Starting phenix.real_space_refine on Wed Jul 24 01:59:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/07_2024/8jns_36450_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/07_2024/8jns_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_36450/07_2024/8jns_36450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/07_2024/8jns_36450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/07_2024/8jns_36450_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jns_36450/07_2024/8jns_36450_neut.cif" } 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-dev-5388/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: 13.56, per 1000 atoms: 0.56 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: 9.40 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... Secondary structure from input PDB file: 171 helices and 13 sheets defined 61.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.758A pdb=" N ALA A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) 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 39 through 46 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.559A pdb=" N ARG A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) 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) removed outlier: 3.540A pdb=" N ALA A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.726A pdb=" N ASP A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) 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) removed outlier: 3.690A pdb=" N ASN A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.022A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.978A pdb=" N ILE A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 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 312 through 327 removed outlier: 4.886A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) 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 386 through 395 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 399 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 458 through 466 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 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) removed outlier: 3.968A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 removed outlier: 3.757A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) 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 39 through 46 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.559A pdb=" N ARG B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) 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) removed outlier: 3.540A pdb=" N ALA B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.620A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) 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) removed outlier: 3.690A pdb=" N ASN B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.597A pdb=" N ARG B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.523A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.022A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.684A pdb=" N ARG B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 4.102A pdb=" N ILE B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 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 312 through 327 removed outlier: 4.886A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.890A pdb=" N ALA B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) 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 386 through 397 removed outlier: 3.775A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 458 through 466 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 469 through 486 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) removed outlier: 3.672A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.757A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) 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 39 through 46 Processing helix chain 'C' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) 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) removed outlier: 3.540A pdb=" N ALA C 65 " --> pdb=" O TYR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 78 removed outlier: 3.531A pdb=" N TYR C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA C 84 " --> pdb=" O GLN C 80 " (cutoff:3.500A) 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) removed outlier: 3.690A pdb=" N ASN C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.597A pdb=" N ARG C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.522A pdb=" N ILE C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) 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) removed outlier: 3.579A pdb=" N SER C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 198 through 212 removed outlier: 4.022A pdb=" N PHE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.118A pdb=" N ILE C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE C 277 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 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 312 through 327 removed outlier: 4.886A pdb=" N VAL C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.892A pdb=" N ALA C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) 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 386 through 399 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) removed outlier: 4.136A pdb=" N MET C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 428 through 440 Processing