Starting phenix.real_space_refine on Tue Aug 26 16:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8y_36968/08_2025/8k8y_36968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8y_36968/08_2025/8k8y_36968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8y_36968/08_2025/8k8y_36968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8y_36968/08_2025/8k8y_36968.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8y_36968/08_2025/8k8y_36968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8y_36968/08_2025/8k8y_36968.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.065 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 7 5.49 5 S 56 5.16 5 C 24675 2.51 5 N 7000 2.21 5 O 7329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39067 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "G" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.37, per 1000 atoms: 0.21 Number of scatterers: 39067 At special positions: 0 Unit cell: (151.7, 150.88, 172.2, 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 56 16.00 P 7 15.00 O 7329 8.00 N 7000 7.00 C 24675 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 - 3.00 Amino acid : True - 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: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 73 sheets defined 54.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 97 through 120 removed outlier: 4.144A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.811A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.043A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.506A pdb=" N PHE A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.668A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.801A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.213A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 32 through 46 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.768A pdb=" N THR G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 120 removed outlier: 4.130A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASN G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 153 Processing helix chain 'G' and resid 173 through 221 removed outlier: 4.068A pdb=" N ASN G 212 " --> pdb=" O HIS G 208 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG G 213 " --> pdb=" O TYR G 209 " (cutoff:3.500A) Proline residue: G 216 - end of helix Processing helix chain 'G' and resid 224 through 242 Processing helix chain 'G' and resid 273 through 279 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 300 through 305 Processing helix chain 'G' and resid 314 through 320 Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 363 through 369 removed outlier: 4.070A pdb=" N GLY G 369 " --> pdb=" O GLU G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 379 Processing helix chain 'G' and resid 393 through 408 Processing helix chain 'G' and resid 412 through 428 Processing helix chain 'G' and resid 436 through 452 Processing helix chain 'G' and resid 456 through 471 removed outlier: 3.834A pdb=" N SER G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 485 Processing helix chain 'G' and resid 543 through 557 Processing helix chain 'G' and resid 585 through 597 Processing helix chain 'G' and resid 621 through 636 Processing helix chain 'G' and resid 649 through 654 removed outlier: 4.269A pdb=" N ALA G 652 " --> pdb=" O ALA G 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 666 Processing helix chain 'G' and resid 676 through 686 Processing helix chain 'G' and resid 694 through 719 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.721A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 removed outlier: 4.131A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 152 Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.018A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 242 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 293 through 297 Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.843A pdb=" N GLY F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 379 Processing helix chain 'F' and resid 393 through 408 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 470 Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 543 through 557 Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 621 through 636 Processing helix chain 'F' and resid 649 through 654 removed outlier: 4.286A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 Processing helix chain 'F' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.793A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 120 removed outlier: 4.176A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 153 Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.107A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.859A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 428 Processing helix chain 'E' and resid 436 through 451 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.885A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 532 through 534 No H-bonds generated for 'chain 'E' and resid 532 through 534' Processing helix chain 'E' and resid 543 through 557 Processing helix chain 'E' and resid 584 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.250A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.807A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 120 removed outlier: 4.230A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 153 removed outlier: 3.776A pdb=" N ALA D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.063A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.863A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.869A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.817A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 543 through 557 Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.312A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 654 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 97 through 120 removed outlier: 4.108A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 152 Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.090A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.104A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.851A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 543 through 557 Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 636 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.307A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.733A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 119 removed outlier: 4.098A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 153 removed outlier: 3.728A pdb=" N ALA B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.106A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 372 removed outlier: 4.054A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.693A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 585 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.339A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 4.827A pdb=" N ILE A 671 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.376A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA9, first strand: chain 'A' and resid 410 through 411 removed outlier: 6.844A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AB2, first strand: chain 'A' and resid 583 through 584 removed outlier: 4.257A pdb=" N ALA A 583 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 266 through 268 removed outlier: 6.490A pdb=" N VAL G 267 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASP G 313 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 310 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL G 361 " --> pdb=" O LEU G 310 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU G 312 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA G 49 " --> pdb=" O LEU G 360 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY G 362 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU G 51 " --> pdb=" O GLY G 362 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N HIS G 48 " --> pdb=" O PHE G 380 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE G 382 " --> pdb=" O HIS G 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 77 through 82 Processing sheet with id=AB5, first strand: chain 'G' and resid 156 through 158 Processing sheet with id=AB6, first strand: chain 'G' and resid 280 through 281 Processing sheet with id=AB7, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AB8, first strand: chain 'G' and resid 334 through 335 Processing sheet with id=AB9, first strand: chain 'G' and resid 389 through 391 Processing sheet with id=AC1, first strand: chain 'G' and resid 410 through 411 removed outlier: 6.866A pdb=" N GLN G 410 " --> pdb=" O LEU G 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 494 through 496 Processing sheet with id=AC3, first strand: chain 'G' and resid 528 through 530 removed outlier: 6.706A pdb=" N ILE G 529 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N PHE G 571 " --> pdb=" O ILE G 529 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N GLU G 498 " --> pdb=" O LEU G 604 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N VAL G 606 " --> pdb=" O GLU G 498 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN G 500 " --> pdb=" O VAL G 606 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA G 605 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL G 644 " --> pdb=" O TYR G 672 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL G 674 " --> pdb=" O VAL G 644 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU G 646 " --> pdb=" O VAL G 674 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 583 through 584 removed outlier: 4.304A pdb=" N ALA G 583 " --> pdb=" O VAL G 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.776A pdb=" N ILE F 671 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE F 529 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N PHE F 571 " --> pdb=" O ILE F 529 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 266 through 268 removed outlier: 6.391A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N HIS F 48 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 382 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 77 through 82 Processing sheet with id=AC8, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC9, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AD1, first strand: chain 'F' and resid 334 through 335 Processing sheet with id=AD2, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AD3, first strand: chain 'F' and resid 410 through 411 removed outlier: 6.902A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AD5, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AD6, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.762A pdb=" N ILE E 671 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N GLU E 498 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N VAL E 606 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASN E 500 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE E 571 " --> pdb=" O ILE E 529 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.407A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA E 49 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLY E 362 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU E 51 " --> pdb=" O GLY E 362 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AD9, first strand: chain 'E' and resid 156 through 158 Processing sheet with id=AE1, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AE2, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AE3, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AE4, first strand: chain 'E' and resid 410 through 411 removed outlier: 6.998A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AE6, first strand: chain 'E' and resid 609 through 610 Processing sheet with id=AE7, first strand: chain 'D' and resid 2 through 3 removed outlier: 4.755A pdb=" N ILE D 671 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 644 " --> pdb=" O TYR D 672 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL D 674 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.406A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AF1, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AF2, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AF3, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AF4, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AF5, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AF6, first strand: chain 'D' and resid 410 through 411 removed outlier: 6.922A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AF8, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.194A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.804A pdb=" N ILE C 671 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.599A pdb=" N VAL C 267 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASP C 313 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 77 through 82 Processing sheet with id=AG3, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AG4, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AG5, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AG6, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AG7, first strand: chain 'C' and resid 410 through 411 removed outlier: 6.933A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AG9, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.321A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.406A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 49 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLY B 362 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 51 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 77 through 82 removed outlier: 3.813A pdb=" N VAL B 88 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AH4, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AH5, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AH6, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AH7, first strand: chain 'B' and resid 410 through 411 removed outlier: 6.869A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AH9, first strand: chain 'B' and resid 528 through 530 removed outlier: 9.886A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 583 through 584 removed outlier: 4.262A pdb=" N ALA B 583 " --> pdb=" O VAL B 610 " (cutoff:3.500A) 2207 hydrogen bonds defined for protein. 