Starting phenix.real_space_refine on Sun Jul 5 19:08:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fxi_29534/07_2026/8fxi_29534_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fxi_29534/07_2026/8fxi_29534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fxi_29534/07_2026/8fxi_29534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fxi_29534/07_2026/8fxi_29534.map" model { file = "/net/cci-nas-00/data/ceres_data/8fxi_29534/07_2026/8fxi_29534_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fxi_29534/07_2026/8fxi_29534_neut.cif" } resolution = 2.7 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= 0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 18884 2.51 5 N 4983 2.21 5 O 5680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29641 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4777 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain breaks: 3 Chain: "B" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4921 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 25, 'TRANS': 589} Chain breaks: 1 Chain: "C" Number of atoms: 5033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5033 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 25, 'TRANS': 604} Chain: "D" Number of atoms: 5033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5033 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 25, 'TRANS': 604} Chain: "E" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4921 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 25, 'TRANS': 589} Chain breaks: 1 Chain: "F" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4777 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain breaks: 3 Chain: "G" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'YHZ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.77, per 1000 atoms: 0.23 Number of scatterers: 29641 At special positions: 0 Unit cell: (146.475, 180.225, 159.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 6 15.00 Mg 4 11.99 O 5680 8.00 N 4983 7.00 C 18884 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6952 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 30 sheets defined 34.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.876A pdb=" N TYR A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.824A pdb=" N ILE A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.650A pdb=" N LEU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 135 removed outlier: 3.625A pdb=" N ILE A 135 " --> pdb=" O TRP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.971A pdb=" N GLN A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.788A pdb=" N SER A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 336 through 345 removed outlier: 4.148A pdb=" N SER A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 408 through 420 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.909A pdb=" N PHE A 478 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.701A pdb=" N ALA A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'A' and resid 496 through 509 Processing helix chain 'A' and resid 536 through 547 removed outlier: 4.164A pdb=" N ASN A 540 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 624 through 630 removed outlier: 3.667A pdb=" N TYR A 628 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.919A pdb=" N TYR B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.756A pdb=" N LEU B 69 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 71 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.706A pdb=" N LEU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 137 removed outlier: 3.570A pdb=" N THR B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.561A pdb=" N ASN B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.940A pdb=" N ALA B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.700A pdb=" N SER B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.955A pdb=" N LEU B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.679A pdb=" N GLY B 287 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.556A pdb=" N HIS B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 Processing helix chain 'B' and resid 456 through 461 removed outlier: 3.708A pdb=" N LEU B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.196A pdb=" N ARG B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.846A pdb=" N ARG B 486 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.515A pdb=" N MET B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.648A pdb=" N TYR B 628 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU B 631 " --> pdb=" O VAL B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 636 removed outlier: 3.556A pdb=" N SER B 636 " --> pdb=" O GLY B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 636' Processing helix chain 'C' and resid 54 through 64 removed outlier: 4.008A pdb=" N TYR C 58 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.680A pdb=" N LYS C 70 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.573A pdb=" N LEU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 137 removed outlier: 3.737A pdb=" N GLN C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.817A pdb=" N ALA C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.793A pdb=" N SER C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 239 through 250 removed outlier: 3.534A pdb=" N GLU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.727A pdb=" N LEU C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.130A pdb=" N GLU C 370 " --> pdb=" O HIS C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 420 Processing helix chain 'C' and resid 469 through 476 removed outlier: 3.917A pdb=" N ARG C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.937A pdb=" N ARG C 486 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.615A pdb=" N LYS C 502 " --> pdb=" O ARG C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 