helix chain 'C' and resid 457 through 466 Processing helix chain 'C' and resid 469 through 485 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 532 through 536 removed outlier: 3.851A pdb=" N LEU C 535 " --> pdb=" O PHE C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 198 through 212 removed outlier: 4.021A pdb=" N PHE D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.946A pdb=" N ILE D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE D 277 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 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 312 through 327 Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 344 through 355 Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) 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 386 through 396 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) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 428 through 440 Processing helix chain 'D' and resid 458 through 466 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 469 through 485 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) removed outlier: 3.797A pdb=" N LEU D 485 " --> pdb=" O GLU D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU D 535 " --> pdb=" O PHE D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.636A pdb=" N ARG E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 164 through 176 removed outlier: 3.522A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 212 removed outlier: 4.038A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 240 Processing helix chain 'E' and resid 254 through 264 removed outlier: 4.063A pdb=" N ILE E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 281 removed outlier: 3.916A pdb=" N ILE E 277 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 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 312 through 327 Processing helix chain 'E' and resid 329 through 340 Processing helix chain 'E' and resid 344 through 355 Processing helix chain 'E' and resid 358 through 363 Processing helix chain 'E' and resid 373 through 384 removed outlier: 3.892A pdb=" N ALA E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) 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 388 through 397 removed outlier: 3.531A pdb=" N VAL E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 428 through 440 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'E' and resid 469 through 484 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 532 through 536 removed outlier: 3.852A pdb=" N LEU E 535 " --> pdb=" O PHE E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER E 542 " --> pdb=" O LYS E 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 146 Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 212 removed outlier: 3.959A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 254 through 265 removed outlier: 4.066A pdb=" N ILE F 258 " --> pdb=" O GLN F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 281 removed outlier: 3.915A pdb=" N ILE F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 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 312 through 327 removed outlier: 4.886A pdb=" N VAL F 318 " --> pdb=" O LYS F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 338 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA F 377 " --> pdb=" O SER F 373 " (cutoff:3.500A) 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 386 through 396 removed outlier: 3.711A pdb=" N SER F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 428 through 440 Processing helix chain 'F' and resid 457 through 468 Processing helix chain 'F' and resid 469 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 532 through 536 removed outlier: 3.851A pdb=" N LEU F 535 " --> pdb=" O PHE F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER F 542 " --> pdb=" O LYS F 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU G 10 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.774A pdb=" N ALA G 26 " --> pdb=" O GLU G 22 " (cutoff:3.500A) 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 39 through 46 Processing helix chain 'G' and resid 49 through 65 removed outlier: 3.552A pdb=" N ARG G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) 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) removed outlier: 3.507A pdb=" N ALA G 65 " --> pdb=" O TYR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 78 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) 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 3 through 13 removed outlier: 3.630A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS H 19 " --> pdb=" O THR H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.774A pdb=" N ALA H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) 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 39 through 46 Processing helix chain 'H' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) 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) removed outlier: 3.507A pdb=" N ALA H 65 " --> pdb=" O TYR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 Processing helix chain 'H' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) 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 3 through 13 removed outlier: 3.630A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) 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 39 through 46 Processing helix chain 'I' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) 