6363 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: 8.25 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 13676 1.35 - 1.50: 11198 1.50 - 1.65: 14872 1.65 - 1.80: 71 1.80 - 1.95: 20 Bond restraints: 39837 Sorted by residual: bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.945 0.330 2.00e-02 2.50e+03 2.73e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.945 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 2.275 1.945 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.945 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.71e+02 ... (remaining 39832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 53753 3.43 - 6.85: 292 6.85 - 10.28: 13 10.28 - 13.71: 20 13.71 - 17.13: 11 Bond angle restraints: 54089 Sorted by residual: angle pdb=" O1P TS6 G 801 " pdb=" P TS6 G 801 " pdb=" S2P TS6 G 801 " ideal model delta sigma weight residual 98.15 115.28 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O1P TS6 F 801 " pdb=" P TS6 F 801 " pdb=" S2P TS6 F 801 " ideal model delta sigma weight residual 98.15 115.28 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O1P TS6 B 801 " pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 98.15 115.27 -17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O1P TS6 A 801 " pdb=" P TS6 A 801 " pdb=" S2P TS6 A 801 " ideal model delta sigma weight residual 98.15 115.25 -17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.25 -17.10 3.00e+00 1.11e-01 3.25e+01 ... (remaining 54084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 22096 18.02 - 36.04: 1587 36.04 - 54.06: 287 54.06 - 72.08: 121 72.08 - 90.10: 87 Dihedral angle restraints: 24178 sinusoidal: 9793 harmonic: 14385 Sorted by residual: dihedral pdb=" CA ALA A 535 " pdb=" C ALA A 535 " pdb=" N GLY A 536 " pdb=" CA GLY A 536 " ideal model delta harmonic sigma weight residual -180.00 -149.33 -30.67 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA PHE F 571 " pdb=" C PHE F 571 " pdb=" N GLU F 572 " pdb=" CA GLU F 572 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PHE D 571 " pdb=" C PHE D 571 " pdb=" N GLU D 572 " pdb=" CA GLU D 572 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 24175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 5215 0.062 - 0.125: 752 0.125 - 0.187: 33 0.187 - 0.250: 20 0.250 - 0.312: 7 Chirality restraints: 6027 Sorted by residual: chirality pdb=" CB VAL B 438 " pdb=" CA VAL B 438 " pdb=" CG1 VAL B 438 " pdb=" CG2 VAL B 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL D 438 " pdb=" CA VAL D 438 " pdb=" CG1 VAL D 438 " pdb=" CG2 VAL D 438 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA SER A 56 " pdb=" N SER A 56 " pdb=" C SER A 56 " pdb=" CB SER A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 6024 not shown) Planarity restraints: 7217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 572 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C GLU B 572 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU B 572 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN B 573 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 572 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C GLU G 572 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU G 572 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN G 573 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 572 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C GLU E 572 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU E 572 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN E 573 " -0.009 2.00e-02 2.50e+03 ... (remaining 7214 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 915 2.68 - 3.24: 40211 3.24 - 3.79: 66510 3.79 - 4.35: 88900 4.35 - 4.90: 144664 Nonbonded interactions: 341200 Sorted by model distance: nonbonded pdb=" OG SER C 593 " pdb=" O LEU C 598 " model vdw 2.125 3.040 nonbonded pdb=" OG SER B 593 " pdb=" O LEU B 598 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 593 " pdb=" O LEU A 598 " model vdw 2.155 3.040 nonbonded pdb=" OG SER D 593 " pdb=" O LEU D 598 " model vdw 2.167 3.040 nonbonded pdb=" OG SER G 593 " pdb=" O LEU G 598 " model vdw 2.180 3.040 ... (remaining 341195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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' } 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=0.00 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.250 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 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 : 0.009 0.330 39837 Z= 0.447 Angle : 0.836 17.133 54089 Z= 0.478 Chirality : 0.045 0.312 6027 Planarity : 0.003 0.032 7217 Dihedral : 14.694 90.103 14938 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 0.30 % Allowed : 4.23 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.11), residues: 5019 helix: -0.62 (0.09), residues: 2562 sheet: -1.03 (0.19), residues: 637 loop : -1.00 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 381 TYR 0.016 0.002 TYR D 557 PHE 0.019 0.001 PHE B 135 TRP 0.015 0.002 TRP G 250 HIS 0.010 0.001 HIS C 527 Details of bonding type rmsd covalent geometry : bond 0.00917 (39837) covalent geometry : angle 0.83604 (54089) hydrogen bonds : bond 0.11647 ( 2207) hydrogen bonds : angle 6.36419 ( 6363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 721 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 140 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6215 (mt-10) REVERT: A 213 ARG cc_start: 0.6712 (mmm160) cc_final: 0.6454 (mmm160) REVERT: A 278 PHE cc_start: 0.5791 (m-80) cc_final: 0.5385 (m-80) REVERT: A 302 VAL cc_start: 0.6999 (t) cc_final: 0.6764 (p) REVERT: A 327 LYS cc_start: 0.5335 (ttpp) cc_final: 0.4945 (ttmt) REVERT: A 331 ARG cc_start: 0.6063 (tpp-160) cc_final: 0.5841 (mtp-110) REVERT: A 334 GLN cc_start: 0.6248 (mt0) cc_final: 0.5974 (pt0) REVERT: A 336 GLU cc_start: 0.6341 (mp0) cc_final: 0.6141 (mt-10) REVERT: A 365 GLU cc_start: 0.6150 (mp0) cc_final: 0.5903 (mp0) REVERT: A 381 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6169 (mtt-85) REVERT: A 395 GLU cc_start: 0.5824 (mp0) cc_final: 0.5581 (mp0) REVERT: A 426 MET cc_start: 0.5986 (mtp) cc_final: 0.5720 (mtp) REVERT: A 461 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5661 (mt-10) REVERT: A 494 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7203 (mtt-85) REVERT: A 544 LYS cc_start: 0.5932 (ttmt) cc_final: 0.5668 (ttmp) REVERT: A 556 ARG cc_start: 0.5925 (tpt90) cc_final: 0.5397 (tpp-160) REVERT: A 597 ASN cc_start: 0.7028 (t0) cc_final: 0.6653 (t0) REVERT: A 634 LYS cc_start: 0.6697 (tttt) cc_final: 0.6258 (ttpt) REVERT: A 648 GLU cc_start: 0.6410 (tt0) cc_final: 0.5609 (tt0) REVERT: A 659 GLU cc_start: 0.6592 (pt0) cc_final: 0.5500 (pm20) REVERT: A 675 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6562 (mt-10) REVERT: A 688 ARG cc_start: 0.5417 (mtm110) cc_final: 0.4759 (mtp85) REVERT: A 708 ARG cc_start: 0.4323 (mtm-85) cc_final: 0.4028 (mtm-85) REVERT: G 1 MET cc_start: 0.4157 (ttp) cc_final: 0.3828 (tmm) REVERT: G 19 GLU cc_start: 0.5573 (mp0) cc_final: 0.5323 (pm20) REVERT: G 33 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6513 (mm-30) REVERT: G 37 GLU cc_start: 0.5783 (mt-10) cc_final: 0.5454 (mt-10) REVERT: G 40 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6254 (mt-10) REVERT: G 61 GLU cc_start: 0.5966 (mt-10) cc_final: 0.5359 (mp0) REVERT: G 243 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6250 (mt-10) REVERT: G 271 TYR cc_start: 0.6642 (t80) cc_final: 0.6164 (t80) REVERT: G 320 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6481 (mm-30) REVERT: G 331 ARG cc_start: 0.5565 (tpp-160) cc_final: 0.5318 (mtp180) REVERT: G 334 GLN cc_start: 0.6104 (mt0) cc_final: 0.5514 (pt0) REVERT: G 365 GLU cc_start: 0.6037 (mp0) cc_final: 0.5687 (mp0) REVERT: G 381 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.5883 (mtt-85) REVERT: G 385 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6212 (tp30) REVERT: G 426 MET cc_start: 0.5974 (mtt) cc_final: 0.5646 (mtp) REVERT: G 458 GLU cc_start: 0.5706 (mp0) cc_final: 0.5342 (mp0) REVERT: G 476 GLU cc_start: 0.5591 (tt0) cc_final: 0.5143 (mt-10) REVERT: G 488 ARG cc_start: 0.6622 (mmt180) cc_final: 0.6340 (mmt90) REVERT: G 494 ARG cc_start: 0.7389 (mtt180) cc_final: 0.6720 (mtt-85) REVERT: G 556 ARG cc_start: 0.5746 (tpt90) cc_final: 0.5203 (tpt170) REVERT: G 560 HIS cc_start: 0.6604 (m-70) cc_final: 0.6238 (m-70) REVERT: G 662 GLU cc_start: 0.6039 (tp30) cc_final: 0.5578 (mm-30) REVERT: G 688 ARG cc_start: 0.5556 (mtm-85) cc_final: 0.4614 (mtp85) REVERT: G 704 GLU cc_start: 0.4484 (tp30) cc_final: 0.3711 (mt-10) REVERT: F 1 MET cc_start: 0.4042 (ptt) cc_final: 0.3302 (tmm) REVERT: F 37 GLU cc_start: 0.5684 (mt-10) cc_final: 0.5414 (mt-10) REVERT: F 61 GLU cc_start: 0.5691 (mt-10) cc_final: 0.5194 (mp0) REVERT: F 69 THR cc_start: 0.7508 (t) cc_final: 0.7290 (p) REVERT: F 97 GLN cc_start: 0.5858 (mm110) cc_final: 0.5544 (mm-40) REVERT: F 219 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6424 (mm-40) REVERT: F 249 GLN cc_start: 0.7027 (tt0) cc_final: 0.6596 (tt0) REVERT: F 298 ARG cc_start: 0.6924 (mmt180) cc_final: 0.6658 (mpt180) REVERT: F 327 LYS cc_start: 0.5424 (ttpp) cc_final: 0.4698 (ttmt) REVERT: F 331 ARG cc_start: 0.6242 (ttm-80) cc_final: 0.6042 (ttt180) REVERT: F 334 GLN cc_start: 0.6099 (mt0) cc_final: 0.5556 (pt0) REVERT: F 365 GLU cc_start: 0.6083 (mp0) cc_final: 0.5763 (mp0) REVERT: F 381 ARG cc_start: 0.6843 (mtm180) cc_final: 0.6140 (mtt-85) REVERT: F 425 ARG cc_start: 0.5937 (tpt90) cc_final: 0.5694 (ttt180) REVERT: F 426 MET cc_start: 0.6160 (mtt) cc_final: 0.5932 (mtp) REVERT: F 488 ARG cc_start: 0.6915 (mtt-85) cc_final: 0.6670 (mtt90) REVERT: F 494 ARG cc_start: 0.7526 (mtt-85) cc_final: 0.7012 (mtt-85) REVERT: F 541 ILE cc_start: 0.4119 (OUTLIER) cc_final: 0.3735 (mm) REVERT: F 544 LYS cc_start: 0.5936 (tttt) cc_final: 0.5627 (ttmp) REVERT: F 556 ARG cc_start: 0.5898 (tpt90) cc_final: 0.5457 (tpp80) REVERT: F 568 SER cc_start: 0.7467 (m) cc_final: 0.6875 (p) REVERT: F 634 LYS cc_start: 0.6583 (tttm) cc_final: 0.6236 (ttpt) REVERT: F 659 GLU cc_start: 0.6163 (pt0) cc_final: 0.5186 (pm20) REVERT: F 665 ARG cc_start: 0.6312 (ttp80) cc_final: 0.5928 (ttm-80) REVERT: F 676 THR cc_start: 0.6337 (m) cc_final: 0.6133 (p) REVERT: F 688 ARG cc_start: 0.5304 (mmm-85) cc_final: 0.4796 (mmp-170) REVERT: F 697 GLU cc_start: 0.4835 (pp20) cc_final: 0.4397 (mm-30) REVERT: F 704 GLU cc_start: 0.4280 (tp30) cc_final: 0.3487 (mt-10) REVERT: E 1 MET cc_start: 0.3942 (ptt) cc_final: 0.3357 (tmm) REVERT: E 37 GLU cc_start: 0.5759 (mt-10) cc_final: 0.5436 (mt-10) REVERT: E 97 GLN cc_start: 0.6076 (mm-40) cc_final: 0.5847 (mm110) REVERT: E 120 ARG cc_start: 0.4734 (mtt90) cc_final: 0.4460 (mtm-85) REVERT: E 243 GLU cc_start: 0.6722 (tp30) cc_final: 0.6463 (tt0) REVERT: E 278 PHE cc_start: 0.5935 (m-80) cc_final: 0.5124 (m-80) REVERT: E 302 VAL cc_start: 0.7114 (t) cc_final: 0.6808 (p) REVERT: E 331 ARG cc_start: 0.5900 (ttm170) cc_final: 0.5429 (ttp80) REVERT: E 334 GLN cc_start: 0.6158 (mt0) cc_final: 0.5471 (pt0) REVERT: E 365 GLU cc_start: 0.6361 (mp0) cc_final: 0.5947 (mp0) REVERT: E 410 GLN cc_start: 0.6702 (mt0) cc_final: 0.5774 (mp10) REVERT: E 428 GLU cc_start: 0.4802 (tt0) cc_final: 0.4539 (mm-30) REVERT: E 429 GLN cc_start: 0.7293 (mt0) cc_final: 0.6927 (mt0) REVERT: E 458 GLU cc_start: 0.5645 (mp0) cc_final: 0.5205 (mp0) REVERT: E 488 ARG cc_start: 0.7018 (mtt-85) cc_final: 0.6777 (mtt90) REVERT: E 494 ARG cc_start: 0.7486 (mtt-85) cc_final: 0.7047 (mtt-85) REVERT: E 556 ARG cc_start: 0.5989 (tpt90) cc_final: 0.5493 (tpp80) REVERT: E 634 LYS cc_start: 0.6434 (tttt) cc_final: 0.6083 (ttpt) REVERT: E 648 GLU cc_start: 0.6864 (tt0) cc_final: 0.5986 (tt0) REVERT: E 659 GLU cc_start: 0.6329 (pt0) cc_final: 0.5361 (pm20) REVERT: E 675 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6698 (mt-10) REVERT: E 688 ARG cc_start: 0.5623 (mtm180) cc_final: 0.4708 (mtp85) REVERT: D 61 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5229 (mp0) REVERT: D 69 THR cc_start: 0.7629 (t) cc_final: 0.7418 (p) REVERT: D 219 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6768 (mm-40) REVERT: D 278 PHE cc_start: 0.5919 (m-80) cc_final: 0.5640 (m-80) REVERT: D 302 VAL cc_start: 0.6997 (t) cc_final: 0.6680 (p) REVERT: D 331 ARG cc_start: 0.5966 (ttm-80) cc_final: 0.5349 (ttm110) REVERT: D 334 GLN cc_start: 0.6132 (mt0) cc_final: 0.5809 (pt0) REVERT: D 381 ARG cc_start: 0.6970 (mpp80) cc_final: 0.6437 (mmt180) REVERT: D 476 GLU cc_start: 0.4780 (tp30) cc_final: 0.4540 (mt-10) REVERT: D 488 ARG cc_start: 0.6959 (mtt-85) cc_final: 0.6744 (mpt-90) REVERT: D 494 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6813 (mtt-85) REVERT: D 498 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5439 (tt0) REVERT: D 544 LYS cc_start: 0.5787 (ttmt) cc_final: 0.5554 (ttmp) REVERT: D 556 ARG cc_start: 0.6049 (tpt90) cc_final: 0.5694 (tpt170) REVERT: D 562 SER cc_start: 0.4774 (p) cc_final: 0.4572 (t) REVERT: D 634 LYS cc_start: 0.6368 (tttt) cc_final: 0.5954 (ttpt) REVERT: D 648 GLU cc_start: 0.6622 (tt0) cc_final: 0.5948 (tt0) REVERT: D 659 GLU cc_start: 0.6302 (pt0) cc_final: 0.5574 (pm20) REVERT: D 688 ARG cc_start: 0.5674 (mtm180) cc_final: 0.4881 (mtp85) REVERT: D 696 GLN cc_start: 0.5047 (tt0) cc_final: 0.4843 (mm110) REVERT: D 697 GLU cc_start: 0.4833 (pt0) cc_final: 0.4209 (mm-30) REVERT: D 704 GLU cc_start: 0.3879 (mm-30) cc_final: 0.3409 (mt-10) REVERT: C 1 MET cc_start: 0.3564 (tpt) cc_final: 0.3319 (ptm) REVERT: C 61 GLU cc_start: 0.5958 (mt-10) cc_final: 0.5407 (mp0) REVERT: C 97 GLN cc_start: 0.5678 (mm-40) cc_final: 0.5396 (mm110) REVERT: C 243 GLU cc_start: 0.6334 (tp30) cc_final: 0.5703 (mt-10) REVERT: C 298 ARG cc_start: 0.6983 (mmt180) cc_final: 0.6678 (mpt180) REVERT: C 302 VAL cc_start: 0.6957 (t) cc_final: 0.6725 (p) REVERT: C 304 ARG cc_start: 0.6182 (mtm-85) cc_final: 0.5860 (mtm110) REVERT: C 331 ARG cc_start: 0.5875 (ttm-80) cc_final: 0.5332 (ttp80) REVERT: C 334 GLN cc_start: 0.6351 (mt0) cc_final: 0.5656 (pt0) REVERT: C 365 GLU cc_start: 0.6262 (mp0) cc_final: 0.5916 (mp0) REVERT: C 385 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6195 (tp30) REVERT: C 410 GLN cc_start: 0.5936 (mp10) cc_final: 0.5355 (mp10) REVERT: C 429 GLN cc_start: 0.7474 (mt0) cc_final: 0.7157 (mt0) REVERT: C 431 ASP cc_start: 0.7448 (m-30) cc_final: 0.7014 (m-30) REVERT: C 461 GLU cc_start: 0.5967 (mt-10) cc_final: 0.5632 (mt-10) REVERT: C 462 GLN cc_start: 0.5936 (mt0) cc_final: 0.5715 (mt0) REVERT: C 475 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6218 (mm-30) REVERT: C 476 GLU cc_start: 0.4925 (tp30) cc_final: 0.4377 (tt0) REVERT: C 494 ARG cc_start: 0.7718 (mtt-85) cc_final: 0.7156 (mtt-85) REVERT: C 498 GLU cc_start: 0.6298 (mt-10) cc_final: 0.5321 (tt0) REVERT: C 556 ARG cc_start: 0.5985 (tpt90) cc_final: 0.5483 (tpp80) REVERT: C 560 HIS cc_start: 0.6565 (m-70) cc_final: 0.5796 (m-70) REVERT: C 562 SER cc_start: 0.5449 (p) cc_final: 0.5171 (m) REVERT: C 659 GLU cc_start: 0.6350 (pt0) cc_final: 0.5385 (pm20) REVERT: C 688 ARG cc_start: 0.5704 (mtm110) cc_final: 0.4758 (mtp85) REVERT: C 690 GLU cc_start: 0.5318 (pm20) cc_final: 0.4911 (mp0) REVERT: C 697 GLU cc_start: 0.4864 (mt-10) cc_final: 0.4628 (mm-30) REVERT: C 704 GLU cc_start: 0.3848 (mm-30) cc_final: 0.3414 (mt-10) REVERT: B 19 GLU cc_start: 0.6215 (tp30) cc_final: 0.5962 (mt-10) REVERT: B 36 ARG cc_start: 0.5800 (ttp-170) cc_final: 0.5266 (ttp-170) REVERT: B 37 GLU cc_start: 0.5627 (mt-10) cc_final: 0.5383 (mt-10) REVERT: B 97 GLN cc_start: 0.5767 (mm-40) cc_final: 0.5449 (mm110) REVERT: B 140 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5787 (mt-10) REVERT: B 278 PHE cc_start: 0.5925 (m-80) cc_final: 0.5631 (m-80) REVERT: B 298 ARG cc_start: 0.7026 (mmt180) cc_final: 0.6662 (mpt180) REVERT: B 302 VAL cc_start: 0.7191 (t) cc_final: 0.6947 (p) REVERT: B 331 ARG cc_start: 0.5891 (ttm-80) cc_final: 0.5396 (ttp80) REVERT: B 334 GLN cc_start: 0.6160 (mt0) cc_final: 0.5702 (pt0) REVERT: B 395 GLU cc_start: 0.6279 (mp0) cc_final: 0.6067 (mm-30) REVERT: B 425 ARG cc_start: 0.5947 (tpt90) cc_final: 0.5591 (ttt180) REVERT: B 461 GLU cc_start: 0.5716 (mt-10) cc_final: 0.5380 (mt-10) REVERT: B 498 GLU cc_start: 0.6439 (mt-10) cc_final: 0.5719 (tt0) REVERT: B 544 LYS cc_start: 0.5714 (tttt) cc_final: 0.5368 (ttmt) REVERT: B 556 ARG cc_start: 0.5838 (tpt90) cc_final: 0.5337 (tpp-160) REVERT: B 634 LYS cc_start: 0.6634 (tttt) cc_final: 0.6198 (ttmt) REVERT: B 648 GLU cc_start: 0.6694 (tt0) cc_final: 0.6391 (tt0) REVERT: B 659 GLU cc_start: 0.6720 (pt0) cc_final: 0.5531 (pm20) REVERT: B 665 ARG cc_start: 0.5926 (ttp80) cc_final: 0.5668 (ttp-170) REVERT: B 675 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6767 (mt-10) REVERT: B 688 ARG cc_start: 0.5692 (mtm180) cc_final: 0.4785 (mtp85) REVERT: B 704 GLU cc_start: 0.4391 (tp30) cc_final: 0.3535 (mt-10) outliers start: 12 outliers final: 7 residues processed: 732 average time/residue: 0.9217 time to fit residues: 772.8033 Evaluate side-chains 519 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 511 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain B residue 438 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.0010 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 293 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A 355 GLN A 357 GLN A 396 ASN A 500 ASN A 527 HIS A 573 GLN G 48 HIS G 303 HIS G 334 GLN G 407 GLN G 413 GLN G 429 GLN G 500 ASN G 527 HIS G 679 GLN F 100 HIS ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN F 334 GLN F 429 GLN F 500 ASN F 573 GLN F 670 HIS E 100 HIS E 253 ASN E 334 GLN E 500 ASN E 679 GLN D 160 ASN D 303 HIS D 355 GLN D 462 GLN D 560 HIS D 573 GLN D 696 GLN C 130 GLN C 293 ASN C 429 GLN C 500 ASN C 527 HIS C 560 HIS C 679 GLN B 121 GLN B 223 GLN B 249 GLN B 342 GLN B 396 ASN B 429 GLN B 462 GLN B 500 ASN B 653 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145652 restraints weight = 41605.813| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.73 r_work: 0.3496 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39837 Z= 0.135 Angle : 0.567 9.681 54089 Z= 0.290 Chirality : 0.039 0.158 6027 Planarity : 0.004 0.049 7217 Dihedral : 4.552 45.152 5610 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.86 % Allowed : 9.58 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.11), residues: 5019 helix: 0.81 (0.10), residues: 2653 sheet: -0.56 (0.20), residues: 616 loop : -0.55 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 120 TYR 0.017 0.002 TYR A 50 PHE 0.013 0.001 PHE C 571 TRP 0.013 0.001 TRP C 250 HIS 0.004 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00288 (39837) covalent geometry : angle 0.56748 (54089) hydrogen bonds : bond 0.04318 ( 2207) hydrogen bonds : angle 4.89444 ( 6363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 559 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7762 (tp) REVERT: A 140 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6964 (mt-10) REVERT: A 223 GLN cc_start: 0.8608 (mp10) cc_final: 0.8282 (mp10) REVERT: A 326 PHE cc_start: 0.7525 (t80) cc_final: 0.7280 (t80) REVERT: A 327 LYS cc_start: 0.7176 (ttpp) cc_final: 0.6830 (ttmt) REVERT: A 410 GLN cc_start: 0.7740 (mm110) cc_final: 0.7363 (mp10) REVERT: A 597 ASN cc_start: 0.8663 (t0) cc_final: 0.8461 (t0) REVERT: A 659 GLU cc_start: 0.8076 (pt0) cc_final: 0.7698 (pm20) REVERT: A 688 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7202 (mtp85) REVERT: A 696 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8382 (tp-100) REVERT: A 708 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6927 (mtp180) REVERT: G 1 MET cc_start: 0.6264 (ttp) cc_final: 0.6053 (tmm) REVERT: G 179 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6738 (mmm160) REVERT: G 334 GLN cc_start: 0.7385 (mt0) cc_final: 0.7042 (pt0) REVERT: G 355 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: G 381 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7638 (mtt-85) REVERT: G 659 GLU cc_start: 0.8280 (pt0) cc_final: 0.7853 (pm20) REVERT: G 688 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7145 (mtp85) REVERT: G 696 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8175 (tp-100) REVERT: G 704 GLU cc_start: 0.7761 (tp30) cc_final: 0.7004 (mt-10) REVERT: F 1 MET cc_start: 0.6121 (ptt) cc_final: 0.5418 (tmm) REVERT: F 40 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8272 (mt-10) REVERT: F 97 GLN cc_start: 0.7871 (mm110) cc_final: 0.7406 (mm-40) REVERT: F 162 GLU cc_start: 0.2356 (OUTLIER) cc_final: 0.2009 (mt-10) REVERT: F 219 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7379 (mm-40) REVERT: F 249 GLN cc_start: 0.8375 (tt0) cc_final: 0.8054 (tt0) REVERT: F 331 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6518 (ttp80) REVERT: F 334 GLN cc_start: 0.7300 (mt0) cc_final: 0.7043 (pt0) REVERT: F 410 GLN cc_start: 0.7656 (mm110) cc_final: 0.7378 (mp10) REVERT: F 541 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5346 (mm) REVERT: F 659 GLU cc_start: 0.8021 (pt0) cc_final: 0.7573 (pm20) REVERT: F 688 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7197 (mmp-170) REVERT: F 696 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8338 (tp-100) REVERT: F 697 GLU cc_start: 0.7661 (pp20) cc_final: 0.7304 (mm-30) REVERT: F 704 GLU cc_start: 0.7737 (tp30) cc_final: 0.6915 (mt-10) REVERT: E 1 MET cc_start: 0.6038 (ptt) cc_final: 0.5525 (tmm) REVERT: E 140 GLU cc_start: 0.6638 (pp20) cc_final: 0.6369 (pt0) REVERT: E 278 PHE cc_start: 0.6908 (m-80) cc_final: 0.6642 (m-80) REVERT: E 298 ARG cc_start: 0.7937 (mpt180) cc_final: 0.7674 (mmt-90) REVERT: E 320 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6329 (mm-30) REVERT: E 331 ARG cc_start: 0.6969 (ttm170) cc_final: 0.6733 (ttp80) REVERT: E 334 GLN cc_start: 0.7400 (mt0) cc_final: 0.7068 (pt0) REVERT: E 410 GLN cc_start: 0.7781 (mt0) cc_final: 0.7419 (mp10) REVERT: E 648 GLU cc_start: 0.8519 (tt0) cc_final: 0.8166 (tt0) REVERT: E 659 GLU cc_start: 0.8175 (pt0) cc_final: 0.7816 (pm20) REVERT: E 688 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7268 (mtp85) REVERT: E 696 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8341 (tp-100) REVERT: D 1 MET cc_start: 0.6378 (tmm) cc_final: 0.6100 (tmm) REVERT: D 61 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7391 (mp0) REVERT: D 118 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7913 (tp) REVERT: D 140 GLU cc_start: 0.6739 (pp20) cc_final: 0.6395 (pt0) REVERT: D 355 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: D 410 GLN cc_start: 0.7304 (mp10) cc_final: 0.7068 (mp10) REVERT: D 527 HIS cc_start: 0.7519 (t-170) cc_final: 0.7249 (t70) REVERT: D 562 SER cc_start: 0.6576 (p) cc_final: 0.6191 (t) REVERT: D 574 ASN cc_start: 0.7377 (p0) cc_final: 0.7175 (p0) REVERT: D 648 GLU cc_start: 0.8383 (tt0) cc_final: 0.8176 (tt0) REVERT: D 659 GLU cc_start: 0.8081 (pt0) cc_final: 0.7879 (pm20) REVERT: D 688 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7284 (mtp85) REVERT: D 697 GLU cc_start: 0.7739 (pt0) cc_final: 0.7054 (mm-30) REVERT: D 704 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6789 (mt-10) REVERT: C 61 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7522 (mp0) REVERT: C 97 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7720 (mm110) REVERT: C 304 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7485 (mtm110) REVERT: C 320 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: C 331 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6733 (ttp80) REVERT: C 334 GLN cc_start: 0.7463 (mt0) cc_final: 0.7111 (pt0) REVERT: C 410 GLN cc_start: 0.7526 (mp10) cc_final: 0.7244 (mp10) REVERT: C 541 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6066 (tt) REVERT: C 560 HIS cc_start: 0.8060 (m90) cc_final: 0.7827 (m-70) REVERT: C 562 SER cc_start: 0.7164 (p) cc_final: 0.6815 (m) REVERT: C 659 GLU cc_start: 0.8038 (pt0) cc_final: 0.7584 (pm20) REVERT: C 688 ARG cc_start: 0.7618 (mtm110) cc_final: 0.6892 (mtp85) REVERT: C 697 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7402 (mm-30) REVERT: C 704 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6858 (mt-10) REVERT: B 97 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7527 (mm-40) REVERT: B 118 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7731 (tp) REVERT: B 140 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6600 (mt-10) REVERT: B 179 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6779 (mmm-85) REVERT: B 331 ARG cc_start: 0.7102 (ttm-80) cc_final: 0.6668 (ttp80) REVERT: B 410 GLN cc_start: 0.7562 (mp10) cc_final: 0.7334 (mp10) REVERT: B 659 GLU cc_start: 0.8308 (pt0) cc_final: 0.7826 (pm20) REVERT: B 688 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7122 (mtp85) REVERT: B 704 GLU cc_start: 0.7926 (tp30) cc_final: 0.6998 (mt-10) outliers start: 74 outliers final: 25 residues processed: 601 average time/residue: 0.8430 time to fit residues: 586.9681 Evaluate side-chains 482 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 445 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 355 GLN Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 488 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 97 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 479 optimal weight: 8.9990 chunk 384 