Starting phenix.real_space_refine on Fri Mar 22 10:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7o_29818/03_2024/8g7o_29818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7o_29818/03_2024/8g7o_29818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7o_29818/03_2024/8g7o_29818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7o_29818/03_2024/8g7o_29818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7o_29818/03_2024/8g7o_29818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7o_29818/03_2024/8g7o_29818_updated.pdb" } resolution = 3.4 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= 0.092 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: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 105 5.16 5 C 20734 2.51 5 N 5621 2.21 5 O 6566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 394": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 264": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 344": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 394": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 444": "NH1" <-> "NH2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F ARG 34": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F ARG 242": "NH1" <-> "NH2" Residue "F ARG 264": "NH1" <-> "NH2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "F ARG 344": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 394": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "F ARG 444": "NH1" <-> "NH2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G ARG 264": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 500": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H ARG 20": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "J ARG 7": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 92": "NH1" <-> "NH2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K ARG 92": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "M ARG 7": "NH1" <-> "NH2" Residue "M ARG 15": "NH1" <-> "NH2" Residue "M ARG 20": "NH1" <-> "NH2" Residue "M ARG 92": "NH1" <-> "NH2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "N ARG 15": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 92": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33047 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "B" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "C" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "D" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "E" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "F" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "G" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "I" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "K" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "M" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "N" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.98, per 1000 atoms: 0.54 Number of scatterers: 33047 At special positions: 0 Unit cell: (162.225, 165.006, 156.663, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 21 15.00 O 6566 8.00 N 5621 7.00 C 20734 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: 13.87 Conformation dependent library (CDL) restraints added in 6.6 seconds 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 56 sheets defined 46.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.884A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.568A pdb=" N SER A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.850A pdb=" N GLY A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 228 through 241 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 338 through 354 removed outlier: 3.548A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 385 through 407 removed outlier: 3.533A pdb=" N ARG A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.835A pdb=" N CYS A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.805A pdb=" N ASP A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 456 removed outlier: 4.611A pdb=" N LYS A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 487 through 490 No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 496 through 515 removed outlier: 3.797A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 4.054A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.518A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 87 through 103 Processing helix chain 'B' and resid 111 through 132 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 154 through 166 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.523A pdb=" N THR B 294 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 338 through 353 removed outlier: 3.584A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 Processing helix chain 'B' and resid 385 through 407 removed outlier: 3.603A pdb=" N ARG B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.655A pdb=" N CYS B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.740A pdb=" N ASP B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 457 removed outlier: 4.560A pdb=" N LYS B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix removed outlier: 3.593A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 496 through 515 removed outlier: 3.582A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 28 removed outlier: 4.002A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 Processing helix chain 'C' and resid 63 through 83 removed outlier: 3.847A pdb=" N GLY C 68 " --> pdb=" O TYR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 104 removed outlier: 3.514A pdb=" N LYS C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 132 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 154 through 166 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 228 through 241 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 358 through 372 Processing helix chain 'C' and resid 385 through 407 removed outlier: 3.620A pdb=" N ARG C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.878A pdb=" N CYS C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.686A pdb=" N ASP C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 457 removed outlier: 4.590A pdb=" N LYS C 447 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) Proline residue: C 449 - end of helix removed outlier: 3.553A pdb=" N ALA C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 487 through 490 No H-bonds generated for 'chain 'C' and resid 487 through 490' Processing helix chain 'C' and resid 496 through 515 removed outlier: 3.502A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 28 removed outlier: 3.947A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 