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) removed outlier: 3.507A pdb=" N ALA I 65 " --> pdb=" O TYR I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) 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=AA1, first strand: chain 'A' and resid 186 through 191 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: 6.204A pdb=" N PHE A 153 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 270 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 155 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 272 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 157 " --> pdb=" O THR A 272 " (cutoff:3.500A) 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) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 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: 6.203A pdb=" N PHE B 153 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 270 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 155 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B 272 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 157 " --> pdb=" O THR B 272 " (cutoff:3.500A) 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) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 191 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: 6.204A pdb=" N PHE C 153 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 270 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 155 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR C 272 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 157 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 186 through 191 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: 6.204A pdb=" N PHE C 153 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 270 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 155 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR C 272 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 157 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 290 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS C 158 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AA8, first strand: chain 'D' and resid 186 through 191 removed outlier: 4.780A pdb=" N ARG D 267 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE D 153 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL D 270 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU D 155 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR D 272 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU D 157 " --> pdb=" O THR D 272 " (cutoff:3.500A) 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) Processing sheet with id=AA9, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AB1, first strand: chain 'E' and resid 186 through 191 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: 6.203A pdb=" N PHE E 153 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL E 270 " --> pdb=" O PHE E 153 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU E 155 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR E 272 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU E 157 " --> pdb=" O THR E 272 " (cutoff:3.500A) 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) Processing sheet with id=AB2, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'F' and resid 186 through 191 removed outlier: 4.819A pdb=" N ARG F 267 " --> pdb=" O THR F 245 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE F 153 " --> pdb=" O CYS F 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL F 270 " --> pdb=" O PHE F 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU F 155 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR F 272 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU F 157 " --> pdb=" O THR F 272 " (cutoff:3.500A) 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) Processing sheet with id=AB4, first strand: chain 'F' and resid 405 through 406 1066 hydrogen bonds defined for protein. 3000 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: 7.44 Time building geometry restraints manager: 10.34 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: 6391 2.79 - 3.50: 34751 3.50 - 4.20: 59519 4.20 - 4.90: 100478 Nonbonded interactions: 201145 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 201140 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: 0.700 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: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 64.450 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.120 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.170 ------------------------------------------------------------------------------- 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= 0.618 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 : 3.012 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 REVERT: A 8 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7888 (ttt90) REVERT: A 47 MET cc_start: 0.8044 (mmm) cc_final: 0.6338 (mmm) REVERT: A 58 LEU cc_start: 0.9049 (mt) cc_final: 0.8559 (pp) REVERT: A 173 LEU cc_start: 0.8974 (mt) cc_final: 0.8764 (pp) REVERT: A 180 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 255 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: A 290 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 332 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 434 LEU cc_start: 0.9225 (mt) cc_final: 0.8977 (mt) REVERT: B 8 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7950 (tpt170) REVERT: B 216 ASP cc_start: 0.8988 (m-30) cc_final: 0.8115 (t0) REVERT: B 307 MET cc_start: 0.8125 (tpp) cc_final: 0.7869 (tpp) REVERT: B 369 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (t80) REVERT: B 459 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8886 (mm) REVERT: C 47 MET cc_start: 0.8417 (mmm) cc_final: 0.8179 (mmm) REVERT: C 49 THR cc_start: 0.9057 (m) cc_final: 0.8631 (p) REVERT: C 58 LEU cc_start: 0.9132 (mt) cc_final: 0.8734 (pp) REVERT: C 290 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9007 (p) REVERT: C 296 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8391 (p0) REVERT: C 348 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8915 (tmm) REVERT: C 355 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9278 (mm) REVERT: C 363 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8722 (p) REVERT: C 437 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8960 (tp) REVERT: D 175 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8382 (ttpp) REVERT: D 226 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 290 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9214 (t) REVERT: D 296 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8576 (p0) REVERT: D 355 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9227 (tp) REVERT: D 369 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7891 (t80) REVERT: F 113 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: F 144 LEU cc_start: 0.9412 (mt) cc_final: 0.9171 (mt) REVERT: F 207 ILE cc_start: 0.9599 (mt) cc_final: 0.9340 (mt) REVERT: F 277 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8910 (pt) REVERT: F 334 MET cc_start: 0.9429 (tpt) cc_final: 0.9188 (tpp) REVERT: F 344 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 369 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7642 (t80) REVERT: F 381 CYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8585 (t) REVERT: F 437 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9377 (mt) REVERT: H 88 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8841 (mm-30) REVERT: I 45 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.6564 (p) REVERT: I 68 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7377 (tt) REVERT: I 76 ASN cc_start: 0.8256 (m-40) cc_final: 0.7594 (p0) outliers start: 484 outliers final: 101 residues processed: 759 average time/residue: 0.3602 time to fit residues: 417.6172 Evaluate side-chains 338 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 209 time to evaluate : 2.941 ------------------------------------------------------------------------------- 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: 3.9990 chunk 225 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS 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 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 536 HIS B 34 ASN B 40 HIS B 219 ASN ** 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 283 GLN C 482 GLN D 123 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 254 GLN D 262 GLN D 283 GLN E 123 ASN E 244 ASN E 482 GLN F 123 ASN F 244 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 HIS G 34 ASN G 56 ASN H 14 HIS H 19 HIS I 34 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24606 Z= 0.227 Angle : 0.741 10.452 33282 Z= 0.373 Chirality : 0.043 0.199 3819 Planarity : 0.006 0.072 4233 Dihedral : 10.673 77.023 3411 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.22 % Allowed : 4.67 % Favored : 95.11 % 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: -2.56 (0.14), residues: 2943 helix: -1.26 (0.11), residues: 1722 sheet: -2.41 (0.29), residues: 219 loop : -2.03 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP F 189 HIS 0.005 0.001 HIS H 14 PHE 0.018 0.002 PHE I 74 TYR 0.021 0.002 TYR B 90 ARG 0.006 0.001 ARG H 8 *********************** 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 254 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 248 time to evaluate : 2.743 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: A 30 LEU cc_start: 0.7277 (mm) cc_final: 0.7034 (mt) REVERT: A 128 MET cc_start: 0.7253 (mmp) cc_final: 0.6838 (tpp) REVERT: A 157 LEU cc_start: 0.8866 (tp) cc_final: 0.8628 (tp) REVERT: B 140 VAL cc_start: 0.9302 (t) cc_final: 0.9041 (t) REVERT: B 335 MET cc_start: 0.9203 (mtp) cc_final: 0.8838 (ttm) REVERT: C 1 MET cc_start: 0.9054 (mpp) cc_final: 0.8234 (ppp) REVERT: C 144 LEU cc_start: 0.9604 (mt) cc_final: 0.9375 (mt) REVERT: C 462 MET cc_start: 0.9177 (mtp) cc_final: 0.8893 (ttp) REVERT: C 533 MET cc_start: 0.7897 (ppp) cc_final: 0.7565 (ppp) REVERT: D 334 MET cc_start: 0.9112 (tpp) cc_final: 0.8890 (tpp) REVERT: E 144 LEU cc_start: 0.9263 (tp) cc_final: 0.9042 (tp) REVERT: E 302 LEU cc_start: 0.9151 (mt) cc_final: 0.8770 (mt) REVERT: F 144 LEU cc_start: 0.9352 (mt) cc_final: 0.9095 (tp) REVERT: G 75 PHE cc_start: 0.8677 (m-10) cc_final: 0.8385 (m-80) REVERT: I 1 MET cc_start: 0.8073 (mmm) cc_final: 0.7854 (mmm) outliers start: 6 outliers final: 0 residues processed: 254 average time/residue: 0.3738 time to fit residues: 150.2873 Evaluate side-chains 180 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.984 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 267 optimal weight: 30.0000 chunk 92 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 171 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN F 262 GLN F 283 GLN H 19 HIS ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24606 Z= 0.230 Angle : 0.644 9.196 33282 Z= 0.324 Chirality : 0.039 0.158 3819 Planarity : 0.005 0.064 4233 Dihedral : 10.143 88.435 3411 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: -1.06 (0.15), residues: 2943 helix: -0.06 (0.13), residues: 1734 sheet: -1.96 (0.29), residues: 246 loop : -1.32 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP C 189 HIS 0.005 0.001 HIS B 158 PHE 0.021 0.002 PHE H 74 TYR 0.018 0.002 TYR B 90 ARG 0.011 0.000 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 212 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.409 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: A 30 LEU cc_start: 0.7634 (mm) cc_final: 0.7374 (mt) REVERT: A 128 MET cc_start: 0.8139 (mmp) cc_final: 0.7814 (tpp) REVERT: A 157 LEU cc_start: 0.8916 (tp) cc_final: 0.8701 (tp) REVERT: A 399 MET cc_start: 0.8535 (tpp) cc_final: 0.8151 (tmm) REVERT: B 216 ASP cc_start: 0.7963 (t0) cc_final: 0.7684 (t0) REVERT: B 533 MET cc_start: 0.8702 (ppp) cc_final: 0.7976 (ppp) REVERT: C 533 MET cc_start: 0.7709 (ppp) cc_final: 0.7343 (ppp) REVERT: D 307 MET cc_start: 0.8094 (mmt) cc_final: 0.7819 (mmp) REVERT: D 334 MET cc_start: 0.9172 (tpp) cc_final: 0.8969 (tpp) REVERT: D 348 MET cc_start: 0.9533 (ptm) cc_final: 0.9250 (ptm) REVERT: E 114 MET cc_start: 0.9261 (pmm) cc_final: 0.8733 (pmm) REVERT: E 225 HIS cc_start: 0.7549 (p90) cc_final: 0.7284 (p-80) REVERT: E 449 MET cc_start: 0.8495 (pmm) cc_final: 0.8287 (pmm) REVERT: E 533 MET cc_start: 0.8320 (ppp) cc_final: 0.7477 (mmm) REVERT: F 309 MET cc_start: 0.7954 (ppp) cc_final: 0.7370 (ppp) REVERT: F 348 MET cc_start: 0.8682 (ttm) cc_final: 0.8392 (ttp) REVERT: F 399 MET cc_start: 0.8625 (mmp) cc_final: 0.8415 (mmt) REVERT: F 462 MET cc_start: 0.8836 (tmm) cc_final: 0.8573 (tmm) REVERT: G 88 GLU cc_start: 0.8833 (pt0) cc_final: 0.7870 (mm-30) REVERT: H 7 CYS cc_start: 0.8692 (m) cc_final: 0.8338 (m) REVERT: H 29 TYR cc_start: 0.3991 (t80) cc_final: 0.2959 (m-80) REVERT: I 1 MET cc_start: 0.8118 (mmm) cc_final: 0.7399 (mmm) REVERT: I 76 ASN cc_start: 0.8192 (m-40) cc_final: 0.7978 (m-40) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3478 time to fit residues: 119.3615 Evaluate side-chains 162 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.078 ------------------------------------------------------------------------------- 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: 0.2980 chunk 203 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 287 optimal weight: 50.0000 chunk 141 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 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** G 56 ASN H 19 HIS H 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24606 Z= 0.175 Angle : 0.592 11.902 33282 Z= 0.292 Chirality : 0.038 0.163 3819 Planarity : 0.005 0.057 4233 Dihedral : 9.836 86.561 3411 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: -0.34 (0.16), residues: 2943 helix: 0.55 (0.13), residues: 1719 sheet: -1.53 (0.32), residues: 219 loop : -1.13 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 410 HIS 0.005 0.001 HIS B 466 PHE 0.018 0.001 PHE H 74 TYR 0.025 0.001 TYR I 29 ARG 0.006 0.000 ARG C 380 *********************** 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 199 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.005 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: A 30 LEU cc_start: 0.7565 (mm) cc_final: 0.7271 (mt) REVERT: A 128 MET cc_start: 0.8232 (mmp) cc_final: 0.7767 (mmm) REVERT: B 216 ASP cc_start: 0.7981 (t0) cc_final: 0.7718 (t0) REVERT: C 128 MET cc_start: 0.9182 (ptp) cc_final: 0.8710 (ptp) REVERT: C 374 LEU cc_start: 0.8958 (tp) cc_final: 0.8742 (tp) REVERT: D 234 MET cc_start: 0.9029 (mtm) cc_final: 0.8823 (mtp) REVERT: D 334 MET cc_start: 0.9165 (tpp) cc_final: 0.8944 (tpp) REVERT: E 114 MET cc_start: 0.9271 (pmm) cc_final: 0.8810 (pmm) REVERT: E 225 HIS cc_start: 0.7438 (p90) cc_final: 0.7213 (p-80) REVERT: E 307 MET cc_start: 0.7575 (tpp) cc_final: 0.7305 (tpp) REVERT: F 147 MET cc_start: 0.9372 (mmt) cc_final: 0.9011 (mmp) REVERT: F 348 MET cc_start: 0.8831 (ttm) cc_final: 0.8427 (ttt) REVERT: F 462 MET cc_start: 0.8761 (tmm) cc_final: 0.8544 (tmm) REVERT: G 88 GLU cc_start: 0.8967 (pt0) cc_final: 0.7833 (mm-30) REVERT: H 7 CYS cc_start: 0.8642 (m) cc_final: 0.8325 (m) REVERT: H 29 TYR cc_start: 0.3998 (t80) cc_final: 0.3203 (m-80) REVERT: I 1 MET cc_start: 0.8072 (mmm) cc_final: 0.7340 (mmm) REVERT: I 46 LYS cc_start: 0.8910 (pptt) cc_final: 0.8650 (pttm) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3415 time to fit residues: 111.8342 Evaluate side-chains 169 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.201 ------------------------------------------------------------------------------- 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: 9.9990 chunk 162 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 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 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 534 GLN B 96 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 19 HIS H 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24606 Z= 0.270 Angle : 0.664 10.422 33282 Z= 0.330 Chirality : 0.039 0.142 3819 Planarity : 0.005 0.056 4233 Dihedral : 9.807 88.918 3411 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % 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: -0.29 (0.16), residues: 2943 