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 489 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 462 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 527 HIS G 342 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** F 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN E 429 GLN D 249 GLN ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN B 429 GLN B 527 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.182327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136098 restraints weight = 41007.821| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.84 r_work: 0.3487 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39837 Z= 0.183 Angle : 0.577 8.167 54089 Z= 0.294 Chirality : 0.040 0.159 6027 Planarity : 0.004 0.054 7217 Dihedral : 4.641 47.297 5610 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 12.95 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.11), residues: 5019 helix: 1.10 (0.10), residues: 2660 sheet: -0.38 (0.20), residues: 616 loop : -0.28 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 114 TYR 0.020 0.002 TYR G 557 PHE 0.016 0.002 PHE B 221 TRP 0.013 0.002 TRP G 323 HIS 0.010 0.001 HIS F 560 Details of bonding type rmsd covalent geometry : bond 0.00414 (39837) covalent geometry : angle 0.57728 (54089) hydrogen bonds : bond 0.04317 ( 2207) hydrogen bonds : angle 4.66087 ( 6363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 467 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6919 (mt-10) REVERT: A 179 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6904 (mtp180) REVERT: A 223 GLN cc_start: 0.8586 (mp10) cc_final: 0.8190 (mp10) REVERT: A 327 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6934 (ttmt) REVERT: A 365 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: A 378 GLU cc_start: 0.7889 (tt0) cc_final: 0.7117 (tp30) REVERT: A 410 GLN cc_start: 0.7739 (mm110) cc_final: 0.7359 (mp10) REVERT: A 541 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6029 (mm) REVERT: A 597 ASN cc_start: 0.8732 (t0) cc_final: 0.8504 (t0) REVERT: A 659 GLU cc_start: 0.8128 (pt0) cc_final: 0.7711 (pm20) REVERT: A 665 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8116 (ttp-170) REVERT: A 688 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7223 (mtp85) REVERT: A 696 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8285 (tp-100) REVERT: A 708 ARG cc_start: 0.7210 (mtm-85) cc_final: 0.6892 (mtp180) REVERT: G 1 MET cc_start: 0.6540 (ttp) cc_final: 0.6086 (tmm) REVERT: G 118 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7985 (tp) REVERT: G 179 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6664 (mmm160) REVERT: G 181 GLU cc_start: 0.7248 (tp30) cc_final: 0.6943 (tp30) REVERT: G 334 GLN cc_start: 0.7391 (mt0) cc_final: 0.7113 (pt0) REVERT: G 365 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: G 381 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7627 (mtt-85) REVERT: G 581 ASP cc_start: 0.6498 (p0) cc_final: 0.5767 (t70) REVERT: G 688 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7149 (mtp85) REVERT: G 696 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8057 (tp-100) REVERT: G 704 GLU cc_start: 0.7668 (tp30) cc_final: 0.6887 (mt-10) REVERT: G 710 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6528 (mm-30) REVERT: F 1 MET cc_start: 0.6298 (ptt) cc_final: 0.5684 (tmm) REVERT: F 40 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8211 (mt-10) REVERT: F 97 GLN cc_start: 0.7895 (mm110) cc_final: 0.7601 (mm-40) REVERT: F 219 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7339 (mm-40) REVERT: F 331 ARG cc_start: 0.7017 (ttm-80) cc_final: 0.6554 (ttp80) REVERT: F 355 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: F 365 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: F 410 GLN cc_start: 0.7766 (mm110) cc_final: 0.7490 (mp10) REVERT: F 541 ILE cc_start: 0.6327 (OUTLIER) cc_final: 0.5376 (mm) REVERT: F 659 GLU cc_start: 0.8012 (pt0) cc_final: 0.7612 (pm20) REVERT: F 688 ARG cc_start: 0.7491 (mmm-85) cc_final: 0.7067 (mmp-170) REVERT: F 696 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8277 (tp-100) REVERT: F 697 GLU cc_start: 0.7672 (pp20) cc_final: 0.7299 (mm-30) REVERT: F 704 GLU cc_start: 0.7767 (tp30) cc_final: 0.6918 (mt-10) REVERT: E 1 MET cc_start: 0.6409 (ptt) cc_final: 0.5841 (tmm) REVERT: E 118 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7740 (tp) REVERT: E 140 GLU cc_start: 0.6663 (pp20) cc_final: 0.6392 (pt0) REVERT: E 179 ARG cc_start: 0.7205 (mmm160) cc_final: 0.6933 (mmm160) REVERT: E 278 PHE cc_start: 0.6832 (m-80) cc_final: 0.6505 (m-80) REVERT: E 320 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: E 334 GLN cc_start: 0.7404 (mt0) cc_final: 0.7118 (pt0) REVERT: E 410 GLN cc_start: 0.7753 (mt0) cc_final: 0.7391 (mp10) REVERT: E 488 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8426 (mtt90) REVERT: E 648 GLU cc_start: 0.8466 (tt0) cc_final: 0.8098 (tt0) REVERT: E 659 GLU cc_start: 0.8210 (pt0) cc_final: 0.7849 (pm20) REVERT: E 688 ARG cc_start: 0.7746 (mtm180) cc_final: 0.7227 (mtp85) REVERT: E 696 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8319 (tp-100) REVERT: D 1 MET cc_start: 0.6627 (tmm) cc_final: 0.6408 (tmm) REVERT: D 61 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7338 (mp0) REVERT: D 140 GLU cc_start: 0.6643 (pp20) cc_final: 0.6296 (pt0) REVERT: D 223 GLN cc_start: 0.8687 (mp10) cc_final: 0.8380 (mp-120) REVERT: D 410 GLN cc_start: 0.7356 (mp10) cc_final: 0.7123 (mp10) REVERT: D 488 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7810 (mtt90) REVERT: D 498 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: D 562 SER cc_start: 0.6622 (p) cc_final: 0.6173 (t) REVERT: D 648 GLU cc_start: 0.8377 (tt0) cc_final: 0.8131 (tt0) REVERT: D 659 GLU cc_start: 0.8060 (pt0) cc_final: 0.7849 (pm20) REVERT: D 688 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7285 (mtp85) REVERT: D 697 GLU cc_start: 0.7903 (pt0) cc_final: 0.7159 (mm-30) REVERT: D 704 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6828 (mt-10) REVERT: C 61 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 97 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7761 (mm110) REVERT: C 320 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: C 331 ARG cc_start: 0.7052 (ttm-80) cc_final: 0.6605 (ttp80) REVERT: C 334 GLN cc_start: 0.7503 (mt0) cc_final: 0.7181 (pt0) REVERT: C 355 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: C 365 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: C 410 GLN cc_start: 0.7536 (mp10) cc_final: 0.7305 (mp10) REVERT: C 428 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 541 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6068 (tt) REVERT: C 659 GLU cc_start: 0.8123 (pt0) cc_final: 0.7662 (pm20) REVERT: C 665 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8057 (ttp-170) REVERT: C 688 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7037 (mtp85) REVERT: C 697 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7349 (mm-30) REVERT: C 704 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6797 (mt-10) REVERT: B 36 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.8024 (ttp-170) REVERT: B 97 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7475 (mm-40) REVERT: B 118 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7863 (tp) REVERT: B 140 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6547 (mt-10) REVERT: B 179 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6712 (mmm-85) REVERT: B 181 GLU cc_start: 0.7418 (tp30) cc_final: 0.7196 (tp30) REVERT: B 331 ARG cc_start: 0.7037 (ttm-80) cc_final: 0.6636 (ttp80) REVERT: B 410 GLN cc_start: 0.7593 (mp10) cc_final: 0.7386 (mp10) REVERT: B 688 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7078 (mtp85) REVERT: B 704 GLU cc_start: 0.7989 (tp30) cc_final: 0.7048 (mt-10) outliers start: 97 outliers final: 34 residues processed: 529 average time/residue: 0.8179 time to fit residues: 505.3115 Evaluate side-chains 487 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 433 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 355 GLN Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 665 ARG Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 305 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 446 optimal weight: 9.9990 chunk 490 optimal weight: 1.9990 chunk 333 optimal weight: 4.9990 chunk 442 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 413 GLN A 560 HIS G 413 GLN F 151 GLN F 355 GLN ** F 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN D 249 GLN D 413 GLN ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 355 GLN B 413 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137750 restraints weight = 41560.237| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.83 r_work: 0.3483 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39837 Z= 0.181 Angle : 0.566 6.859 54089 Z= 0.287 Chirality : 0.040 0.157 6027 Planarity : 0.004 0.053 7217 Dihedral : 4.573 48.837 5608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.09 % Allowed : 13.81 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.12), residues: 5019 helix: 1.28 (0.10), residues: 2653 sheet: -0.23 (0.21), residues: 616 loop : -0.12 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 114 TYR 0.022 0.002 TYR D 557 PHE 0.016 0.002 PHE B 221 TRP 0.012 0.002 TRP G 250 HIS 0.008 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00411 (39837) covalent geometry : angle 0.56575 (54089) hydrogen bonds : bond 0.04197 ( 2207) hydrogen bonds : angle 4.53077 ( 6363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 457 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (tp) REVERT: A 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6930 (mt-10) REVERT: A 179 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6885 (mtp180) REVERT: A 223 GLN cc_start: 0.8599 (mp10) cc_final: 0.8277 (mp-120) REVERT: A 327 LYS cc_start: 0.7463 (ttpp) cc_final: 0.7001 (ttmt) REVERT: A 365 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: A 410 GLN cc_start: 0.7709 (mm110) cc_final: 0.7350 (mp10) REVERT: A 541 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6168 (mm) REVERT: A 597 ASN cc_start: 0.8723 (t0) cc_final: 0.8514 (t0) REVERT: A 659 GLU cc_start: 0.8251 (pt0) cc_final: 0.7841 (pm20) REVERT: A 665 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: A 688 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7277 (mtp85) REVERT: A 696 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8308 (tp-100) REVERT: A 708 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6890 (mtp180) REVERT: G 1 MET cc_start: 0.6830 (ttp) cc_final: 0.6296 (tmm) REVERT: G 118 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8017 (tp) REVERT: G 181 GLU cc_start: 0.7419 (tp30) cc_final: 0.7112 (tp30) REVERT: G 334 GLN cc_start: 0.7378 (mt0) cc_final: 0.7109 (pt0) REVERT: G 365 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: G 378 GLU cc_start: 0.7789 (tt0) cc_final: 0.7145 (tp30) REVERT: G 418 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7003 (mmm160) REVERT: G 581 ASP cc_start: 0.6657 (p0) cc_final: 0.5821 (t70) REVERT: G 688 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7212 (mtp85) REVERT: G 696 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8108 (tp-100) REVERT: G 704 GLU cc_start: 0.7696 (tp30) cc_final: 0.6878 (mt-10) REVERT: F 1 MET cc_start: 0.6427 (ptt) cc_final: 0.5778 (tmm) REVERT: F 40 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8232 (mt-10) REVERT: F 97 GLN cc_start: 0.7940 (mm110) cc_final: 0.7632 (mm-40) REVERT: F 118 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7713 (tp) REVERT: F 162 GLU cc_start: 0.2726 (OUTLIER) cc_final: 0.2426 (mt-10) REVERT: F 181 GLU cc_start: 0.7344 (tp30) cc_final: 0.7071 (tp30) REVERT: F 219 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7372 (mm-40) REVERT: F 331 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6407 (ttt-90) REVERT: F 355 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: F 365 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: F 410 GLN cc_start: 0.7735 (mm110) cc_final: 0.7449 (mp10) REVERT: F 425 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6363 (ttp80) REVERT: F 467 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8309 (ttt90) REVERT: F 541 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.5401 (mm) REVERT: F 659 GLU cc_start: 0.8087 (pt0) cc_final: 0.7695 (pm20) REVERT: F 688 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7106 (mmp-170) REVERT: F 696 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8296 (tp-100) REVERT: F 697 GLU cc_start: 0.7618 (pp20) cc_final: 0.7216 (mm-30) REVERT: F 704 GLU cc_start: 0.7828 (tp30) cc_final: 0.6963 (mt-10) REVERT: E 1 MET cc_start: 0.6523 (ptt) cc_final: 0.5805 (tmm) REVERT: E 140 GLU cc_start: 0.6727 (pp20) cc_final: 0.6458 (pt0) REVERT: E 320 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6263 (mm-30) REVERT: E 334 GLN cc_start: 0.7451 (mt0) cc_final: 0.7195 (pt0) REVERT: E 410 GLN cc_start: 0.7776 (mt0) cc_final: 0.7408 (mp10) REVERT: E 659 GLU cc_start: 0.8213 (pt0) cc_final: 0.7856 (pm20) REVERT: E 688 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7288 (mmp-170) REVERT: D 61 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7396 (mp0) REVERT: D 140 GLU cc_start: 0.6692 (pp20) cc_final: 0.6296 (pt0) REVERT: D 160 ASN cc_start: 0.5483 (OUTLIER) cc_final: 0.4878 (t0) REVERT: D 188 LEU cc_start: 0.7571 (mt) cc_final: 0.7319 (mp) REVERT: D 213 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6994 (tpt90) REVERT: D 410 GLN cc_start: 0.7406 (mp10) cc_final: 0.7155 (mp10) REVERT: D 455 LEU cc_start: 0.8335 (mp) cc_final: 0.8095 (mt) REVERT: D 488 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7864 (mtt90) REVERT: D 648 GLU cc_start: 0.8412 (tt0) cc_final: 0.8134 (tt0) REVERT: D 659 GLU cc_start: 0.8135 (pt0) cc_final: 0.7884 (pm20) REVERT: D 688 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7312 (mtp85) REVERT: D 697 GLU cc_start: 0.7964 (pt0) cc_final: 0.7216 (mm-30) REVERT: D 704 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6878 (mt-10) REVERT: C 1 MET cc_start: 0.7217 (ptm) cc_final: 0.6730 (ppp) REVERT: C 97 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7752 (mm-40) REVERT: C 118 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (tp) REVERT: C 243 GLU cc_start: 0.7551 (tt0) cc_final: 0.7094 (tt0) REVERT: C 298 ARG cc_start: 0.7873 (mpt180) cc_final: 0.7627 (mmp-170) REVERT: C 320 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: C 331 ARG cc_start: 0.7019 (ttm-80) cc_final: 0.6593 (ttp80) REVERT: C 334 GLN cc_start: 0.7491 (mt0) cc_final: 0.7141 (pt0) REVERT: C 355 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: C 365 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: C 410 GLN cc_start: 0.7559 (mp10) cc_final: 0.7340 (mp10) REVERT: C 541 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6234 (tt) REVERT: C 559 GLU cc_start: 0.6023 (mp0) cc_final: 0.5774 (mp0) REVERT: C 560 HIS cc_start: 0.8033 (m90) cc_final: 0.7827 (m-70) REVERT: C 581 ASP cc_start: 0.6503 (p0) cc_final: 0.5752 (t0) REVERT: C 659 GLU cc_start: 0.8211 (pt0) cc_final: 0.7738 (pm20) REVERT: C 665 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8056 (ttp-170) REVERT: C 688 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7023 (mtp85) REVERT: C 697 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7390 (mm-30) REVERT: C 704 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6810 (mt-10) REVERT: B 97 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7522 (mm-40) REVERT: B 106 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: B 118 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 140 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6547 (mt-10) REVERT: B 181 GLU cc_start: 0.7498 (tp30) cc_final: 0.7203 (tp30) REVERT: B 331 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6656 (ttp80) REVERT: B 348 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6683 (pp20) REVERT: B 355 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8337 (mt0) REVERT: B 410 GLN cc_start: 0.7589 (mp10) cc_final: 0.7345 (mp10) REVERT: B 488 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7869 (mtt90) REVERT: B 688 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7087 (mtp85) REVERT: B 704 GLU cc_start: 0.7945 (tp30) cc_final: 0.7033 (mt-10) outliers start: 123 outliers final: 51 residues processed: 545 average time/residue: 0.7536 time to fit residues: 482.1275 Evaluate side-chains 502 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 423 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 418 ARG Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain G residue 610 VAL Chi-restraints excluded: chain G residue 713 HIS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 417 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 665 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 355 GLN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 634 LYS Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 85 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 349 optimal weight: 4.9990 chunk 310 optimal weight: 0.2980 chunk 150 optimal weight: 0.0570 chunk 47 optimal weight: 0.7980 chunk 486 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN G 413 GLN F 151 GLN F 160 ASN ** F 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN E 527 HIS D 249 GLN D 413 GLN D 527 HIS ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 429 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139683 restraints weight = 40907.675| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.85 r_work: 0.3524 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 39837 Z= 0.111 Angle : 0.507 6.558 54089 Z= 0.257 Chirality : 0.037 0.157 6027 Planarity : 0.004 0.051 7217 Dihedral : 4.330 51.831 5608 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.64 % Allowed : 14.99 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.12), residues: 5019 helix: 1.56 (0.10), residues: 2653 sheet: -0.17 (0.21), residues: 616 loop : 0.01 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 114 TYR 0.018 0.001 TYR E 557 PHE 0.017 0.001 PHE B 221 TRP 0.011 0.001 TRP B 511 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00236 (39837) covalent geometry : angle 0.50713 (54089) hydrogen bonds : bond 0.03813 ( 2207) hydrogen bonds : angle 4.33935 ( 6363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 445 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7882 (tp) REVERT: A 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6875 (mt-10) REVERT: A 179 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6900 (mtp180) REVERT: A 223 GLN cc_start: 0.8530 (mp10) cc_final: 0.8184 (mp10) REVERT: A 327 LYS cc_start: 0.7564 (ttpp) cc_final: 0.6994 (ttmt) REVERT: A 365 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: A 410 GLN cc_start: 0.7668 (mm110) cc_final: 0.7353 (mp10) REVERT: A 541 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6088 (mm) REVERT: A 597 ASN cc_start: 0.8660 (t0) cc_final: 0.8437 (t0) REVERT: A 659 GLU cc_start: 0.8108 (pt0) cc_final: 0.7754 (pm20) REVERT: A 688 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7124 (mtp85) REVERT: A 696 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8230 (tp-100) REVERT: A 708 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6756 (mtp180) REVERT: G 1 MET cc_start: 0.6676 (ttp) cc_final: 0.6238 (tmm) REVERT: G 118 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7950 (tp) REVERT: G 181 GLU cc_start: 0.7505 (tp30) cc_final: 0.7203 (tp30) REVERT: G 334 GLN cc_start: 0.7289 (mt0) cc_final: 0.7065 (pt0) REVERT: G 365 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: G 378 GLU cc_start: 0.7748 (tt0) cc_final: 0.7056 (tp30) REVERT: G 581 ASP cc_start: 0.6541 (p0) cc_final: 0.5780 (t70) REVERT: G 659 GLU cc_start: 0.8222 (pt0) cc_final: 0.7775 (pm20) REVERT: G 688 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7151 (mtp85) REVERT: G 696 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7854 (tp-100) REVERT: G 704 GLU cc_start: 0.7637 (tp30) cc_final: 0.6810 (mt-10) REVERT: F 1 MET cc_start: 0.6305 (ptt) cc_final: 0.5699 (tmm) REVERT: F 97 GLN cc_start: 0.7889 (mm110) cc_final: 0.7624 (mm-40) REVERT: F 118 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7676 (tp) REVERT: F 160 ASN cc_start: 0.5706 (OUTLIER) cc_final: 0.5491 (t0) REVERT: F 181 GLU cc_start: 0.7361 (tp30) cc_final: 0.7099 (tp30) REVERT: F 219 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7378 (mm-40) REVERT: F 355 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: F 365 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: F 410 GLN cc_start: 0.7785 (mm110) cc_final: 0.7451 (mp10) REVERT: F 425 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.6256 (ttp80) REVERT: F 541 ILE cc_start: 0.6336 (OUTLIER) cc_final: 0.5721 (tt) REVERT: F 659 GLU cc_start: 0.8062 (pt0) cc_final: 0.7664 (pm20) REVERT: F 696 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8155 (tp-100) REVERT: F 697 GLU cc_start: 0.7549 (pp20) cc_final: 0.7156 (mm-30) REVERT: F 704 GLU cc_start: 0.7744 (tp30) cc_final: 0.6887 (mt-10) REVERT: E 1 MET cc_start: 0.6444 (ptt) cc_final: 0.5909 (tmm) REVERT: E 140 GLU cc_start: 0.6707 (pp20) cc_final: 0.6478 (pt0) REVERT: E 334 GLN cc_start: 0.7359 (mt0) cc_final: 0.7145 (pt0) REVERT: E 410 GLN cc_start: 0.7767 (mt0) cc_final: 0.7380 (mp10) REVERT: E 648 GLU cc_start: 0.8399 (tt0) cc_final: 0.8063 (tt0) REVERT: E 659 GLU cc_start: 0.8139 (pt0) cc_final: 0.7782 (pm20) REVERT: E 688 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7337 (mtp85) REVERT: D 61 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7364 (mp0) REVERT: D 140 GLU cc_start: 0.6693 (pp20) cc_final: 0.6224 (pt0) REVERT: D 160 ASN cc_start: 0.5456 (OUTLIER) cc_final: 0.4879 (t0) REVERT: D 188 LEU cc_start: 0.7519 (mt) cc_final: 0.7257 (mp) REVERT: D 213 ARG cc_start: 0.7171 (mmm160) cc_final: 0.6795 (tpt90) REVERT: D 410 GLN cc_start: 0.7423 (mp10) cc_final: 0.7217 (mp10) REVERT: D 455 LEU cc_start: 0.8274 (mp) cc_final: 0.8018 (mt) REVERT: D 488 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7781 (mtt90) REVERT: D 659 GLU cc_start: 0.8010 (pt0) cc_final: 0.7753 (pm20) REVERT: D 688 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7343 (mtp85) REVERT: D 697 GLU cc_start: 0.7877 (pt0) cc_final: 0.7112 (mm-30) REVERT: D 704 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6798 (mt-10) REVERT: C 97 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7676 (mm-40) REVERT: C 118 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 179 ARG cc_start: 0.6913 (mmm-85) cc_final: 0.6497 (tpt90) REVERT: C 243 GLU cc_start: 0.7511 (tt0) cc_final: 0.7073 (tt0) REVERT: C 331 ARG cc_start: 0.7047 (ttm-80) cc_final: 0.6559 (ttp80) REVERT: C 334 GLN cc_start: 0.7463 (mt0) cc_final: 0.7162 (pt0) REVERT: C 355 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: C 365 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: C 410 GLN cc_start: 0.7514 (mp10) cc_final: 0.7282 (mp10) REVERT: C 541 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6118 (tt) REVERT: C 581 ASP cc_start: 0.6445 (p0) cc_final: 0.5771 (t0) REVERT: C 659 GLU cc_start: 0.8158 (pt0) cc_final: 0.7661 (pm20) REVERT: C 688 ARG cc_start: 0.7570 (mtm110) cc_final: 0.7075 (mtp85) REVERT: C 690 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6436 (pm20) REVERT: C 697 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7263 (mm-30) REVERT: C 704 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6702 (mt-10) REVERT: B 78 LEU cc_start: 0.8569 (mp) cc_final: 0.8367 (mm) REVERT: B 97 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7406 (mm-40) REVERT: B 106 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: B 118 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 140 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6541 (mt-10) REVERT: B 179 ARG cc_start: 0.7160 (mmm160) cc_final: 0.6389 (mmp80) REVERT: B 181 GLU cc_start: 0.7518 (tp30) cc_final: 0.7219 (tp30) REVERT: B 193 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6079 (tp30) REVERT: B 331 ARG cc_start: 0.7067 (ttm-80) cc_final: 0.6623 (ttp80) REVERT: B 410 GLN cc_start: 0.7627 (mp10) cc_final: 0.7376 (mp10) REVERT: B 688 ARG cc_start: 0.7723 (mtm180) cc_final: 0.7053 (mtp85) REVERT: B 704 GLU cc_start: 0.7828 (tp30) cc_final: 0.6908 (mt-10) outliers start: 105 outliers final: 41 residues processed: 523 average time/residue: 0.7352 time to fit residues: 452.0436 Evaluate side-chains 474 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 413 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain G residue 713 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 271 TYR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ARG Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 336 optimal weight: 4.9990 chunk 157 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 325 optimal weight: 0.9990 chunk 475 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 315 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 334 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 413 GLN F 151 GLN F 429 GLN F 527 HIS ** F 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN E 429 GLN E 527 HIS D 249 GLN D 413 GLN D 527 HIS ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN B 413 GLN B 429 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.181587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135234 restraints weight = 40948.248| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.86 r_work: 0.3475 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39837 Z= 0.195 Angle : 0.569 6.840 54089 Z= 0.288 Chirality : 0.040 0.157 6027 Planarity : 0.004 0.050 7217 Dihedral : 4.549 50.325 5608 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.74 % Allowed : 15.82 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.12), residues: 5019 helix: 1.41 (0.10), residues: 2660 sheet: -0.07 (0.21), residues: 616 loop : 0.01 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 114 TYR 0.023 0.002 TYR D 557 PHE 0.021 0.002 PHE A 352 TRP 0.012 0.002 TRP F 250 HIS 0.009 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00442 (39837) covalent geometry : angle 0.56870 (54089) hydrogen bonds : bond 0.04156 ( 2207) hydrogen bonds : angle 4.43449 ( 6363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 