 3411 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.08 (0.16), residues: 2943 helix: 0.73 (0.13), residues: 1710 sheet: -1.32 (0.34), residues: 219 loop : -0.99 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP F 410 HIS 0.006 0.001 HIS F 158 PHE 0.025 0.002 PHE H 74 TYR 0.018 0.002 TYR B 540 ARG 0.006 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3429 time to fit residues: 99.1411 Evaluate side-chains 135 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 86 optimal weight: 0.0370 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 overall best weight: 1.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 19 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.8346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24606 Z= 0.160 Angle : 0.600 11.283 33282 Z= 0.285 Chirality : 0.038 0.170 3819 Planarity : 0.004 0.050 4233 Dihedral : 9.049 89.156 3411 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.16), residues: 2943 helix: 0.93 (0.13), residues: 1713 sheet: -1.23 (0.34), residues: 219 loop : -0.91 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 410 HIS 0.004 0.001 HIS H 19 PHE 0.023 0.001 PHE G 75 TYR 0.017 0.001 TYR D 540 ARG 0.003 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3374 time to fit residues: 97.9363 Evaluate side-chains 143 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 265 optimal weight: 20.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.8490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24606 Z= 0.143 Angle : 0.582 10.849 33282 Z= 0.278 Chirality : 0.038 0.144 3819 Planarity : 0.004 0.048 4233 Dihedral : 8.753 89.826 3411 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2943 helix: 1.05 (0.13), residues: 1698 sheet: -1.08 (0.34), residues: 219 loop : -0.70 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 410 HIS 0.002 0.000 HIS C 458 PHE 0.023 0.001 PHE I 93 TYR 0.014 0.001 TYR A 77 ARG 0.002 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3519 time to fit residues: 103.1186 Evaluate side-chains 141 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.0270 chunk 282 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 196 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 HIS I 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.8746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24606 Z= 0.210 Angle : 0.622 13.380 33282 Z= 0.300 Chirality : 0.038 0.198 3819 Planarity : 0.004 0.047 4233 Dihedral : 8.849 88.825 3411 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2943 helix: 1.00 (0.13), residues: 1713 sheet: -1.07 (0.34), residues: 219 loop : -0.82 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 410 HIS 0.005 0.001 HIS H 19 PHE 0.025 0.001 PHE D 301 TYR 0.015 0.001 TYR D 540 ARG 0.004 0.000 ARG C 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3024 time to fit residues: 86.4723 Evaluate side-chains 138 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.1980 chunk 250 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.025584 restraints weight = 265848.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.026347 restraints weight = 160907.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.026878 restraints weight = 113407.002| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.8896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24606 Z= 0.156 Angle : 0.595 11.172 33282 Z= 0.286 Chirality : 0.038 0.202 3819 Planarity : 0.004 0.048 4233 Dihedral : 8.714 88.294 3411 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.36 (0.16), residues: 2943 helix: 1.05 (0.13), residues: 1716 sheet: -0.98 (0.34), residues: 219 loop : -0.78 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 410 HIS 0.002 0.001 HIS F 158 PHE 0.015 0.001 PHE D 532 TYR 0.015 0.001 TYR B 540 ARG 0.003 0.000 ARG C 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4089.02 seconds wall clock time: 79 minutes 49.42 seconds (4789.42 seconds total)