87 through 104 Processing helix chain 'D' and resid 111 through 132 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 232 through 241 Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.596A pdb=" N THR D 294 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 338 through 354 removed outlier: 3.696A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 372 Processing helix chain 'D' and resid 385 through 407 removed outlier: 3.544A pdb=" N ARG D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.867A pdb=" N CYS D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.961A pdb=" N ASP D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 456 removed outlier: 4.519A pdb=" N LYS D 447 " --> pdb=" O LYS D 443 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE D 448 " --> pdb=" O ARG D 444 " (cutoff:3.500A) Proline residue: D 449 - end of helix Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'D' and resid 487 through 490 No H-bonds generated for 'chain 'D' and resid 487 through 490' Processing helix chain 'D' and resid 496 through 515 removed outlier: 3.527A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.627A pdb=" N ALA E 26 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL E 27 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E 28 " --> pdb=" O VAL E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'E' and resid 63 through 82 removed outlier: 3.677A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 104 Processing helix chain 'E' and resid 111 through 132 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 154 through 166 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 228 through 241 removed outlier: 3.909A pdb=" N VAL E 232 " --> pdb=" O GLN E 229 " (cutoff:3.500A) Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.503A pdb=" N THR E 294 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 310 No H-bonds generated for 'chain 'E' and resid 308 through 310' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 338 through 354 removed outlier: 3.583A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 372 Processing helix chain 'E' and resid 385 through 407 removed outlier: 3.535A pdb=" N ARG E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 427 removed outlier: 3.780A pdb=" N CYS E 421 " --> pdb=" O ALA E 417 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Proline residue: E 423 - end of helix removed outlier: 3.775A pdb=" N ASP E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER E 427 " --> pdb=" O PRO E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 457 removed outlier: 4.656A pdb=" N LYS E 447 " --> pdb=" O LYS E 443 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) Proline residue: E 449 - end of helix Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'E' and resid 487 through 490 No H-bonds generated for 'chain 'E' and resid 487 through 490' Processing helix chain 'E' and resid 496 through 515 removed outlier: 3.608A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 28 removed outlier: 4.068A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 63 through 83 removed outlier: 3.761A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY F 68 " --> pdb=" O TYR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 111 through 132 Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'F' and resid 154 through 166 Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 228 through 241 removed outlier: 4.030A pdb=" N VAL F 232 " --> pdb=" O GLN F 229 " (cutoff:3.500A) Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 308 through 310 No H-bonds generated for 'chain 'F' and resid 308 through 310' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 338 through 353 removed outlier: 3.539A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 372 Processing helix chain 'F' and resid 385 through 407 removed outlier: 3.574A pdb=" N ARG F 394 " --> pdb=" O GLU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 427 removed outlier: 3.823A pdb=" N CYS F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Proline residue: F 423 - end of helix removed outlier: 3.551A pdb=" N ASP F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 457 removed outlier: 4.535A pdb=" N LYS F 447 " --> pdb=" O LYS F 443 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE F 448 " --> pdb=" O ARG F 444 " (cutoff:3.500A) Proline residue: F 449 - end of helix Processing helix chain 'F' and resid 461 through 469 Processing helix chain 'F' and resid 487 through 490 No H-bonds generated for 'chain 'F' and resid 487 through 490' Processing helix chain 'F' and resid 496 through 515 removed outlier: 4.142A pdb=" N THR F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 28 removed outlier: 4.019A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.522A pdb=" N SER G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 83 Processing helix chain 'G' and resid 87 through 104 removed outlier: 3.505A pdb=" N LYS G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 132 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 154 through 166 Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 228 through 241 removed outlier: 4.079A pdb=" N VAL G 232 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Proline residue: G 233 - end of helix Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.656A pdb=" N LYS G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 310 No H-bonds generated for 'chain 'G' and resid 308 through 310' Processing helix chain 'G' and resid 313 through 315 No H-bonds generated for 'chain 'G' and resid 313 through 315' Processing helix chain 'G' and resid 338 through 353 removed outlier: 3.522A pdb=" N ASP G 353 " --> pdb=" O ILE G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 372 Processing helix chain 'G' and resid 385 through 407 removed outlier: 3.508A pdb=" N ARG G 394 " --> pdb=" O GLU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.601A pdb=" N CYS G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) Proline residue: G 423 - end of helix removed outlier: 3.926A pdb=" N ASP G 426 " --> pdb=" O ILE G 422 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER G 427 " --> pdb=" O PRO G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 457 removed outlier: 4.497A pdb=" N LYS G 447 " --> pdb=" O LYS G 443 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE G 448 " --> pdb=" O ARG G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 461 through 469 Processing helix chain 'G' and resid 487 through 490 No H-bonds generated for 'chain 'G' and resid 487 