413 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6935 (mt-10) REVERT: A 179 ARG cc_start: 0.7103 (mtp180) cc_final: 0.6243 (ttt-90) REVERT: A 223 GLN cc_start: 0.8589 (mp10) cc_final: 0.8220 (mp10) REVERT: A 225 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7549 (ttm-80) REVERT: A 327 LYS cc_start: 0.7518 (ttpp) cc_final: 0.6956 (ttmt) REVERT: A 356 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.6770 (pmm) REVERT: A 365 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: A 410 GLN cc_start: 0.7732 (mm110) cc_final: 0.7385 (mp10) REVERT: A 541 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6187 (mm) REVERT: A 597 ASN cc_start: 0.8720 (t0) cc_final: 0.8496 (t0) REVERT: A 659 GLU cc_start: 0.8212 (pt0) cc_final: 0.7810 (pm20) REVERT: A 665 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8153 (ttp-170) REVERT: A 688 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7238 (mtp85) REVERT: A 696 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8296 (tp-100) REVERT: A 708 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6714 (mtp180) REVERT: G 1 MET cc_start: 0.6882 (ttp) cc_final: 0.6310 (tmm) REVERT: G 118 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8052 (tp) REVERT: G 181 GLU cc_start: 0.7538 (tp30) cc_final: 0.7300 (tp30) REVERT: G 334 GLN cc_start: 0.7401 (mt0) cc_final: 0.7145 (pt0) REVERT: G 365 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: G 378 GLU cc_start: 0.7833 (tt0) cc_final: 0.7166 (tp30) REVERT: G 425 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: G 581 ASP cc_start: 0.6681 (p0) cc_final: 0.5865 (t70) REVERT: G 688 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7193 (mtp85) REVERT: G 696 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8094 (tp-100) REVERT: G 704 GLU cc_start: 0.7705 (tp30) cc_final: 0.6840 (mt-10) REVERT: F 1 MET cc_start: 0.6344 (ptt) cc_final: 0.5668 (tmm) REVERT: F 97 GLN cc_start: 0.7946 (mm110) cc_final: 0.7655 (mm-40) REVERT: F 118 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7702 (tp) REVERT: F 162 GLU cc_start: 0.3070 (OUTLIER) cc_final: 0.2294 (pp20) REVERT: F 181 GLU cc_start: 0.7406 (tp30) cc_final: 0.7126 (tp30) REVERT: F 219 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7372 (mm-40) REVERT: F 365 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: F 410 GLN cc_start: 0.7748 (mm110) cc_final: 0.7437 (mp10) REVERT: F 425 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6313 (ttp80) REVERT: F 490 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.6832 (mtp-110) REVERT: F 541 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.5809 (tt) REVERT: F 574 ASN cc_start: 0.7469 (p0) cc_final: 0.7254 (p0) REVERT: F 659 GLU cc_start: 0.8073 (pt0) cc_final: 0.7669 (pm20) REVERT: F 696 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8254 (tp-100) REVERT: F 697 GLU cc_start: 0.7587 (pp20) cc_final: 0.7171 (mm-30) REVERT: F 704 GLU cc_start: 0.7776 (tp30) cc_final: 0.6870 (mt-10) REVERT: E 1 MET cc_start: 0.6629 (ptt) cc_final: 0.5911 (tmm) REVERT: E 140 GLU cc_start: 0.6758 (pp20) cc_final: 0.6533 (pt0) REVERT: E 298 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7584 (mmp80) REVERT: E 334 GLN cc_start: 0.7450 (mt0) cc_final: 0.7191 (pt0) REVERT: E 410 GLN cc_start: 0.7801 (mt0) cc_final: 0.7391 (mp10) REVERT: E 659 GLU cc_start: 0.8243 (pt0) cc_final: 0.7880 (pm20) REVERT: E 688 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7344 (mtp85) REVERT: D 61 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7404 (mp0) REVERT: D 87 LYS cc_start: 0.7564 (tttt) cc_final: 0.7364 (tttt) REVERT: D 140 GLU cc_start: 0.6652 (pp20) cc_final: 0.6195 (pt0) REVERT: D 160 ASN cc_start: 0.5431 (OUTLIER) cc_final: 0.4842 (t0) REVERT: D 188 LEU cc_start: 0.7556 (mt) cc_final: 0.7288 (mp) REVERT: D 213 ARG cc_start: 0.7144 (mmm160) cc_final: 0.6890 (tpt90) REVERT: D 223 GLN cc_start: 0.8633 (mp10) cc_final: 0.8276 (mp-120) REVERT: D 410 GLN cc_start: 0.7443 (mp10) cc_final: 0.7220 (mp10) REVERT: D 455 LEU cc_start: 0.8422 (mp) cc_final: 0.8188 (mt) REVERT: D 488 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7776 (mtt90) REVERT: D 659 GLU cc_start: 0.8080 (pt0) cc_final: 0.7846 (pm20) REVERT: D 688 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7318 (mtp85) REVERT: D 697 GLU cc_start: 0.7942 (pt0) cc_final: 0.7135 (mm-30) REVERT: D 704 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6794 (mt-10) REVERT: C 97 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7691 (mm-40) REVERT: C 179 ARG cc_start: 0.6992 (mmm-85) cc_final: 0.6571 (tpt90) REVERT: C 225 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7531 (ttm-80) REVERT: C 243 GLU cc_start: 0.7549 (tt0) cc_final: 0.7090 (tt0) REVERT: C 320 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: C 331 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6625 (ttp80) REVERT: C 334 GLN cc_start: 0.7516 (mt0) cc_final: 0.7178 (pt0) REVERT: C 355 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: C 365 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: C 410 GLN cc_start: 0.7539 (mp10) cc_final: 0.7305 (mp10) REVERT: C 541 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6203 (tt) REVERT: C 581 ASP cc_start: 0.6543 (p0) cc_final: 0.5798 (t0) REVERT: C 659 GLU cc_start: 0.8185 (pt0) cc_final: 0.7717 (pm20) REVERT: C 665 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8069 (ttp-170) REVERT: C 688 ARG cc_start: 0.7682 (mtm110) cc_final: 0.7160 (mtp85) REVERT: C 690 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6455 (pm20) REVERT: C 697 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7332 (mm-30) REVERT: C 704 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6768 (mt-10) REVERT: B 97 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7498 (mm-40) REVERT: B 106 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: B 118 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7835 (tp) REVERT: B 140 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6515 (mt-10) REVERT: B 181 GLU cc_start: 0.7542 (tp30) cc_final: 0.7245 (tp30) REVERT: B 193 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6118 (tp30) REVERT: B 331 ARG cc_start: 0.7069 (ttm-80) cc_final: 0.6593 (ttp80) REVERT: B 410 GLN cc_start: 0.7611 (mp10) cc_final: 0.7351 (mp10) REVERT: B 688 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7099 (mtp85) REVERT: B 704 GLU cc_start: 0.7936 (tp30) cc_final: 0.7002 (mt-10) outliers start: 109 outliers final: 54 residues processed: 502 average time/residue: 0.7604 time to fit residues: 448.2038 Evaluate side-chains 474 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 410 GLN Chi-restraints excluded: chain G residue 425 ARG Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 713 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 417 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 619 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 665 ARG Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 110 optimal weight: 0.0570 chunk 67 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 chunk 193 optimal weight: 0.3980 chunk 288 optimal weight: 0.9980 chunk 447 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 486 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 413 GLN F 151 GLN E 413 GLN E 527 HIS D 249 GLN D 413 GLN D 527 HIS ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 429 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.186667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142546 restraints weight = 41254.762| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.88 r_work: 0.3566 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39837 Z= 0.114 Angle : 0.509 11.630 54089 Z= 0.256 Chirality : 0.037 0.156 6027 Planarity : 0.004 0.049 7217 Dihedral : 4.302 53.761 5608 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.36 % Allowed : 16.55 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.12), residues: 5019 helix: 1.67 (0.10), residues: 2653 sheet: -0.11 (0.21), residues: 630 loop : 0.11 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 114 TYR 0.018 0.002 TYR E 557 PHE 0.019 0.001 PHE E 221 TRP 0.011 0.001 TRP B 511 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00243 (39837) covalent geometry : angle 0.50892 (54089) hydrogen bonds : bond 0.03753 ( 2207) hydrogen bonds : angle 4.25738 ( 6363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 428 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6957 (mt-10) REVERT: A 188 LEU cc_start: 0.7733 (mt) cc_final: 0.7431 (mm) REVERT: A 223 GLN cc_start: 0.8518 (mp10) cc_final: 0.8207 (mp10) REVERT: A 327 LYS cc_start: 0.7520 (ttpp) cc_final: 0.6856 (ttmt) REVERT: A 331 ARG cc_start: 0.7299 (mmm160) cc_final: 0.6534 (ttt-90) REVERT: A 356 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.6661 (pmm) REVERT: A 365 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: A 410 GLN cc_start: 0.7675 (mm110) cc_final: 0.7431 (mp10) REVERT: A 541 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6179 (mm) REVERT: A 597 ASN cc_start: 0.8696 (t0) cc_final: 0.8471 (t0) REVERT: A 659 GLU cc_start: 0.8124 (pt0) cc_final: 0.7771 (pm20) REVERT: A 688 ARG cc_start: 0.7575 (mtm110) cc_final: 0.7174 (mtp85) REVERT: A 696 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8202 (tp-100) REVERT: A 708 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6802 (mtp180) REVERT: G 118 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8006 (tp) REVERT: G 181 GLU cc_start: 0.7527 (tp30) cc_final: 0.7233 (tp30) REVERT: G 298 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7553 (mpt180) REVERT: G 365 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: G 378 GLU cc_start: 0.7721 (tt0) cc_final: 0.7083 (tp30) REVERT: G 581 ASP cc_start: 0.6564 (p0) cc_final: 0.5788 (t70) REVERT: G 659 GLU cc_start: 0.8180 (pt0) cc_final: 0.7775 (pm20) REVERT: G 688 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7217 (mtp85) REVERT: G 696 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7947 (tp-100) REVERT: G 704 GLU cc_start: 0.7700 (tp30) cc_final: 0.6928 (mt-10) REVERT: F 1 MET cc_start: 0.6280 (ptt) cc_final: 0.5671 (tmm) REVERT: F 97 GLN cc_start: 0.7917 (mm110) cc_final: 0.7645 (mm-40) REVERT: F 118 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7688 (tp) REVERT: F 140 GLU cc_start: 0.6717 (pp20) cc_final: 0.6400 (pt0) REVERT: F 181 GLU cc_start: 0.7534 (tp30) cc_final: 0.7217 (tp30) REVERT: F 219 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7471 (mm-40) REVERT: F 365 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: F 410 GLN cc_start: 0.7797 (mm110) cc_final: 0.7525 (mp10) REVERT: F 425 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6179 (ttp80) REVERT: F 541 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.5804 (tt) REVERT: F 574 ASN cc_start: 0.7209 (p0) cc_final: 0.6999 (p0) REVERT: F 659 GLU cc_start: 0.8095 (pt0) cc_final: 0.7734 (pm20) REVERT: F 697 GLU cc_start: 0.7528 (pp20) cc_final: 0.7187 (mm-30) REVERT: F 704 GLU cc_start: 0.7867 (tp30) cc_final: 0.7004 (mt-10) REVERT: E 1 MET cc_start: 0.6545 (ptt) cc_final: 0.6006 (tmm) REVERT: E 140 GLU cc_start: 0.6754 (pp20) cc_final: 0.6552 (pt0) REVERT: E 298 ARG cc_start: 0.7875 (mmt-90) cc_final: 0.7606 (mmp80) REVERT: E 410 GLN cc_start: 0.7799 (mt0) cc_final: 0.7399 (mp10) REVERT: E 648 GLU cc_start: 0.8379 (tt0) cc_final: 0.8055 (tt0) REVERT: E 659 GLU cc_start: 0.8143 (pt0) cc_final: 0.7832 (pm20) REVERT: E 688 ARG cc_start: 0.7838 (mtm180) cc_final: 0.7407 (mtp85) REVERT: D 61 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7353 (mp0) REVERT: D 140 GLU cc_start: 0.6698 (pp20) cc_final: 0.6246 (pt0) REVERT: D 160 ASN cc_start: 0.5452 (OUTLIER) cc_final: 0.4898 (t0) REVERT: D 188 LEU cc_start: 0.7658 (mt) cc_final: 0.7385 (mp) REVERT: D 213 ARG cc_start: 0.7110 (mmm160) cc_final: 0.6725 (tpt90) REVERT: D 223 GLN cc_start: 0.8601 (mp10) cc_final: 0.8257 (mp-120) REVERT: D 273 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6696 (p) REVERT: D 455 LEU cc_start: 0.8319 (mp) cc_final: 0.8063 (mt) REVERT: D 488 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7773 (mtt90) REVERT: D 688 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7392 (mtp85) REVERT: D 697 GLU cc_start: 0.7939 (pt0) cc_final: 0.7141 (mm-30) REVERT: D 704 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6852 (mt-10) REVERT: C 97 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7664 (mm-40) REVERT: C 179 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6680 (tpt90) REVERT: C 225 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7487 (ttm-80) REVERT: C 243 GLU cc_start: 0.7486 (tt0) cc_final: 0.7046 (tt0) REVERT: C 331 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6594 (ttp80) REVERT: C 355 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: C 365 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: C 410 GLN cc_start: 0.7532 (mp10) cc_final: 0.7305 (mp10) REVERT: C 581 ASP cc_start: 0.6413 (p0) cc_final: 0.5753 (t0) REVERT: C 659 GLU cc_start: 0.8128 (pt0) cc_final: 0.7701 (pm20) REVERT: C 688 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7194 (mtp85) REVERT: C 690 