removed outlier: 4.323A pdb=" N VAL C 541 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 542 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 565 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 624 through 629 removed outlier: 3.676A pdb=" N TYR C 628 " --> pdb=" O ILE C 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 4.008A pdb=" N TYR D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 removed outlier: 3.680A pdb=" N LYS D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.573A pdb=" N LEU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 3.737A pdb=" N GLN D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 Processing helix chain 'D' and resid 161 through 174 removed outlier: 3.818A pdb=" N ALA D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.793A pdb=" N SER D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 239 through 250 removed outlier: 3.535A pdb=" N GLU D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.727A pdb=" N LEU D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 Processing helix chain 'D' and resid 366 through 371 removed outlier: 4.130A pdb=" N GLU D 370 " --> pdb=" O HIS D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 420 Processing helix chain 'D' and resid 469 through 476 removed outlier: 3.918A pdb=" N ARG D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 486 removed outlier: 3.937A pdb=" N ARG D 486 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 508 removed outlier: 3.615A pdb=" N LYS D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 547 removed outlier: 4.323A pdb=" N VAL D 541 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 565 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 624 through 629 removed outlier: 3.676A pdb=" N TYR D 628 " --> pdb=" O ILE D 624 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.918A pdb=" N TYR E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.756A pdb=" N LEU E 69 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU E 71 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.707A pdb=" N LEU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 137 removed outlier: 3.571A pdb=" N THR E 121 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.561A pdb=" N ASN E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 removed outlier: 3.939A pdb=" N ALA E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.700A pdb=" N SER E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 227 removed outlier: 3.955A pdb=" N LEU E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.679A pdb=" N GLY E 287 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 344 Processing helix chain 'E' and resid 345 through 349 Processing helix chain 'E' and resid 362 through 369 removed outlier: 3.556A pdb=" N HIS E 366 " --> pdb=" O ASP E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 420 Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.707A pdb=" N LEU E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 479 removed outlier: 4.197A pdb=" N ARG E 473 " --> pdb=" O ASP E 469 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE E 478 " --> pdb=" O ILE E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 486 removed outlier: 3.846A pdb=" N ARG E 486 " --> pdb=" O LYS E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 509 removed outlier: 3.516A pdb=" N MET E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 545 Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'E' and resid 583 through 589 Processing helix chain 'E' and resid 624 through 632 removed outlier: 3.648A pdb=" N TYR E 628 " --> pdb=" O ILE E 624 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS E 630 " --> pdb=" O GLN E 626 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU E 631 " --> pdb=" O VAL E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 636 removed outlier: 3.556A pdb=" N SER E 636 " --> pdb=" O GLY E 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 633 through 636' Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.876A pdb=" N TYR F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.825A pdb=" N ILE F 72 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 90 removed outlier: 3.649A pdb=" N LEU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 135 removed outlier: 3.624A pdb=" N ILE F 135 " --> pdb=" O TRP F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 156 removed outlier: 3.971A pdb=" N GLN F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE F 149 " --> pdb=" O LYS F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 175 Processing helix chain 'F' and resid 207 through 214 removed outlier: 3.788A pdb=" N SER F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 336 through 345 removed outlier: 4.148A pdb=" N SER F 345 " --> pdb=" O LYS F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 373 Processing helix chain 'F' and resid 408 through 420 Processing helix chain 'F' and resid 470 through 479 removed outlier: 3.909A pdb=" N PHE F 478 " --> pdb=" O ILE F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 486 removed outlier: 3.702A pdb=" N ALA F 485 " --> pdb=" O GLU F 482 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG F 486 " --> pdb=" O LYS F 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 482 through 486' Processing helix chain 'F' and resid 496 through 509 Processing helix chain 'F' and resid 536 through 547 removed outlier: 4.163A pdb=" N ASN F 540 " --> pdb=" O HIS F 536 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL F 541 " --> pdb=" O TYR F 537 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 542 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN F 547 " --> pdb=" O ASN F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'F' and resid 585 through 589 Processing helix chain 'F' and resid 624 through 630 removed outlier: 3.668A pdb=" N TYR F 628 " --> pdb=" O ILE F 624 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS F 630 " --> pdb=" O GLN F 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 28 removed outlier: 5.287A pdb=" N ILE A 22 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 45 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN A 24 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP A 43 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 402 removed outlier: 5.282A pdb=" N PHE A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 312 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA A 318 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 310 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP A 306 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 449 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE A 432 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 447 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 492 removed outlier: 6.228A pdb=" N ILE A 490 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 556 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 574 through 578 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 28 removed outlier: 5.708A pdb=" N ILE B 22 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA B 45 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN B 24 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 109 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 105 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.621A pdb=" N LEU B 186 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 399 through 402 removed outlier: 5.451A pdb=" N PHE B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 312 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 318 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 310 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP B 306 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 433 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 428 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 450 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP B 430 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 524 through 526 removed outlier: 3.653A pdb=" N GLU B 556 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 490 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 489 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 574 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN B 573 " --> pdb=" O ASP B 594 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 596 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 28 removed outlier: 4.220A pdb=" N VAL C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 41 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN C 27 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 39 " --> pdb=" O GLN C 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 179 through 180 Processing sheet with id=AB3, first strand: chain 'C' and resid 234 through 237 removed outlier: 3.724A pdb=" N ASP C 235 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.957A pdb=" N LEU C 310 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA C 319 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG C 308 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU C 321 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP C 306 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 449 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE C 432 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE C 447 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 326 through 327 Processing sheet with id=AB6, first strand: chain 'C' and resid 529 through 530 removed outlier: 3.539A pdb=" N GLU C 556 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 490 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 489 " --> pdb=" O SER C 572 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 574 " --> pdb=" O ILE C 489 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN C 573 " --> pdb=" O ASP C 594 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 28 removed outlier: 4.220A pdb=" N VAL D 25 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 41 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN D 27 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA D 39 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AB9, first strand: chain 'D' and resid 234 through 237 removed outlier: 3.723A pdb=" N ASP D 235 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 398 through 402 removed outlier: 6.957A pdb=" N LEU D 310 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 319 " --> pdb=" O ARG D 308 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG D 308 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU D 321 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP D 306 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 449 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 432 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE D 447 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 326 through 327 Processing sheet with id=AC3, first strand: chain 'D' and resid 529 through 530 removed outlier: 3.539A pdb=" N GLU D 556 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE D 490 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 489 " --> pdb=" O SER D 572 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 574 " --> pdb=" O ILE D 489 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN D 573 " --> pdb=" O ASP D 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 20 through 28 removed outlier: 5.708A pdb=" N ILE E 22 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA E 45 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN E 24 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN E 109 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 105 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 