through 490' Processing helix chain 'G' and resid 496 through 515 removed outlier: 3.611A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'K' and resid 93 through 95 No H-bonds generated for 'chain 'K' and resid 93 through 95' Processing helix chain 'L' and resid 93 through 95 No H-bonds generated for 'chain 'L' and resid 93 through 95' Processing helix chain 'N' and resid 93 through 95 No H-bonds generated for 'chain 'N' and resid 93 through 95' Processing sheet with id= A, first strand: chain 'A' and resid 2 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 211 through 214 Processing sheet with id= E, first strand: chain 'A' and resid 317 through 319 removed outlier: 3.532A pdb=" N VAL A 246 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= G, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.511A pdb=" N ASP A 483 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 6 Processing sheet with id= I, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= J, first strand: chain 'B' and resid 172 through 177 Processing sheet with id= K, first strand: chain 'B' and resid 211 through 214 Processing sheet with id= L, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.563A pdb=" N ALA B 249 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 410 through 412 Processing sheet with id= N, first strand: chain 'B' and resid 475 through 478 Processing sheet with id= O, first strand: chain 'C' and resid 2 through 6 Processing sheet with id= P, first strand: chain 'C' and resid 36 through 38 Processing sheet with id= Q, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= R, first strand: chain 'C' and resid 211 through 214 Processing sheet with id= S, first strand: chain 'C' and resid 317 through 319 removed outlier: 3.520A pdb=" N ALA C 249 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 410 through 412 Processing sheet with id= U, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.744A pdb=" N ASP C 483 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 2 through 6 Processing sheet with id= W, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= X, first strand: chain 'D' and resid 172 through 177 Processing sheet with id= Y, first strand: chain 'D' and resid 211 through 214 removed outlier: 3.857A pdb=" N VAL D 322 " --> pdb=" O PHE D 213 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= AA, first strand: chain 'D' and resid 410 through 412 Processing sheet with id= AB, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.577A pdb=" N ASP D 483 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= AD, first strand: chain 'E' and resid 36 through 38 Processing sheet with id= AE, first strand: chain 'E' and resid 172 through 177 Processing sheet with id= AF, first strand: chain 'E' and resid 211 through 214 Processing sheet with id= AG, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= AH, first strand: chain 'E' and resid 410 through 412 Processing sheet with id= AI, first strand: chain 'E' and resid 475 through 478 Processing sheet with id= AJ, first strand: chain 'F' and resid 2 through 6 Processing sheet with id= AK, first strand: chain 'F' and resid 36 through 38 Processing sheet with id= AL, first strand: chain 'F' and resid 172 through 177 removed outlier: 3.519A pdb=" N VAL F 380 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 211 through 214 Processing sheet with id= AN, first strand: chain 'F' and resid 317 through 319 removed outlier: 3.584A pdb=" N ALA F 249 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 410 through 412 Processing sheet with id= AP, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.537A pdb=" N ASP F 483 " --> pdb=" O ASP F 478 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= AR, first strand: chain 'G' and resid 36 through 38 Processing sheet with id= AS, first strand: chain 'G' and resid 172 through 177 Processing sheet with id= AT, first strand: chain 'G' and resid 211 through 214 Processing sheet with id= AU, first strand: chain 'G' and resid 317 through 319 Processing sheet with id= AV, first strand: chain 'G' and resid 410 through 412 Processing sheet with id= AW, first strand: chain 'G' and resid 475 through 478 removed outlier: 3.534A pdb=" N ASP G 483 " --> pdb=" O ASP G 478 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 79 through 83 removed outlier: 8.600A pdb=" N ASP H 87 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG H 20 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU H 19 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL H 46 " --> pdb=" O GLU H 19 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS H 70 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY H 98 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 79 through 83 removed outlier: 8.888A pdb=" N ASP I 87 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG I 20 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU I 19 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL I 46 " --> pdb=" O GLU I 19 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'J' and resid 79 through 83 removed outlier: 8.245A pdb=" N ASP J 87 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG J 20 " --> pdb=" O ASP J 87 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU J 19 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL J 46 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS J 70 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY J 98 " --> pdb=" O LEU J 72 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 79 through 83 removed outlier: 8.803A pdb=" N ASP K 87 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG K 20 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU K 19 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL K 46 " --> pdb=" O GLU K 19 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA K 44 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'L' and resid 79 through 83 removed outlier: 8.532A pdb=" N ASP L 87 " --> pdb=" O ARG L 20 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG L 20 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA L 48 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU L 19 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL L 46 " --> pdb=" O GLU L 19 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 79 through 83 removed outlier: 8.749A pdb=" N ASP M 87 " --> pdb=" O ARG M 20 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG M 20 " --> pdb=" O ASP M 87 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU M 19 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL M 46 " --> pdb=" O GLU M 19 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA M 44 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS M 70 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY M 98 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 79 through 83 removed outlier: 8.461A pdb=" N ASP N 87 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG N 20 " --> pdb=" O ASP N 87 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU N 19 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL N 46 " --> pdb=" O GLU N 19 " (cutoff:3.500A) 1672 hydrogen bonds defined for protein. 