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6584 (pm20) REVERT: C 697 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7322 (mm-30) REVERT: C 704 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6846 (mt-10) REVERT: B 78 LEU cc_start: 0.8569 (mp) cc_final: 0.8358 (mm) REVERT: B 97 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7489 (mm-40) REVERT: B 106 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: B 118 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 140 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6533 (mt-10) REVERT: B 181 GLU cc_start: 0.7588 (tp30) cc_final: 0.7335 (tp30) REVERT: B 193 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6250 (tp30) REVERT: B 331 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6577 (ttp80) REVERT: B 350 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: B 410 GLN cc_start: 0.7576 (mp10) cc_final: 0.7330 (mp10) REVERT: B 659 GLU cc_start: 0.8248 (pt0) cc_final: 0.7812 (pm20) REVERT: B 688 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7113 (mtp85) REVERT: B 704 GLU cc_start: 0.7941 (tp30) cc_final: 0.7037 (mt-10) outliers start: 94 outliers final: 47 residues processed: 504 average time/residue: 0.7510 time to fit residues: 446.5455 Evaluate side-chains 462 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 397 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain G residue 713 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 271 TYR Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 271 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 84 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 340 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 479 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 443 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN G 429 GLN G 713 HIS F 560 HIS E 527 HIS D 413 GLN ** D 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN B 413 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133318 restraints weight = 41325.188| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.90 r_work: 0.3446 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 39837 Z= 0.260 Angle : 0.624 11.060 54089 Z= 0.316 Chirality : 0.042 0.163 6027 Planarity : 0.005 0.049 7217 Dihedral : 4.702 49.015 5608 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.79 % Allowed : 16.70 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.12), residues: 5019 helix: 1.31 (0.10), residues: 2646 sheet: -0.04 (0.21), residues: 616 loop : 0.08 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 114 TYR 0.027 0.003 TYR D 557 PHE 0.029 0.002 PHE A 352 TRP 0.016 0.002 TRP G 250 HIS 0.011 0.002 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00596 (39837) covalent geometry : angle 0.62437 (54089) hydrogen bonds : bond 0.04414 ( 2207) hydrogen bonds : angle 4.53244 ( 6363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 414 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 140 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6924 (mt-10) REVERT: A 188 LEU cc_start: 0.7683 (mt) cc_final: 0.7351 (mm) REVERT: A 223 GLN cc_start: 0.8624 (mp10) cc_final: 0.8292 (mp-120) REVERT: A 225 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7520 (ttm-80) REVERT: A 327 LYS cc_start: 0.7480 (ttpp) cc_final: 0.6801 (ttmt) REVERT: A 331 ARG cc_start: 0.7392 (mmm160) cc_final: 0.6656 (ttt-90) REVERT: A 356 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6779 (pmm) REVERT: A 365 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: A 410 GLN cc_start: 0.7693 (mm110) cc_final: 0.7392 (mp10) REVERT: A 541 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6182 (mm) REVERT: A 597 ASN cc_start: 0.8745 (t0) cc_final: 0.8530 (t0) REVERT: A 659 GLU cc_start: 0.8242 (pt0) cc_final: 0.7868 (pm20) REVERT: A 665 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8118 (ttp-170) REVERT: A 688 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7252 (mtp85) REVERT: A 696 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8344 (tp-100) REVERT: A 708 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6833 (mtp180) REVERT: G 118 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8054 (tp) REVERT: G 181 GLU cc_start: 0.7526 (tp30) cc_final: 0.7223 (tp30) REVERT: G 365 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: G 418 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7023 (mmm160) REVERT: G 581 ASP cc_start: 0.6801 (p0) cc_final: 0.5938 (t70) REVERT: G 688 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7245 (mtp85) REVERT: G 696 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8139 (tp-100) REVERT: G 704 GLU cc_start: 0.7760 (tp30) cc_final: 0.6895 (mt-10) REVERT: F 1 MET cc_start: 0.6697 (ptt) cc_final: 0.5856 (tmm) REVERT: F 97 GLN cc_start: 0.8012 (mm110) cc_final: 0.7712 (mm-40) REVERT: F 140 GLU cc_start: 0.6659 (pp20) cc_final: 0.6264 (pt0) REVERT: F 181 GLU cc_start: 0.7443 (tp30) cc_final: 0.7081 (tp30) REVERT: F 219 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7364 (mm-40) REVERT: F 365 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: F 410 GLN cc_start: 0.7719 (mm110) cc_final: 0.7434 (mp10) REVERT: F 425 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6386 (ttp80) REVERT: F 490 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6652 (mtp-110) REVERT: F 541 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6236 (tt) REVERT: F 574 ASN cc_start: 0.7609 (p0) cc_final: 0.7382 (p0) REVERT: F 659 GLU cc_start: 0.8183 (pt0) cc_final: 0.7783 (pm20) REVERT: F 697 GLU cc_start: 0.7675 (pp20) cc_final: 0.7273 (mm-30) REVERT: F 704 GLU cc_start: 0.7894 (tp30) cc_final: 0.6963 (mt-10) REVERT: E 1 MET cc_start: 0.6859 (ptt) cc_final: 0.6095 (tmm) REVERT: E 140 GLU cc_start: 0.6745 (pp20) cc_final: 0.6513 (pt0) REVERT: E 298 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7565 (mmp80) REVERT: E 410 GLN cc_start: 0.7829 (mt0) cc_final: 0.7404 (mp10) REVERT: E 659 GLU cc_start: 0.8304 (pt0) cc_final: 0.7925 (pm20) REVERT: E 688 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7360 (mmp-170) REVERT: D 61 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7369 (mp0) REVERT: D 140 GLU cc_start: 0.6628 (pp20) cc_final: 0.6176 (pt0) REVERT: D 188 LEU cc_start: 0.7570 (mt) cc_final: 0.7296 (mp) REVERT: D 213 ARG cc_start: 0.7198 (mmm160) cc_final: 0.6884 (tpt90) REVERT: D 223 GLN cc_start: 0.8655 (mp10) cc_final: 0.8327 (mp-120) REVERT: D 276 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7302 (mtp180) REVERT: D 455 LEU cc_start: 0.8488 (mp) cc_final: 0.8256 (mt) REVERT: D 488 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7921 (mtt90) REVERT: D 688 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7375 (mmp-170) REVERT: D 697 GLU cc_start: 0.7994 (pt0) cc_final: 0.7126 (mm-30) REVERT: D 704 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6908 (mt-10) REVERT: C 1 MET cc_start: 0.7026 (ptm) cc_final: 0.6543 (ppp) REVERT: C 97 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7752 (mm-40) REVERT: C 108 LEU cc_start: 0.8309 (mt) cc_final: 0.8088 (mp) REVERT: C 179 ARG cc_start: 0.7043 (mmm-85) cc_final: 0.6594 (tpt90) REVERT: C 243 GLU cc_start: 0.7602 (tt0) cc_final: 0.7132 (tt0) REVERT: C 331 ARG cc_start: 0.7132 (ttm-80) cc_final: 0.6688 (ttp80) REVERT: C 355 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8433 (mt0) REVERT: C 365 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: C 410 GLN cc_start: 0.7504 (mp10) cc_final: 0.7288 (mp10) REVERT: C 429 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: C 541 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6358 (tt) REVERT: C 581 ASP cc_start: 0.6561 (p0) cc_final: 0.5825 (t0) REVERT: C 659 GLU cc_start: 0.8180 (pt0) cc_final: 0.7713 (pm20) REVERT: C 688 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7260 (mtp85) REVERT: C 690 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6574 (pm20) REVERT: C 697 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7356 (mm-30) REVERT: C 704 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7004 (mt-10) REVERT: B 97 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7711 (mm-40) REVERT: B 106 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: B 118 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 140 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6547 (mt-10) REVERT: B 181 GLU cc_start: 0.7483 (tp30) cc_final: 0.7275 (tp30) REVERT: B 331 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6651 (ttm110) REVERT: B 410 GLN cc_start: 0.7604 (mp10) cc_final: 0.7357 (mp10) REVERT: B 688 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7130 (mmp-170) REVERT: B 704 GLU cc_start: 0.8003 (tp30) cc_final: 0.7087 (mt-10) outliers start: 111 outliers final: 60 residues processed: 498 average time/residue: 0.8072 time to fit residues: 470.6132 Evaluate side-chains 479 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 397 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 410 GLN Chi-restraints excluded: chain G residue 418 ARG Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 713 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 417 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 490 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 469 optimal weight: 2.9990 chunk 489 optimal weight: 0.0870 chunk 406 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 470 optimal weight: 0.9980 chunk 443 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 380 optimal weight: 10.0000 chunk 384 optimal weight: 0.0980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN F 413 GLN F 560 HIS E 527 HIS D 293 ASN D 527 HIS ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN B 560 HIS B 597 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.184413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139437 restraints weight = 41091.836| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.89 r_work: 0.3515 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39837 Z= 0.113 Angle : 0.522 10.949 54089 Z= 0.263 Chirality : 0.038 0.157 6027 Planarity : 0.004 0.048 7217 Dihedral : 4.370 54.194 5608 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.04 % Allowed : 17.61 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.12), residues: 5019 helix: 1.61 (0.10), residues: 2660 sheet: -0.01 (0.21), residues: 602 loop : 0.25 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 114 TYR 0.018 0.002 TYR B 557 PHE 0.022 0.001 PHE E 221 TRP 0.016 0.001 TRP B 323 HIS 0.021 0.001 HIS G 713 Details of bonding type rmsd covalent geometry : bond 0.00239 (39837) covalent geometry : angle 0.52236 (54089) hydrogen bonds : bond 0.03805 ( 2207) hydrogen bonds : angle 4.29103 ( 6363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 418 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7903 (tp) REVERT: A 140 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6899 (mt-10) REVERT: A 188 LEU cc_start: 0.7676 (mt) cc_final: 0.7395 (mm) REVERT: A 223 GLN cc_start: 0.8533 (mp10) cc_final: 0.8173 (mp10) REVERT: A 225 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7486 (ttm-80) REVERT: A 327 LYS cc_start: 0.7502 (ttpp) cc_final: 0.6833 (ttmt) REVERT: A 331 ARG cc_start: 0.7386 (mmm160) cc_final: 0.6666 (ttt-90) REVERT: A 356 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.6713 (pmm) REVERT: A 365 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: A 410 GLN cc_start: 0.7724 (mm110) cc_final: 0.7450 (mp10) REVERT: A 541 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6189 (mm) REVERT: A 597 ASN cc_start: 0.8664 (t0) cc_final: 0.8445 (t0) REVERT: A 659 GLU cc_start: 0.8151 (pt0) cc_final: 0.7833 (pm20) REVERT: A 688 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7154 (mtp85) REVERT: A 708 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6818 (mtp180) REVERT: G 118 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8042 (tp) REVERT: G 181 GLU cc_start: 0.7580 (tp30) cc_final: 0.7296 (tp30) REVERT: G 298 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.7486 (mpt180) REVERT: G 365 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: G 418 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7046 (mmm160) REVERT: G 581 ASP cc_start: 0.6624 (p0) cc_final: 0.5849 (t70) REVERT: G 659 GLU cc_start: 0.8200 (pt0) cc_final: 0.7781 (pm20) REVERT: G 688 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7176 (mtp85) REVERT: G 696 GLN cc_start: 0.8290 (tp-100) cc_final: 0.8033 (tp-100) REVERT: G 704 GLU cc_start: 0.7727 (tp30) cc_final: 0.6871 (mt-10) REVERT: F 1 MET cc_start: 0.6512 (ptt) cc_final: 0.5704 (tmm) REVERT: F 97 GLN cc_start: 0.7923 (mm110) cc_final: 0.7634 (mm-40) REVERT: F 140 GLU cc_start: 0.6721 (pp20) cc_final: 0.6378 (pt0) REVERT: F 181 GLU cc_start: 0.7517 (tp30) cc_final: 0.7194 (tp30) REVERT: F 219 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7385 (mm-40) REVERT: F 365 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: F 410 GLN cc_start: 0.7772 (mm110) cc_final: 0.7515 (mp10) REVERT: F 425 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6139 (ttp80) REVERT: F 541 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.5939 (tt) REVERT: F 544 LYS cc_start: 0.8453 (ttmp) cc_final: 0.8223 (ttmt) REVERT: F 574 ASN cc_start: 0.7312 (p0) cc_final: 0.7105 (p0) REVERT: F 659 GLU cc_start: 0.8114 (pt0) cc_final: 0.7730 (pm20) REVERT: F 697 GLU cc_start: 0.7620 (pp20) cc_final: 0.7211 (mm-30) REVERT: F 704 GLU cc_start: 0.7832 (tp30) cc_final: 0.6949 (mt-10) REVERT: E 1 MET cc_start: 0.6629 (ptt) cc_final: 0.6022 (tmm) REVERT: E 106 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7357 (mm-30) REVERT: E 298 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7603 (mmp80) REVERT: E 410 GLN cc_start: 0.7816 (mt0) cc_final: 0.7355 (mp10) REVERT: E 429 GLN cc_start: 0.8647 (mt0) cc_final: 0.8405 (mp10) REVERT: E 648 GLU cc_start: 0.8423 (tt0) cc_final: 0.8097 (tt0) REVERT: E 659 GLU cc_start: 0.8156 (pt0) cc_final: 0.7793 (pm20) REVERT: E 688 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7425 (mmp-170) REVERT: E 696 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8377 (tp40) REVERT: D 61 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7339 (mp0) REVERT: D 140 GLU cc_start: 0.6655 (pp20) cc_final: 0.6220 (pt0) REVERT: D 160 ASN cc_start: 0.5378 (OUTLIER) cc_final: 0.4823 (t0) REVERT: D 188 LEU cc_start: 0.7519 (mt) cc_final: 0.7249 (mp) REVERT: D 193 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6233 (tp30) REVERT: D 213 ARG cc_start: 0.7048 (mmm160) cc_final: 0.6761 (tpt90) REVERT: D 273 THR cc_start: 0.7190 (OUTLIER) cc_final: 0.6732 (p) REVERT: D 298 ARG cc_start: 0.7972 (mpt180) cc_final: 0.7700 (mpt180) REVERT: D 455 LEU cc_start: 0.8409 (mp) cc_final: 0.8178 (mt) REVERT: D 488 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7784 (mtt90) REVERT: D 688 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7334 (mtp85) REVERT: D 697 GLU cc_start: 0.7925 (pt0) cc_final: 0.7094 (mm-30) REVERT: D 704 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6792 (mt-10) REVERT: C 97 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7710 (mm-40) REVERT: C 179 ARG cc_start: 0.7043 (mmm-85) cc_final: 0.6627 (tpt90) REVERT: C 225 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7453 (ttm-80) REVERT: C 243 GLU cc_start: 0.7521 (tt0) cc_final: 0.7094 (tt0) REVERT: C 331 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6583 (ttp80) REVERT: C 365 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: C 410 GLN cc_start: 0.7469 (mp10) cc_final: 0.7231 (mp10) REVERT: C 541 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6288 (tt) REVERT: C 581 ASP cc_start: 0.6481 (p0) cc_final: 0.5799 (t0) REVERT: C 659 GLU cc_start: 0.8193 (pt0) cc_final: 0.7739 (pm20) REVERT: C 688 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7244 (mtp85) REVERT: C 690 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6519 (pm20) REVERT: C 697 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7306 (mm-30) REVERT: C 704 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6884 (mt-10) REVERT: B 97 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7699 (mm-40) REVERT: B 106 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: B 114 ARG cc_start: 0.7399 (mmp80) cc_final: 0.7168 (mmp80) REVERT: B 118 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7832 (tp) REVERT: B 140 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6541 (mt-10) REVERT: B 181 GLU cc_start: 0.7502 (tp30) cc_final: 0.7277 (tp30) REVERT: B 331 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6686 (ttm110) REVERT: B 350 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: B 410 GLN cc_start: 0.7575 (mp10) cc_final: 0.7328 (mp10) REVERT: B 455 LEU cc_start: 0.8434 (mp) cc_final: 0.8199 (mt) REVERT: B 581 ASP cc_start: 0.7004 (p0) cc_final: 0.6138 (t0) REVERT: B 659 GLU cc_start: 0.8289 (pt0) cc_final: 0.7826 (pm20) REVERT: B 688 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7053 (mmp-170) REVERT: B 704 GLU cc_start: 0.7899 (tp30) cc_final: 0.6963 (mt-10) outliers start: 81 outliers final: 47 residues processed: 482 average time/residue: 0.7633 time to fit residues: 431.4297 Evaluate side-chains 466 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 418 ARG Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain G residue 713 HIS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 271 TYR Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 329 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 469 optimal weight: 4.9990 chunk 456 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 350 optimal weight: 7.9990 chunk 412 optimal weight: 1.9990 chunk 407 optimal weight: 2.9990 chunk 445 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN F 355 GLN F 560 HIS E 413 GLN E 527 HIS D 293 ASN ** D 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.181335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136779 restraints weight = 41231.783| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.86 r_work: 0.3466 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 39837 Z= 0.242 Angle : 0.606 10.690 54089 Z= 0.306 Chirality : 0.042 0.233 6027 Planarity : 0.005 0.049 7217 Dihedral : 4.639 50.329 5608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.99 % Allowed : 18.01 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.12), residues: 5019 helix: 1.33 (0.10), residues: 2702 sheet: -0.05 (0.21), residues: 616 loop : 0.12 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 114 TYR 0.026 0.002 TYR D 557 PHE 0.031 0.002 PHE A 352 TRP 0.023 0.002 TRP B 323 HIS 0.009 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00558 (39837) covalent geometry : angle 0.60567 (54089) hydrogen bonds : bond 0.04287 ( 2207) hydrogen bonds : angle 4.45893 ( 6363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 406 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 140 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6916 (mt-10) REVERT: A 188 LEU cc_start: 0.7714 (mt) cc_final: 0.7413 (mm) REVERT: A 223 GLN cc_start: 0.8630 (mp10) cc_final: 0.8297 (mp-120) REVERT: A 225 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7533 (ttm-80) REVERT: A 327 LYS cc_start: 0.7448 (ttpp) cc_final: 0.6791 (ttmt) REVERT: A 331 ARG cc_start: 0.7373 (mmm160) cc_final: 0.6668 (ttt-90) REVERT: A 356 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.6783 (pmm) REVERT: A 365 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: A 410 GLN cc_start: 0.7720 (mm110) cc_final: 0.7422 (mp10) REVERT: A 541 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6224 (mm) REVERT: A 597 ASN cc_start: 0.8737 (t0) cc_final: 0.8523 (t0) REVERT: A 659 GLU cc_start: 0.8206 (pt0) cc_final: 0.7857 (pm20) REVERT: A 688 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7246 (mtp85) REVERT: A 708 ARG cc_start: 0.7130 (mtm-85) cc_final: 0.6868 (mtp180) REVERT: G 118 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8055 (tp) REVERT: G 181 GLU cc_start: 0.7574 (tp30) cc_final: 0.7280 (tp30) REVERT: G 298 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7583 (mpt180) REVERT: G 365 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: G 418 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7053 (mmm160) REVERT: G 581 ASP cc_start: 0.6807 (p0) cc_final: 0.5973 (t70) REVERT: G 688 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7259 (mtp85) REVERT: G 696 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8094 (tp-100) REVERT: G 704 GLU cc_start: 0.7773 (tp30) cc_final: 0.6931 (mt-10) REVERT: F 1 MET cc_start: 0.6662 (ptt) cc_final: 0.5853 (tmm) REVERT: F 97 GLN cc_start: 0.8016 (mm110) cc_final: 0.7716 (mm-40) REVERT: F 140 GLU cc_start: 0.6694 (pp20) cc_final: 0.6323 (pt0) REVERT: F 181 GLU cc_start: 0.7476 (tp30) cc_final: 0.7141 (tp30) REVERT: F 219 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7340 (mm-40) REVERT: F 365 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: F 410 GLN cc_start: 0.7737 (mm110) cc_final: 0.7494 (mp10) REVERT: F 425 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6332 (ttp80) REVERT: F 541 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.5639 (mm) REVERT: F 574 ASN cc_start: 0.7565 (p0) cc_final: 0.7342 (p0) REVERT: F 659 GLU cc_start: 0.8096 (pt0) cc_final: 0.7710 (pm20) REVERT: F 697 GLU cc_start: 0.7627 (pp20) cc_final: 0.7249 (mm-30) REVERT: F 704 GLU cc_start: 0.7909 (tp30) cc_final: 0.6969 (mt-10) REVERT: E 1 MET cc_start: 0.6862 (ptt) cc_final: 0.6106 (tmm) REVERT: E 298 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7574 (mmp80) REVERT: E 410 GLN cc_start: 0.7837 (mt0) cc_final: 0.7387 (mp10) REVERT: E 659 GLU cc_start: 0.8240 (pt0) cc_final: 0.7881 (pm20) REVERT: E 688 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7384 (mmp-170) REVERT: D 61 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7380 (mp0) REVERT: D 140 GLU cc_start: 0.6707 (pp20) cc_final: 0.6273 (pt0) REVERT: D 188 LEU cc_start: 0.7584 (mt) cc_final: 0.7308 (mp) REVERT: D 193 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6229 (tp30) REVERT: D 213 ARG cc_start: 0.7148 (mmm160) cc_final: 0.6902 (tpt90) REVERT: D 223 GLN cc_start: 0.8655 (mp10) cc_final: 0.8327 (mp-120) REVERT: D 488 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7910 (mtt90) REVERT: D 688 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7309 (mmp-170) REVERT: D 690 GLU cc_start: 0.7433 (pm20) cc_final: 0.7032 (pm20) REVERT: D 697 GLU cc_start: 0.7949 (pt0) cc_final: 0.7096 (mm-30) REVERT: D 704 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6929 (mt-10) REVERT: C 1 MET cc_start: 0.7031 (ptm) cc_final: 0.6604 (ppp) REVERT: C 97 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7742 (mm-40) REVERT: C 179 ARG cc_start: 0.7093 (mmm-85) cc_final: 0.6634 (tpt90) REVERT: C 243 GLU cc_start: 0.7585 (tt0) cc_final: 0.7135 (tt0) REVERT: C 331 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6674 (ttp80) REVERT: C 365 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: C 455 LEU cc_start: 0.8458 (mp) cc_final: 0.8210 (mt) REVERT: C 541 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6410 (tt) REVERT: C 581 ASP cc_start: 0.6579 (p0) cc_final: 0.5853 (t0) REVERT: C 659 GLU cc_start: 0.8145 (pt0) cc_final: 0.7696 (pm20) REVERT: C 688 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7379 (mtp85) REVERT: C 690 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6728 (pm20) REVERT: C 697 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7375 (mm-30) REVERT: C 704 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6920 (mt-10) REVERT: B 97 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7702 (mm-40) REVERT: B 106 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: B 118 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 140 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6620 (mt-10) REVERT: B 181 GLU cc_start: 0.7497 (tp30) cc_final: 0.7260 (tp30) REVERT: B 331 ARG cc_start: 0.7131 (ttm-80) cc_final: 0.6712 (ttm110) REVERT: B 410 GLN cc_start: 0.7568 (mp10) cc_final: 0.7342 (mp10) REVERT: B 559 GLU cc_start: 0.5842 (pm20) cc_final: 0.5639 (mp0) REVERT: B 688 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7123 (mmp-170) REVERT: B 704 GLU cc_start: 0.7979 (tp30) cc_final: 0.7067 (mt-10) outliers start: 79 outliers final: 49 residues processed: 470 average time/residue: 0.7507 time to fit residues: 412.9701 Evaluate side-chains 465 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 399 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 365 GLU Chi-restraints excluded: chain G residue 418 ARG Chi-restraints excluded: chain G residue 438 VAL Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 568 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 271 TYR Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 488 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 713 HIS Chi-restraints excluded: chain B residue 718 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 444 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 447 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 chunk 360 optimal weight: 0.5980 chunk 495 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** F 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN E 527 HIS D 293 ASN D 527 HIS ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.184646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140565 restraints weight = 41633.892| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.74 r_work: 0.3504 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39837 Z= 0.127 Angle : 0.530 14.413 54089 Z= 0.266 Chirality : 0.038 0.157 6027 Planarity : 0.004 0.048 7217 Dihedral : 4.382 54.919 5608 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.96 % Allowed : 18.08 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.12), residues: 5019 helix: 1.58 (0.10), residues: 2702 sheet: -0.06 (0.21), residues: 616 loop : 0.26 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 114 TYR 0.021 0.002 TYR D 557 PHE 0.022 0.001 PHE E 221 TRP 0.021 0.001 TRP C 323 HIS 0.003 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00275 (39837) covalent geometry : angle 0.53027 (54089) hydrogen bonds : bond 0.03822 ( 2207) hydrogen bonds : angle 4.26116 ( 6363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15356.75 seconds wall clock time: 260 minutes 47.99 seconds (15647.99 seconds total)