helix: 0.50 (0.13), residues: 1755 sheet: -1.52 (0.32), residues: 246 loop : -0.93 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 410 HIS 0.007 0.001 HIS B 536 PHE 0.025 0.002 PHE H 74 TYR 0.014 0.002 TYR A 77 ARG 0.008 0.001 ARG G 16 *********************** 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 190 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 2.945 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: B 307 MET cc_start: 0.8260 (mmp) cc_final: 0.7811 (mmm) REVERT: C 1 MET cc_start: 0.8553 (mmp) cc_final: 0.8095 (ppp) REVERT: C 128 MET cc_start: 0.8980 (ptp) cc_final: 0.8565 (ptp) REVERT: C 374 LEU cc_start: 0.9028 (tp) cc_final: 0.8821 (tp) REVERT: D 234 MET cc_start: 0.9111 (mtm) cc_final: 0.8884 (mtp) REVERT: D 307 MET cc_start: 0.7780 (mmt) cc_final: 0.7554 (mmp) REVERT: D 462 MET cc_start: 0.8955 (ptp) cc_final: 0.8660 (tmm) REVERT: E 225 HIS cc_start: 0.7622 (p90) cc_final: 0.7399 (p-80) REVERT: F 348 MET cc_start: 0.8992 (ttm) cc_final: 0.8594 (ttt) REVERT: F 399 MET cc_start: 0.8963 (mmp) cc_final: 0.8690 (mmt) REVERT: H 7 CYS cc_start: 0.8549 (m) cc_final: 0.8223 (m) REVERT: H 19 HIS cc_start: 0.9216 (m90) cc_final: 0.8965 (m-70) REVERT: I 1 MET cc_start: 0.8421 (mmm) cc_final: 0.8145 (tpp) REVERT: I 46 LYS cc_start: 0.9137 (pptt) cc_final: 0.8768 (pttm) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.3494 time to fit residues: 106.6322 Evaluate side-chains 149 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.042 ------------------------------------------------------------------------------- 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: 0.9980 chunk 258 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 287 optimal weight: 50.0000 chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS E 536 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.7892 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= 0.227 Angle : 0.627 11.176 33282 Z= 0.310 Chirality : 0.038 0.138 3819 Planarity : 0.004 0.050 4233 Dihedral : 9.570 88.269 3411 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.07 (0.16), residues: 2943 helix: 0.71 (0.13), residues: 1752 sheet: -1.26 (0.34), residues: 219 loop : -1.01 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 410 HIS 0.004 0.001 HIS B 158 PHE 0.018 0.001 PHE I 75 TYR 0.017 0.001 TYR I 29 ARG 0.005 0.000 ARG A 63 *********************** 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 182 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 3.059 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: B 147 MET cc_start: 0.9135 (mmm) cc_final: 0.8880 (mmm) REVERT: B 307 MET cc_start: 0.8318 (mmp) cc_final: 0.8088 (mpp) REVERT: B 335 MET cc_start: 0.9150 (mtp) cc_final: 0.8261 (tpp) REVERT: B 533 MET cc_start: 0.8946 (ptm) cc_final: 0.8464 (ptm) REVERT: C 1 MET cc_start: 0.8626 (mmp) cc_final: 0.7938 (ppp) REVERT: C 128 MET cc_start: 0.9001 (ptp) cc_final: 0.8522 (ptp) REVERT: C 335 MET cc_start: 0.9108 (ttm) cc_final: 0.8900 (ttm) REVERT: C 374 LEU cc_start: 0.9025 (tp) cc_final: 0.8820 (tp) REVERT: C 462 MET cc_start: 0.9501 (mtp) cc_final: 0.9287 (mtp) REVERT: D 234 MET cc_start: 0.9113 (mtm) cc_final: 0.8888 (mtp) REVERT: D 307 MET cc_start: 0.7885 (mmt) cc_final: 0.7631 (mmp) REVERT: D 348 MET cc_start: 0.9053 (ppp) cc_final: 0.8710 (ppp) REVERT: D 462 MET cc_start: 0.8960 (ptp) cc_final: 0.8628 (tmm) REVERT: E 225 HIS cc_start: 0.7481 (p90) cc_final: 0.7194 (p-80) REVERT: E 309 MET cc_start: 0.7481 (mmm) cc_final: 0.7099 (mmm) REVERT: F 348 MET cc_start: 0.8897 (ttm) cc_final: 0.8451 (ttp) REVERT: F 399 MET cc_start: 0.9053 (mmp) cc_final: 0.8798 (mmt) REVERT: F 462 MET cc_start: 0.8868 (tmm) cc_final: 0.8662 (tmm) REVERT: H 7 CYS cc_start: 0.8545 (m) cc_final: 0.8236 (m) REVERT: H 19 HIS cc_start: 0.9187 (m90) cc_final: 0.8932 (m-70) REVERT: I 1 MET cc_start: 0.8374 (mmm) cc_final: 0.8080 (tpp) REVERT: I 46 LYS cc_start: 0.9174 (pptt) cc_final: 0.8921 (pttm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3274 time to fit residues: 98.4113 Evaluate side-chains 144 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.012 ------------------------------------------------------------------------------- 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: 50.0000 chunk 32 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 179 optimal weight: 0.3980 chunk 174 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN ** 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 536 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.8128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24606 Z= 0.165 Angle : 0.597 10.439 33282 Z= 0.288 Chirality : 0.038 0.182 3819 Planarity : 0.004 0.046 4233 Dihedral : 9.166 83.892 3411 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.23 (0.16), residues: 2943 helix: 0.92 (0.13), residues: 1761 sheet: -1.06 (0.35), residues: 219 loop : -0.86 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 410 HIS 0.004 0.001 HIS E 461 PHE 0.021 0.001 PHE D 532 TYR 0.015 0.001 TYR A 77 ARG 0.003 0.000 ARG G 16 *********************** 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 185 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7960 (mtm) cc_final: 0.7414 (tmm) REVERT: A 462 MET cc_start: 0.8832 (ttt) cc_final: 0.8535 (ptm) REVERT: B 216 ASP cc_start: 0.8079 (t0) cc_final: 0.7857 (t0) REVERT: B 335 MET cc_start: 0.9129 (mtp) cc_final: 0.8240 (tpp) REVERT: B 533 