4563 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: 11.73 Time building geometry restraints manager: 14.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8842 1.33 - 1.45: 4234 1.45 - 1.57: 20063 1.57 - 1.69: 34 1.69 - 1.81: 189 Bond restraints: 33362 Sorted by residual: bond pdb=" ND1 HIS G 241 " pdb=" CE1 HIS G 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.76e+01 bond pdb=" ND1 HIS B 241 " pdb=" CE1 HIS B 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 bond pdb=" ND1 HIS A 241 " pdb=" CE1 HIS A 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.74e+01 bond pdb=" ND1 HIS D 241 " pdb=" CE1 HIS D 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.71e+01 bond pdb=" CG ASN C 80 " pdb=" OD1 ASN C 80 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.44e+01 ... (remaining 33357 not shown) Histogram of bond angle deviations from ideal: 96.27 - 104.98: 467 104.98 - 113.69: 19872 113.69 - 122.41: 20416 122.41 - 131.12: 4237 131.12 - 139.83: 39 Bond angle restraints: 45031 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 124.28 15.59 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 122.60 14.23 1.00e+00 1.00e+00 2.02e+02 angle pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " pdb=" O3G ATP F 601 " ideal model delta sigma weight residual 104.48 113.76 -9.28 1.14e+00 7.76e-01 6.69e+01 angle pdb=" CB HIS D 241 " pdb=" CG HIS D 241 " pdb=" CD2 HIS D 241 " ideal model delta sigma weight residual 131.20 122.60 8.60 1.30e+00 5.92e-01 4.37e+01 angle pdb=" CB HIS G 241 " pdb=" CG HIS G 241 " pdb=" CD2 HIS G 241 " ideal model delta sigma weight residual 131.20 122.61 8.59 1.30e+00 5.92e-01 4.37e+01 ... (remaining 45026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 18987 17.90 - 35.80: 1413 35.80 - 53.70: 256 53.70 - 71.61: 91 71.61 - 89.51: 43 Dihedral angle restraints: 20790 sinusoidal: 8414 harmonic: 12376 Sorted by residual: dihedral pdb=" CA THR F 28 " pdb=" C THR F 28 " pdb=" N MET F 29 " pdb=" CA MET F 29 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP B 337 " pdb=" CB ASP B 337 " pdb=" CG ASP B 337 " pdb=" OD1 ASP B 337 " ideal model delta sinusoidal sigma weight residual -30.00 -88.68 58.68 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA GLY A 7 " pdb=" C GLY A 7 " pdb=" N ALA A 8 " pdb=" CA ALA A 8 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 20787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4694 0.063 - 0.126: 682 0.126 - 0.188: 27 0.188 - 0.251: 2 0.251 - 0.314: 20 Chirality restraints: 5425 Sorted by residual: chirality pdb=" C4' ATP F 601 " pdb=" C3' ATP F 601 " pdb=" C5' ATP F 601 " pdb=" O4' ATP F 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' ATP G 601 " pdb=" C1' ATP G 601 " pdb=" C3' ATP G 601 " pdb=" O2' ATP G 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 5422 not shown) Planarity restraints: 5768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP F 601 " 0.005 2.00e-02 2.50e+03 1.87e-02 9.59e+00 pdb=" C2 ATP F 601 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ATP F 601 " -0.013 2.00e-02 2.50e+03 pdb=" C5 ATP F 601 " -0.033 2.00e-02 2.50e+03 pdb=" C6 ATP F 601 " -0.017 2.00e-02 2.50e+03 pdb=" C8 ATP F 601 " 0.016 2.00e-02 2.50e+03 pdb=" N1 ATP F 601 " 0.001 2.00e-02 2.50e+03 pdb=" N3 ATP F 601 " 0.012 2.00e-02 2.50e+03 pdb=" N6 ATP F 601 " 0.036 2.00e-02 2.50e+03 pdb=" N7 ATP F 601 " -0.017 2.00e-02 2.50e+03 pdb=" N9 ATP F 601 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 96 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C SER F 96 " -0.037 2.00e-02 2.50e+03 pdb=" O SER F 96 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE F 97 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 243 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 244 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 244 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 244 " 0.028 5.00e-02 4.00e+02 ... (remaining 5765 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 616 2.69 - 3.24: 32865 3.24 - 3.79: 48166 3.79 - 4.35: 63717 4.35 - 4.90: 109233 Nonbonded interactions: 254597 Sorted by model distance: nonbonded pdb=" OD1 ASP E 253 " pdb=" N GLY E 254 " model vdw 2.133 2.520 nonbonded pdb=" NH2 ARG A 115 " pdb=" OE1 GLU B 387 " model vdw 2.197 2.520 nonbonded pdb=" OD1 ASP G 177 " pdb=" NZ LYS G 392 " model vdw 2.199 2.520 nonbonded pdb=" OE1 GLU A 387 " pdb=" NH2 ARG G 115 " model vdw 2.221 2.520 nonbonded pdb=" OG SER A 44 " pdb=" OD2 ASP G 74 " model vdw 2.222 2.440 ... (remaining 254592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 20.570 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 87.860 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.003 0.099 33362 Z= 0.201 Angle : 0.572 15.589 45031 Z= 0.350 Chirality : 0.045 0.314 5425 Planarity : 0.003 0.057 5768 Dihedral : 14.091 89.506 12852 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 4361 helix: 2.62 (0.12), residues: 1995 sheet: 0.92 (0.21), residues: 553 loop : -0.51 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 42 HIS 0.003 0.001 HIS A 241 PHE 0.006 0.001 PHE F 279 TYR 0.012 0.001 TYR A 64 ARG 0.012 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8214 (t0) cc_final: 0.7871 (m-30) REVERT: A 215 ASP cc_start: 0.8289 (t0) cc_final: 0.8059 (t0) REVERT: A 257 LEU cc_start: 0.8887 (tt) cc_final: 0.8629 (mt) REVERT: A 290 MET cc_start: 0.8715 (mtm) cc_final: 0.8379 (mtt) REVERT: A 309 GLU cc_start: 0.7789 (tt0) cc_final: 0.7390 (tp30) REVERT: B 281 ASP cc_start: 0.8457 (t70) cc_final: 0.8158 (t0) REVERT: C 487 MET cc_start: 0.9124 (mmm) cc_final: 0.8902 (mmp) REVERT: D 241 HIS cc_start: 0.8369 (m90) cc_final: 0.8006 (m170) REVERT: D 321 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6293 (mm-30) REVERT: D 326 LYS cc_start: 0.8991 (tppt) cc_final: 0.8708 (tppt) REVERT: D 330 MET cc_start: 0.8270 (ttm) cc_final: 0.7982 (ttm) REVERT: D 358 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7635 (pm20) REVERT: E 191 MET cc_start: 0.8503 (mtp) cc_final: 0.8264 (mtp) REVERT: E 223 LYS cc_start: 0.8988 (pttt) cc_final: 0.8476 (mmtp) REVERT: G 218 VAL cc_start: 0.9188 (t) cc_final: 0.8817 (p) REVERT: G 330 MET cc_start: 0.7459 (ttm) cc_final: 0.7134 (ttm) REVERT: H 4 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8367 (mm-40) REVERT: H 61 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7329 (tm-30) REVERT: H 95 ASP cc_start: 0.8928 (m-30) cc_final: 0.8671 (m-30) REVERT: J 84 ASP cc_start: 0.6780 (m-30) cc_final: 0.6488 (m-30) REVERT: J 93 ASP cc_start: 0.8823 (t0) cc_final: 0.8596 (t0) REVERT: K 15 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7654 (mtt90) REVERT: L 4 GLN cc_start: 0.8261 (tp40) cc_final: 0.7626 (mp10) REVERT: L 95 ASP cc_start: 0.9199 (m-30) cc_final: 0.8982 (m-30) REVERT: M 32 MET cc_start: 0.7933 (mmt) cc_final: 0.7569 (mmm) REVERT: M 43 GLN cc_start: 0.8083 (mp10) cc_final: 0.7682 (mp10) REVERT: N 51 SER cc_start: 0.9239 (m) cc_final: 0.9015 (p) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.4444 time to fit residues: 305.1776 Evaluate side-chains 331 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 8.9990 chunk 328 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 394 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 ASN D 314 HIS I 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33362 Z= 0.226 Angle : 0.499 7.903 45031 Z= 0.267 Chirality : 0.043 0.219 5425 Planarity : 0.004 0.046 5768 Dihedral : 8.413 87.668 4837 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.70 % Allowed : 5.35 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.13), residues: 4361 helix: 2.45 (0.11), residues: 1995 sheet: 0.92 (0.21), residues: 553 loop : -0.49 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 42 HIS 0.007 0.001 HIS D 314 PHE 0.010 0.001 PHE N 6 TYR 0.012 0.001 TYR A 64 ARG 0.008 0.000 ARG J 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 358 time to evaluate : 3.616 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8323 (t0) cc_final: 0.7943 (m-30) REVERT: A 215 ASP cc_start: 0.8217 (t0) cc_final: 0.7986 (t0) REVERT: A 290 MET cc_start: 0.8622 (mtm) cc_final: 0.8338 (mtt) REVERT: A 321 GLU cc_start: 0.7703 (tp30) cc_final: 0.7395 (tp30) REVERT: B 290 MET cc_start: 0.8262 (mtm) cc_final: 0.7854 (mtm) REVERT: C 251 ASP cc_start: 0.8492 (t0) cc_final: 0.8204 (t0) REVERT: D 221 SER cc_start: 0.8794 (m) cc_final: 0.8230 (p) REVERT: D 330 MET cc_start: 0.8359 (ttm) cc_final: 0.8068 (ttm) REVERT: D 358 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7634 (pm20) REVERT: E 223 LYS cc_start: 0.8902 (pttt) cc_final: 0.8444 (mmtp) REVERT: E 330 MET cc_start: 0.8627 (mtp) cc_final: 0.8375 (mmm) REVERT: G 218 VAL cc_start: 0.9229 (t) cc_final: 0.8831 (p) REVERT: G 330 MET cc_start: 0.7451 (ttm) cc_final: 0.7063 (ttm) REVERT: H 95 ASP cc_start: 0.8935 (m-30) cc_final: 0.8650 (m-30) REVERT: K 7 ARG cc_start: 0.8291 (tpp80) cc_final: 0.8021 (tpp80) REVERT: K 15 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7597 (mtt90) REVERT: L 4 GLN cc_start: 0.8321 (tp40) cc_final: 0.7646 (mp10) REVERT: L 32 MET cc_start: 0.8179 (ppp) cc_final: 0.7944 (ppp) REVERT: L 51 SER cc_start: 0.8646 (t) cc_final: 0.8416 (m) REVERT: L 95 ASP cc_start: 0.9171 (m-30) cc_final: 0.8950 (m-30) REVERT: M 32 MET cc_start: 0.8028 (mmt) cc_final: 0.7568 (mmm) outliers start: 25 outliers final: 14 residues processed: 372 average time/residue: 0.4261 time to fit residues: 261.7432 Evaluate side-chains 323 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 309 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 394 optimal weight: 9.9990 chunk 426 optimal weight: 20.0000 chunk 351 optimal weight: 0.9990 chunk 391 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS D 314 HIS ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 282 ASN I 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33362 Z= 0.218 Angle : 0.477 8.083 45031 Z= 0.254 Chirality : 0.042 0.156 5425 Planarity : 0.003 0.042 5768 Dihedral : 7.804 79.512 4837 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.18 % Allowed : 7.24 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.13), residues: 4361 helix: 2.30 (0.12), residues: 2009 sheet: 1.03 (0.22), residues: 532 loop : -0.50 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 42 HIS 0.005 0.001 HIS D 314 PHE 0.012 0.001 PHE D 279 TYR 0.010 0.001 TYR A 64 ARG 0.005 0.000 ARG N 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 4.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8342 (t0) cc_final: 0.7924 (m-30) REVERT: A 215 ASP cc_start: 0.8154 (t0) cc_final: 0.7858 (t0) REVERT: A 290 MET cc_start: 0.8638 (mtm) cc_final: 0.8385 (mtm) REVERT: B 290 MET cc_start: 0.8215 (mtm) cc_final: 0.7768 (mtm) REVERT: C 251 ASP cc_start: 0.8445 (t0) cc_final: 0.8167 (t0) REVERT: C 330 MET cc_start: 0.8294 (ttm) cc_final: 0.7906 (ttm) REVERT: D 221 SER cc_start: 0.8692 (m) cc_final: 0.8137 (p) REVERT: D 330 MET cc_start: 0.8356 (ttm) cc_final: 0.8055 (ttm) REVERT: E 223 LYS cc_start: 0.8856 (pttt) cc_final: 0.8401 (mmtp) REVERT: E 282 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8105 (t0) REVERT: E 360 GLU cc_start: 0.8190 (tp30) cc_final: 0.7762 (tp30) REVERT: G 218 VAL cc_start: 0.9143 (t) cc_final: 0.8836 (p) REVERT: G 330 MET cc_start: 0.7453 (ttm) cc_final: 0.7048 (ttm) REVERT: H 35 GLU cc_start: 0.7488 (tp30) cc_final: 0.7249 (tp30) REVERT: H 95 ASP cc_start: 0.8923 (m-30) cc_final: 0.8610 (m-30) REVERT: K 7 ARG cc_start: 0.8313 (tpp80) cc_final: 0.7999 (tpp80) REVERT: L 4 GLN cc_start: 0.8300 (tp40) cc_final: 0.7619 (mp10) REVERT: L 51 SER cc_start: 0.8667 (t) cc_final: 0.8421 (m) REVERT: L 95 ASP cc_start: 0.9210 (m-30) cc_final: 0.8950 (m-30) REVERT: M 87 ASP cc_start: 0.8185 (p0) cc_final: 0.7912 (m-30) outliers start: 42 outliers final: 20 residues processed: 343 average time/residue: 0.4141 time to fit residues: 236.5961 Evaluate side-chains 329 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 308 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 188 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 396 optimal weight: 0.8980 chunk 419 optimal weight: 0.0970 chunk 207 optimal weight: 0.9980 chunk 375 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33362 Z= 0.128 Angle : 0.435 7.055 45031 Z= 0.233 Chirality : 0.041 0.185 5425 Planarity : 0.003 0.041 5768 Dihedral : 6.739 66.441 4837 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 8.06 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.13), residues: 4361 helix: 2.41 (0.12), residues: 2009 sheet: 0.97 (0.22), residues: 546 loop : -0.57 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 42 HIS 0.001 0.001 HIS D 314 PHE 0.010 0.001 PHE F 193 TYR 0.008 0.001 TYR A 64 ARG 0.003 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 335 time to evaluate : 3.805 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8303 (t0) cc_final: 0.7835 (m-30) REVERT: A 215 ASP cc_start: 0.8143 (t0) cc_final: 0.7832 (t0) REVERT: A 290 MET cc_start: 0.8593 (mtm) cc_final: 0.8337 (mtm) REVERT: A 312 GLN cc_start: 0.8206 (mm110) cc_final: 0.7887 (mm110) REVERT: B 294 THR cc_start: 0.8754 (p) cc_final: 0.8298 (t) REVERT: B 326 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8601 (tppt) REVERT: B 390 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 251 ASP cc_start: 0.8431 (t0) cc_final: 0.8103 (t0) REVERT: C 330 MET cc_start: 0.8263 (ttm) cc_final: 0.7892 (ttm) REVERT: D 321 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6189 (mm-30) REVERT: D 330 MET cc_start: 0.8323 (ttm) cc_final: 0.8009 (ttm) REVERT: D 358 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7622 (pm20) REVERT: E 360 GLU cc_start: 0.8188 (tp30) cc_final: 0.7741 (tp30) REVERT: G 218 VAL cc_start: 0.9129 (t) cc_final: 0.8802 (p) REVERT: G 330 MET cc_start: 0.7393 (ttm) cc_final: 0.6986 (ttm) REVERT: H 35 GLU cc_start: 0.7663 (tp30) cc_final: 0.7403 (tp30) REVERT: H 95 ASP cc_start: 0.8908 (m-30) cc_final: 0.8578 (m-30) REVERT: K 7 ARG cc_start: 0.8291 (tpp80) cc_final: 0.8017 (tpp80) REVERT: L 4 GLN cc_start: 0.8353 (tp40) cc_final: 0.7573 (mp10) REVERT: L 51 SER cc_start: 0.8651 (t) cc_final: 0.8424 (m) REVERT: L 95 ASP cc_start: 0.9180 (m-30) cc_final: 0.8929 (m-30) REVERT: M 43 GLN cc_start: 0.8176 (mp10) cc_final: 0.7960 (mp10) REVERT: M 69 ASP cc_start: 0.8810 (m-30) cc_final: 0.8596 (m-30) REVERT: M 87 ASP cc_start: 0.8116 (p0) cc_final: 0.7811 (m-30) REVERT: N 92 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7641 (mmm160) outliers start: 39 outliers final: 22 residues processed: 355 average time/residue: 0.4335 time to fit residues: 256.2071 Evaluate side-chains 327 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 305 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 357 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 376 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN C 80 ASN D 80 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33362 Z= 0.229 Angle : 0.470 8.232 45031 Z= 0.251 Chirality : 0.042 0.243 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.499 69.382 4837 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.38 % Allowed : 8.96 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4361 helix: 2.28 (0.12), residues: 2009 sheet: 0.79 (0.22), residues: 567 loop : -0.56 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.002 0.001 HIS E 241 PHE 0.013 0.001 PHE D 279 TYR 0.010 0.001 TYR A 64 ARG 0.003 0.000 ARG H 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 305 time to evaluate : 3.799 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8354 (t0) cc_final: 0.7876 (m-30) REVERT: A 215 ASP cc_start: 0.8185 (t0) cc_final: 0.7863 (t0) REVERT: A 290 MET cc_start: 0.8648 (mtm) cc_final: 0.8406 (mtm) REVERT: A 312 GLN cc_start: 0.8209 (mm110) cc_final: 0.7853 (mm110) REVERT: B 326 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8610 (tppt) REVERT: C 330 MET cc_start: 0.8286 (ttm) cc_final: 0.7901 (ttm) REVERT: D 330 MET cc_start: 0.8280 (ttm) cc_final: 0.7954 (ttm) REVERT: E 218 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8884 (p) REVERT: E 330 MET cc_start: 0.8298 (mmm) cc_final: 0.8087 (tpp) REVERT: E 360 GLU cc_start: 0.8214 (tp30) cc_final: 0.7884 (tp30) REVERT: F 191 MET cc_start: 0.8284 (ptp) cc_final: 0.8003 (mtm) REVERT: G 218 VAL cc_start: 0.9176 (t) cc_final: 0.8850 (p) REVERT: G 330 MET cc_start: 0.7369 (ttm) cc_final: 0.6989 (ttm) REVERT: H 35 GLU cc_start: 0.7749 (tp30) cc_final: 0.7465 (tp30) REVERT: H 95 ASP cc_start: 0.8876 (m-30) cc_final: 0.8571 (m-30) REVERT: K 4 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8163 (tp-100) REVERT: K 7 ARG cc_start: 0.8365 (tpp80) cc_final: 0.8070 (tpp80) REVERT: L 4 GLN cc_start: 0.8376 (tp40) cc_final: 0.7583 (mp10) REVERT: L 32 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7799 (ppp) REVERT: L 95 ASP cc_start: 0.9196 (m-30) cc_final: 0.8923 (m-30) REVERT: M 69 ASP cc_start: 0.8830 (m-30) cc_final: 0.8605 (m-30) REVERT: M 87 ASP cc_start: 0.8149 (p0) cc_final: 0.7873 (m-30) outliers start: 49 outliers final: 30 residues processed: 335 average time/residue: 0.4039 time to fit residues: 225.4771 Evaluate side-chains 329 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 297 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 32 MET Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 246 optimal weight: 0.0980 chunk 103 optimal weight: 0.0670 chunk 419 optimal weight: 0.4980 chunk 348 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN H 4 GLN K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33362 Z= 0.130 Angle : 0.430 8.691 45031 Z= 0.229 Chirality : 0.041 0.180 5425 Planarity : 0.003 0.038 5768 Dihedral : 5.855 65.316 4837 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.10 % Allowed : 9.55 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.13), residues: 4361 helix: 2.38 (0.12), residues: 2009 sheet: 0.87 (0.22), residues: 567 loop : -0.57 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 42 HIS 0.001 0.000 HIS B 314 PHE 0.012 0.001 PHE F 193 TYR 0.008 0.001 TYR A 197 ARG 0.003 0.000 ARG N 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 326 time to evaluate : 3.643 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8304 (t0) cc_final: 0.7842 (m-30) REVERT: A 215 ASP cc_start: 0.8093 (t0) cc_final: 0.7786 (t0) REVERT: A 290 MET cc_start: 0.8593 (mtm) cc_final: 0.8323 (mtm) REVERT: A 312 GLN cc_start: 0.8140 (mm110) cc_final: 0.7747 (mm110) REVERT: B 222 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7726 (tm-30) REVERT: B 262 LEU cc_start: 0.8657 (tt) cc_final: 0.8101 (mt) REVERT: B 294 THR cc_start: 0.8710 (p) cc_final: 0.8225 (t) REVERT: B 326 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8631 (tppt) REVERT: B 390 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 330 MET cc_start: 0.8251 (ttm) cc_final: 0.7880 (ttm) REVERT: D 330 MET cc_start: 0.8272 (ttm) cc_final: 0.7947 (ttm) REVERT: D 358 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7616 (pm20) REVERT: E 218 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8832 (p) REVERT: E 360 GLU cc_start: 0.8123 (tp30) cc_final: 0.7714 (tp30) REVERT: G 218 VAL cc_start: 