MET cc_start: 0.8852 (ptm) cc_final: 0.8464 (ptm) REVERT: C 1 MET cc_start: 0.8666 (mmp) cc_final: 0.7890 (ppp) REVERT: C 128 MET cc_start: 0.8983 (ptp) cc_final: 0.8414 (ptp) REVERT: C 335 MET cc_start: 0.9071 (ttm) cc_final: 0.8869 (ttm) REVERT: C 374 LEU cc_start: 0.8979 (tp) cc_final: 0.8757 (tp) REVERT: C 462 MET cc_start: 0.9496 (mtp) cc_final: 0.9295 (mtp) REVERT: C 533 MET cc_start: 0.7911 (ptm) cc_final: 0.7628 (ptm) REVERT: D 147 MET cc_start: 0.8589 (mpp) cc_final: 0.8158 (mtp) REVERT: D 307 MET cc_start: 0.7741 (mmt) cc_final: 0.7508 (mmp) REVERT: D 348 MET cc_start: 0.8992 (ppp) cc_final: 0.8638 (ppp) REVERT: D 462 MET cc_start: 0.8942 (ptp) cc_final: 0.8615 (tmm) REVERT: E 309 MET cc_start: 0.7660 (mmm) cc_final: 0.7215 (mmm) REVERT: F 128 MET cc_start: 0.8921 (ptp) cc_final: 0.8553 (ptp) REVERT: F 334 MET cc_start: 0.9500 (tpp) cc_final: 0.9199 (tpp) REVERT: F 348 MET cc_start: 0.8841 (ttm) cc_final: 0.8521 (ttp) REVERT: F 399 MET cc_start: 0.8995 (mmp) cc_final: 0.8741 (mmt) REVERT: F 462 MET cc_start: 0.8868 (tmm) cc_final: 0.8667 (tmm) REVERT: G 47 MET cc_start: 0.6292 (mmm) cc_final: 0.5887 (mmt) REVERT: G 88 GLU cc_start: 0.9206 (pt0) cc_final: 0.8228 (pt0) REVERT: H 7 CYS cc_start: 0.8457 (m) cc_final: 0.8215 (m) REVERT: H 19 HIS cc_start: 0.9252 (m90) cc_final: 0.8940 (m-70) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3266 time to fit residues: 98.6540 Evaluate side-chains 151 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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: 7.9990 chunk 114 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 244 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS E 158 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.8529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24606 Z= 0.259 Angle : 0.655 9.644 33282 Z= 0.322 Chirality : 0.039 0.194 3819 Planarity : 0.004 0.050 4233 Dihedral : 9.215 74.956 3411 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 0.07 (0.16), residues: 2943 helix: 0.82 (0.13), residues: 1740 sheet: -1.06 (0.35), residues: 219 loop : -0.97 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 410 HIS 0.008 0.001 HIS E 158 PHE 0.021 0.002 PHE H 74 TYR 0.015 0.001 TYR D 540 ARG 0.005 0.000 ARG H 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 172 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.997 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: A 128 MET cc_start: 0.8051 (mtm) cc_final: 0.7449 (tmm) REVERT: A 335 MET cc_start: 0.9283 (pmm) cc_final: 0.8987 (pmm) REVERT: A 462 MET cc_start: 0.8861 (ttt) cc_final: 0.8563 (ptm) REVERT: B 309 MET cc_start: 0.7821 (tpt) cc_final: 0.7573 (tpp) REVERT: B 335 MET cc_start: 0.9176 (mtp) cc_final: 0.8313 (tpp) REVERT: B 533 MET cc_start: 0.9007 (ptm) cc_final: 0.8633 (ptp) REVERT: C 1 MET cc_start: 0.8724 (mmp) cc_final: 0.7701 (tmm) REVERT: C 128 MET cc_start: 0.8886 (ptp) cc_final: 0.8352 (ptp) REVERT: C 335 MET cc_start: 0.9099 (ttm) cc_final: 0.8880 (ttm) REVERT: C 374 LEU cc_start: 0.9026 (tp) cc_final: 0.8798 (tp) REVERT: C 462 MET cc_start: 0.9559 (mtp) cc_final: 0.9300 (mtp) REVERT: C 533 MET cc_start: 0.7970 (ptm) cc_final: 0.7730 (ptm) REVERT: D 147 MET cc_start: 0.8611 (mpp) cc_final: 0.8240 (mtp) REVERT: D 234 MET cc_start: 0.9030 (mtm) cc_final: 0.8773 (mtp) REVERT: D 307 MET cc_start: 0.7864 (mmt) cc_final: 0.7631 (mmp) REVERT: D 348 MET cc_start: 0.9095 (ppp) cc_final: 0.8747 (ppp) REVERT: E 147 MET cc_start: 0.8173 (ptp) cc_final: 0.7473 (ptp) REVERT: F 128 MET cc_start: 0.8818 (ptp) cc_final: 0.8474 (ptp) REVERT: F 348 MET cc_start: 0.9005 (ttm) cc_final: 0.8526 (ttp) REVERT: F 399 MET cc_start: 0.9098 (mmp) cc_final: 0.8836 (mmt) REVERT: F 533 MET cc_start: 0.8734 (ppp) cc_final: 0.8484 (ppp) REVERT: G 75 PHE cc_start: 0.8876 (m-10) cc_final: 0.8592 (m-80) REVERT: H 7 CYS cc_start: 0.8501 (m) cc_final: 0.8248 (m) REVERT: H 19 HIS cc_start: 0.9234 (m90) cc_final: 0.8943 (m-70) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3223 time to fit residues: 91.7632 Evaluate side-chains 141 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.155 ------------------------------------------------------------------------------- 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: 8.9990 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 0.0980 chunk 252 optimal weight: 0.9990 chunk 265 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 B 56 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.8669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24606 Z= 0.159 Angle : 0.609 10.586 33282 Z= 0.294 Chirality : 0.039 0.173 3819 Planarity : 0.004 0.047 4233 Dihedral : 9.022 67.842 3411 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 1.01 (0.13), residues: 1737 sheet: -0.92 (0.35), residues: 219 loop : -0.93 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 410 HIS 0.004 0.001 HIS E 461 PHE 0.019 0.001 PHE G 75 TYR 0.015 0.001 TYR E 305 ARG 0.004 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 174 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.972 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: A 335 MET cc_start: 0.9275 (pmm) cc_final: 0.8971 (pmm) REVERT: A 462 MET cc_start: 0.8792 (ttt) cc_final: 0.8168 (tmm) REVERT: B 147 MET cc_start: 0.9152 (mmm) cc_final: 0.8824 (mmm) REVERT: B 335 MET cc_start: 0.9200 (mtp) cc_final: 0.8334 (tpp) REVERT: B 462 MET cc_start: 0.9152 (ppp) cc_final: 