0.9107 (t) cc_final: 0.8799 (p) REVERT: G 330 MET cc_start: 0.7335 (ttm) cc_final: 0.6946 (ttm) REVERT: H 35 GLU cc_start: 0.7744 (tp30) cc_final: 0.7436 (tp30) REVERT: H 95 ASP cc_start: 0.8838 (m-30) cc_final: 0.8551 (m-30) REVERT: K 4 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8177 (tp-100) REVERT: K 7 ARG cc_start: 0.8326 (tpp80) cc_final: 0.8093 (tpp80) REVERT: K 59 GLU cc_start: 0.6967 (tp30) cc_final: 0.6552 (tp30) REVERT: L 4 GLN cc_start: 0.8388 (tp40) cc_final: 0.7599 (mp10) REVERT: L 32 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7750 (ppp) REVERT: L 51 SER cc_start: 0.8708 (t) cc_final: 0.8483 (m) REVERT: L 95 ASP cc_start: 0.9157 (m-30) cc_final: 0.8897 (m-30) REVERT: M 87 ASP cc_start: 0.8094 (p0) cc_final: 0.7840 (m-30) REVERT: N 92 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7622 (mmm160) outliers start: 39 outliers final: 26 residues processed: 348 average time/residue: 0.4128 time to fit residues: 238.5917 Evaluate side-chains 335 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 32 MET Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 418 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 255 optimal weight: 0.0270 chunk 193 optimal weight: 10.0000 overall best weight: 0.5852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN H 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33362 Z= 0.122 Angle : 0.432 8.199 45031 Z= 0.228 Chirality : 0.041 0.175 5425 Planarity : 0.003 0.038 5768 Dihedral : 5.564 64.062 4837 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.24 % Allowed : 9.72 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.13), residues: 4361 helix: 2.43 (0.12), residues: 2002 sheet: 0.94 (0.22), residues: 567 loop : -0.57 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 42 HIS 0.001 0.000 HIS E 241 PHE 0.012 0.001 PHE F 193 TYR 0.008 0.001 TYR A 64 ARG 0.004 0.000 ARG L 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 322 time to evaluate : 3.759 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8250 (t0) cc_final: 0.7797 (m-30) REVERT: A 215 ASP cc_start: 0.8097 (t0) cc_final: 0.7779 (t0) REVERT: A 290 MET cc_start: 0.8552 (mtm) cc_final: 0.8294 (mtm) REVERT: A 312 GLN cc_start: 0.8136 (mm110) cc_final: 0.7729 (mm110) REVERT: A 488 VAL cc_start: 0.9076 (t) cc_final: 0.8820 (m) REVERT: B 222 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 262 LEU cc_start: 0.8649 (tt) cc_final: 0.8091 (mt) REVERT: B 294 THR cc_start: 0.8664 (p) cc_final: 0.8185 (t) REVERT: B 326 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8617 (tppt) REVERT: B 390 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7662 (tm-30) REVERT: C 330 MET cc_start: 0.8296 (ttm) cc_final: 0.7945 (ttm) REVERT: D 330 MET cc_start: 0.8240 (ttm) cc_final: 0.7912 (ttm) REVERT: E 218 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8817 (p) REVERT: E 360 GLU cc_start: 0.8105 (tp30) cc_final: 0.7677 (tp30) REVERT: G 218 VAL cc_start: 0.9057 (t) cc_final: 0.8755 (p) REVERT: G 290 MET cc_start: 0.8352 (mtt) cc_final: 0.8032 (mtt) REVERT: G 330 MET cc_start: 0.7348 (ttm) cc_final: 0.6975 (ttm) REVERT: H 35 GLU cc_start: 0.7754 (tp30) cc_final: 0.7458 (tp30) REVERT: H 95 ASP cc_start: 0.8833 (m-30) cc_final: 0.8528 (m-30) REVERT: I 19 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7778 (mm-30) REVERT: K 7 ARG cc_start: 0.8335 (tpp80) cc_final: 0.8111 (tpp80) REVERT: L 4 GLN cc_start: 0.8391 (tp40) cc_final: 0.7602 (mp10) REVERT: L 32 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7699 (ppp) REVERT: L 51 SER cc_start: 0.8733 (t) cc_final: 0.8505 (m) REVERT: L 73 LEU cc_start: 0.8920 (mm) cc_final: 0.8538 (mt) REVERT: L 95 ASP cc_start: 0.9152 (m-30) cc_final: 0.8913 (m-30) REVERT: M 87 ASP cc_start: 0.8091 (p0) cc_final: 0.7848 (m-30) REVERT: N 92 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7584 (mmm160) outliers start: 44 outliers final: 31 residues processed: 348 average time/residue: 0.4066 time to fit residues: 236.0133 Evaluate side-chains 341 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 249 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 328 optimal weight: 0.0040 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33362 Z= 0.163 Angle : 0.448 8.615 45031 Z= 0.235 Chirality : 0.041 0.178 5425 Planarity : 0.003 0.035 5768 Dihedral : 5.554 64.193 4837 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 10.20 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.13), residues: 4361 helix: 2.41 (0.12), residues: 2002 sheet: 0.93 (0.22), residues: 567 loop : -0.57 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 42 HIS 0.001 0.000 HIS E 241 PHE 0.010 0.001 PHE C 213 TYR 0.010 0.001 TYR A 64 ARG 0.004 0.000 ARG L 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 317 time to evaluate : 3.916 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8294 (t0) cc_final: 0.7830 (m-30) REVERT: A 215 ASP cc_start: 0.8136 (t0) cc_final: 0.7816 (t0) REVERT: A 290 MET cc_start: 0.8572 (mtm) cc_final: 0.8312 (mtm) REVERT: A 488 VAL cc_start: 0.9089 (t) cc_final: 0.8834 (m) REVERT: B 222 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 262 LEU cc_start: 0.8614 (tt) cc_final: 0.8087 (mt) REVERT: B 294 THR cc_start: 0.8674 (p) cc_final: 0.8193 (t) REVERT: B 326 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8659 (tppt) REVERT: B 390 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 330 MET cc_start: 0.8294 (ttm) cc_final: 0.7930 (ttm) REVERT: D 330 MET cc_start: 0.8241 (ttm) cc_final: 0.7938 (ttm) REVERT: E 218 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8840 (p) REVERT: E 360 GLU cc_start: 0.8108 (tp30) cc_final: 0.7688 (tp30) REVERT: G 218 VAL cc_start: 0.9065 (t) cc_final: 0.8765 (p) REVERT: G 330 MET cc_start: 0.7299 (ttm) cc_final: 0.6923 (ttm) REVERT: H 95 ASP cc_start: 0.8828 (m-30) cc_final: 0.8549 (m-30) REVERT: K 4 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8329 (tp-100) REVERT: K 7 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8148 (tpp80) REVERT: L 4 GLN cc_start: 0.8416 (tp40) cc_final: 0.7604 (mp10) REVERT: L 32 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7721 (ppp) REVERT: L 73 LEU cc_start: 0.8913 (mm) cc_final: 0.8530 (mt) REVERT: L 95 ASP cc_start: 0.9151 (m-30) cc_final: 0.8909 (m-30) REVERT: M 87 ASP cc_start: 0.8116 (p0) cc_final: 0.7891 (m-30) REVERT: N 92 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7614 (mmm160) outliers start: 39 outliers final: 33 residues processed: 343 average time/residue: 0.3990 time to fit residues: 228.1641 Evaluate side-chains 340 