0.8944 (ppp) REVERT: B 533 MET cc_start: 0.8871 (ptm) cc_final: 0.8437 (ptp) REVERT: C 1 MET cc_start: 0.8615 (mmp) cc_final: 0.7745 (tmm) REVERT: C 128 MET cc_start: 0.8869 (ptp) cc_final: 0.8490 (ptp) REVERT: C 335 MET cc_start: 0.9068 (ttm) cc_final: 0.8867 (ttm) REVERT: C 348 MET cc_start: 0.9361 (pmm) cc_final: 0.9149 (pmm) REVERT: C 374 LEU cc_start: 0.8995 (tp) cc_final: 0.8762 (tp) REVERT: C 462 MET cc_start: 0.9501 (mtp) cc_final: 0.9279 (mtp) REVERT: C 533 MET cc_start: 0.7773 (ptm) cc_final: 0.7530 (ptm) REVERT: D 147 MET cc_start: 0.8457 (mpp) cc_final: 0.8233 (mtp) REVERT: D 234 MET cc_start: 0.9060 (mtm) cc_final: 0.8834 (mtp) REVERT: D 307 MET cc_start: 0.7780 (mmt) cc_final: 0.7544 (mmp) REVERT: D 348 MET cc_start: 0.9075 (ppp) cc_final: 0.8728 (ppp) REVERT: E 114 MET cc_start: 0.9491 (pmm) cc_final: 0.9231 (pmm) REVERT: F 128 MET cc_start: 0.8840 (ptp) cc_final: 0.8415 (ptp) REVERT: F 147 MET cc_start: 0.9157 (mmp) cc_final: 0.8927 (mpp) REVERT: F 348 MET cc_start: 0.8944 (ttm) cc_final: 0.8483 (ttp) REVERT: F 399 MET cc_start: 0.9016 (mmp) cc_final: 0.8766 (mmt) REVERT: G 47 MET cc_start: 0.6601 (mmm) cc_final: 0.6188 (mmt) REVERT: G 88 GLU cc_start: 0.8841 (pt0) cc_final: 0.8380 (pt0) REVERT: H 7 CYS cc_start: 0.8456 (m) cc_final: 0.8177 (m) REVERT: H 19 HIS cc_start: 0.9283 (m90) cc_final: 0.8969 (m-70) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3206 time to fit residues: 93.0123 Evaluate side-chains 145 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.932 ------------------------------------------------------------------------------- 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: 0.1980 chunk 282 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 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** D 536 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.8931 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= 0.235 Angle : 0.642 9.442 33282 Z= 0.315 Chirality : 0.039 0.163 3819 Planarity : 0.004 0.049 4233 Dihedral : 8.996 67.587 3411 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.17 (0.16), residues: 2943 helix: 0.90 (0.13), residues: 1734 sheet: -0.89 (0.36), residues: 219 loop : -0.93 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 410 HIS 0.004 0.001 HIS F 158 PHE 0.021 0.002 PHE B 301 TYR 0.019 0.001 TYR D 540 ARG 0.009 0.000 ARG H 8 ********************** 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 171 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8675 (mmm) cc_final: 0.8462 (mmp) REVERT: A 128 MET cc_start: 0.8622 (ptp) cc_final: 0.8397 (ptp) REVERT: A 335 MET cc_start: 0.9267 (pmm) cc_final: 0.8945 (pmm) REVERT: A 462 MET cc_start: 0.8864 (ttt) cc_final: 0.8233 (tmm) REVERT: B 147 MET cc_start: 0.9189 (mmm) cc_final: 0.8851 (mmm) REVERT: B 335 MET cc_start: 0.9268 (mtp) cc_final: 0.8512 (tpp) REVERT: B 462 MET cc_start: 0.9198 (ppp) cc_final: 0.8932 (ppp) REVERT: B 533 MET cc_start: 0.8804 (ptm) cc_final: 0.8394 (ptp) REVERT: C 1 MET cc_start: 0.8748 (mmp) cc_final: 0.7746 (tmm) REVERT: C 128 MET cc_start: 0.8889 (ptp) cc_final: 0.8330 (ptp) REVERT: C 348 MET cc_start: 0.9380 (pmm) cc_final: 0.9166 (pmm) REVERT: C 374 LEU cc_start: 0.9015 (tp) cc_final: 0.8773 (tp) REVERT: C 462 MET cc_start: 0.9552 (mtp) cc_final: 0.9295 (mtp) REVERT: C 533 MET cc_start: 0.8098 (ptm) cc_final: 0.7870 (ptm) REVERT: D 234 MET cc_start: 0.9032 (mtm) cc_final: 0.8764 (mtp) REVERT: D 307 MET cc_start: 0.7676 (mmt) cc_final: 0.7102 (mmp) REVERT: D 309 MET cc_start: 0.7387 (mmm) cc_final: 0.6107 (mmt) REVERT: D 348 MET cc_start: 0.9094 (ppp) cc_final: 0.8749 (ppp) REVERT: E 147 MET cc_start: 0.8052 (ptp) cc_final: 0.7573 (ptp) REVERT: E 335 MET cc_start: 0.9550 (mtp) cc_final: 0.9250 (mtp) REVERT: F 128 MET cc_start: 0.8839 (ptp) cc_final: 0.8465 (ptp) REVERT: F 348 MET cc_start: 0.9023 (ttm) cc_final: 0.8559 (ttp) REVERT: G 34 ASN cc_start: 0.8254 (m-40) cc_final: 0.7902 (m-40) REVERT: H 7 CYS cc_start: 0.8463 (m) cc_final: 0.8208 (m) REVERT: H 19 HIS cc_start: 0.9287 (m90) cc_final: 0.8985 (m-70) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3128 time to fit residues: 89.5883 Evaluate side-chains 140 residues out of total 2718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.202 ------------------------------------------------------------------------------- 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: 9.9990 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.035893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.025930 restraints weight = 269445.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.026704 restraints weight = 160722.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027248 restraints weight = 112412.271| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.9022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24606 Z= 0.142 Angle : 0.598 11.980 33282 Z= 0.287 Chirality : 0.039 0.160 3819 Planarity : 0.004 0.049 4233 Dihedral : 8.745 63.582 3411 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: 0.55 (0.16), residues: 2943 helix: 1.25 (0.13), residues: 1695 sheet: -0.85 (0.35), residues: 219 loop : -0.79 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 410 HIS 0.004 0.001 HIS B 40 PHE 0.019 0.001 PHE A 153 TYR 0.013 0.001 TYR D 540 ARG 0.009 0.000 ARG H 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.21 seconds wall clock time: 75 minutes 7.77 seconds (4507.77 seconds total)