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 305 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 0.3980 chunk 400 optimal weight: 0.2980 chunk 365 optimal weight: 1.9990 chunk 389 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 169 optimal weight: 0.0000 chunk 306 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 352 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33362 Z= 0.117 Angle : 0.436 8.684 45031 Z= 0.228 Chirality : 0.041 0.182 5425 Planarity : 0.003 0.036 5768 Dihedral : 5.273 64.207 4837 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.04 % Allowed : 10.37 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.13), residues: 4361 helix: 2.46 (0.12), residues: 2002 sheet: 0.97 (0.22), residues: 567 loop : -0.53 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 42 HIS 0.001 0.000 HIS B 314 PHE 0.010 0.001 PHE B 279 TYR 0.007 0.001 TYR A 64 ARG 0.004 0.000 ARG L 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 333 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8185 (t0) cc_final: 0.7748 (m-30) REVERT: A 215 ASP cc_start: 0.8087 (t0) cc_final: 0.7760 (t0) REVERT: A 290 MET cc_start: 0.8547 (mtm) cc_final: 0.8282 (mtm) REVERT: A 312 GLN cc_start: 0.8154 (mm110) cc_final: 0.7838 (mm110) REVERT: A 488 VAL cc_start: 0.8952 (t) cc_final: 0.8705 (m) REVERT: B 222 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 262 LEU cc_start: 0.8592 (tt) cc_final: 0.8050 (mt) REVERT: B 294 THR cc_start: 0.8579 (p) cc_final: 0.8103 (t) REVERT: B 390 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 330 MET cc_start: 0.8293 (ttm) cc_final: 0.7946 (ttm) REVERT: D 330 MET cc_start: 0.8231 (ttm) cc_final: 0.7947 (ttm) REVERT: E 218 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8788 (p) REVERT: E 330 MET cc_start: 0.8080 (mmt) cc_final: 0.7746 (mmt) REVERT: E 360 GLU cc_start: 0.8065 (tp30) cc_final: 0.7642 (tp30) REVERT: G 218 VAL cc_start: 0.9054 (t) cc_final: 0.8754 (p) REVERT: G 290 MET cc_start: 0.8330 (mtt) cc_final: 0.7981 (mtt) REVERT: G 330 MET cc_start: 0.7301 (ttm) cc_final: 0.6949 (ttm) REVERT: H 95 ASP cc_start: 0.8818 (m-30) cc_final: 0.8533 (m-30) REVERT: I 61 GLN cc_start: 0.8768 (mp10) cc_final: 0.8517 (mp10) REVERT: J 19 GLU cc_start: 0.7967 (tt0) cc_final: 0.7764 (tt0) REVERT: K 4 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8304 (tp-100) REVERT: K 7 ARG cc_start: 0.8341 (tpp80) cc_final: 0.8125 (tpp80) REVERT: L 4 GLN cc_start: 0.8415 (tp40) cc_final: 0.7652 (mp10) REVERT: L 32 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7664 (ppp) REVERT: L 51 SER cc_start: 0.8801 (t) cc_final: 0.8567 (m) REVERT: L 73 LEU cc_start: 0.8870 (mm) cc_final: 0.8468 (mt) REVERT: N 92 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7553 (mmm160) outliers start: 37 outliers final: 28 residues processed: 357 average time/residue: 0.4021 time to fit residues: 239.3324 Evaluate side-chains 342 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 312 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 1.9990 chunk 412 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 432 optimal weight: 5.9990 chunk 397 optimal weight: 0.0270 chunk 344 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33362 Z= 0.158 Angle : 0.451 9.450 45031 Z= 0.236 Chirality : 0.041 0.181 5425 Planarity : 0.003 0.036 5768 Dihedral : 5.326 65.006 4837 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.99 % Allowed : 10.54 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.13), residues: 4361 helix: 2.44 (0.12), residues: 2002 sheet: 0.95 (0.22), residues: 567 loop : -0.53 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 42 HIS 0.001 0.000 HIS G 241 PHE 0.010 0.001 PHE A 279 TYR 0.009 0.001 TYR A 64 ARG 0.004 0.000 ARG L 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 316 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8220 (t0) cc_final: 0.7775 (m-30) REVERT: A 215 ASP cc_start: 0.8128 (t0) cc_final: 0.7805 (t0) REVERT: A 290 MET cc_start: 0.8566 (mtm) cc_final: 0.8297 (mtm) REVERT: B 262 LEU cc_start: 0.8607 (tt) cc_final: 0.8060 (mt) REVERT: B 294 THR cc_start: 0.8616 (p) cc_final: 0.8137 (t) REVERT: B 390 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 330 MET cc_start: 0.8313 (ttm) cc_final: 0.7955 (ttm) REVERT: D 330 MET cc_start: 0.8235 (ttm) cc_final: 0.7954 (ttm) REVERT: E 218 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8832 (p) REVERT: E 360 GLU cc_start: 0.8050 (tp30) cc_final: 0.7617 (tp30) REVERT: G 218 VAL cc_start: 0.9071 (t) cc_final: 0.8766 (p) REVERT: G 290 MET cc_start: 0.8380 (mtt) cc_final: 0.8001 (mtt) REVERT: G 330 MET cc_start: 0.7348 (ttm) cc_final: 0.7000 (ttm) REVERT: H 95 ASP cc_start: 0.8817 (m-30) cc_final: 0.8544 (m-30) REVERT: I 61 GLN cc_start: 0.8769 (mp10) cc_final: 0.8528 (mp10) REVERT: K 4 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8274 (tp-100) REVERT: K 7 ARG cc_start: 0.8407 (tpp80) cc_final: 0.8143 (tpp80) REVERT: L 4 GLN cc_start: 0.8426 (tp40) cc_final: 0.7649 (mp10) REVERT: L 32 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7676 (ppp) REVERT: L 73 LEU cc_start: 0.8892 (mm) cc_final: 0.8490 (mt) REVERT: N 92 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7613 (mmm160) outliers start: 35 outliers final: 31 residues processed: 339 average time/residue: 0.4199 time to fit residues: 237.6289 Evaluate side-chains 341 residues out of total 3549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 317 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 354 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 307 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 282 ASN ** 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 = 0.3526 r_free = 0.3526 target = 0.109242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078665 restraints weight = 63224.934| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.59 r_work: 0.2900 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33362 Z= 0.130 Angle : 0.444 11.694 45031 Z= 0.231 Chirality : 0.041 0.188 5425 Planarity : 0.003 0.037 5768 Dihedral : 5.250 64.930 4837 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.04 % Allowed : 10.74 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.13), residues: 4361 helix: 2.45 (0.12), residues: 2002 sheet: 0.97 (0.22), residues: 567 loop : -0.52 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 42 HIS 0.001 0.000 HIS G 241 PHE 0.010 0.001 PHE B 279 TYR 0.008 0.001 TYR A 64 ARG 0.002 0.000 ARG N 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6695.14 seconds wall clock time: 122 minutes 7.74 seconds (7327.74 seconds total)