179 through 181 removed outlier: 3.620A pdb=" N LEU E 186 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 399 through 402 removed outlier: 5.450A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 312 " --> pdb=" O PHE E 316 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA E 318 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 310 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP E 306 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR E 433 " --> pdb=" O HIS E 305 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY E 428 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE E 450 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP E 430 " --> pdb=" O ILE E 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 524 through 526 removed outlier: 3.654A pdb=" N GLU E 556 " --> pdb=" O VAL E 519 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 490 " --> pdb=" O ALA E 555 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE E 489 " --> pdb=" O SER E 572 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 574 " --> pdb=" O ILE E 489 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN E 573 " --> pdb=" O ASP E 594 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 596 " --> pdb=" O ASN E 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 20 through 28 removed outlier: 5.288A pdb=" N ILE F 22 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA F 45 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASN F 24 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP F 43 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 179 through 181 Processing sheet with id=AD1, first strand: chain 'F' and resid 399 through 402 removed outlier: 5.282A pdb=" N PHE F 316 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL F 312 " --> pdb=" O PHE F 316 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA F 318 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 310 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP F 306 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 449 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE F 432 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE F 447 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 489 through 492 removed outlier: 6.227A pdb=" N ILE F 490 " --> pdb=" O ALA F 555 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 556 " --> pdb=" O VAL F 519 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 574 through 578 1042 hydrogen bonds defined for protein. 2832 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: 4.78 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.35: 9780 1.35 - 1.64: 20313 1.64 - 1.94: 136 1.94 - 2.23: 0 2.23 - 2.52: 1 Bond restraints: 30230 Sorted by residual: bond pdb=" C1' YHZ C 701 " pdb=" C8 YHZ C 701 " ideal model delta sigma weight residual 1.531 2.523 -0.992 2.00e-02 2.50e+03 2.46e+03 bond pdb=" C VAL B 327 " pdb=" N VAL B 328 " ideal model delta sigma weight residual 1.332 1.054 0.278 1.23e-02 6.61e+03 5.12e+02 bond pdb=" C VAL E 327 " pdb=" N VAL E 328 " ideal model delta sigma weight residual 1.332 1.054 0.278 1.23e-02 6.61e+03 5.12e+02 bond pdb=" C LYS D 257 " pdb=" N PRO D 258 " ideal model delta sigma weight residual 1.329 1.582 -0.253 1.20e-02 6.94e+03 4.45e+02 bond pdb=" C LYS C 257 " pdb=" N PRO C 258 " ideal model delta sigma weight residual 1.329 1.581 -0.253 1.20e-02 6.94e+03 4.44e+02 ... (remaining 30225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.67: 40731 11.67 - 23.33: 244 23.33 - 35.00: 38 35.00 - 46.67: 10 46.67 - 58.33: 2 Bond angle restraints: 41025 Sorted by residual: angle pdb=" N LEU C 376 " pdb=" CA LEU C 376 " pdb=" C LEU C 376 " ideal model delta sigma weight residual 112.68 158.89 -46.21 1.33e+00 5.65e-01 1.21e+03 angle pdb=" N LEU D 376 " pdb=" CA LEU D 376 " pdb=" C LEU D 376 " ideal model delta sigma weight residual 112.68 158.89 -46.21 1.33e+00 5.65e-01 1.21e+03 angle pdb=" N ALA E 279 " pdb=" CA ALA E 279 " pdb=" C ALA E 279 " ideal model delta sigma weight residual 111.28 145.49 -34.21 1.09e+00 8.42e-01 9.85e+02 angle pdb=" N ALA B 279 " pdb=" CA ALA B 279 " pdb=" C ALA B 279 " ideal model delta sigma weight residual 111.28 145.48 -34.20 1.09e+00 8.42e-01 9.85e+02 angle pdb=" O ASP A 377 " pdb=" C ASP A 377 " pdb=" N SER A 378 " ideal model delta sigma weight residual 122.48 87.55 34.93 1.21e+00 6.83e-01 8.33e+02 ... (remaining 41020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.74: 17661 27.74 - 55.47: 526 55.47 - 83.21: 65 83.21 - 110.94: 16 110.94 - 138.68: 11 Dihedral angle restraints: 18279 sinusoidal: 7503 harmonic: 10776 Sorted by residual: dihedral pdb=" C GLU A 363 " pdb=" N GLU A 363 " pdb=" CA GLU A 363 " pdb=" CB GLU A 363 " ideal model delta harmonic sigma weight residual -122.60 -80.13 -42.47 0 2.50e+00 1.60e-01 2.89e+02 dihedral pdb=" C GLU F 363 " pdb=" N GLU F 363 " pdb=" CA GLU F 363 " pdb=" CB GLU F 363 " ideal model delta harmonic sigma weight residual -122.60 -80.13 -42.47 0 2.50e+00 1.60e-01 2.89e+02 dihedral pdb=" C ALA B 303 " pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" CB ALA B 303 " ideal model delta harmonic sigma weight residual -122.60 -85.52 -37.08 0 2.50e+00 1.60e-01 2.20e+02 ... (remaining 18276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.455: 4575 0.455 - 0.910: 42 0.910 - 1.365: 8 1.365 - 1.819: 4 1.819 - 2.274: 3 Chirality restraints: 4632 Sorted by residual: chirality pdb=" C1' YHZ C 701 " pdb=" C2' YHZ C 701 " pdb=" C8 YHZ C 701 " pdb=" O4' YHZ C 701 " both_signs ideal model delta sigma weight residual False 2.57 4.84 -2.27 2.00e-01 2.50e+01 1.29e+02 chirality pdb=" CA ILE A 297 " pdb=" N ILE A 297 " pdb=" C ILE A 297 " pdb=" CB ILE A 297 " both_signs ideal model delta sigma weight residual False 2.43 0.35 2.09 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" CA ILE F 297 " pdb=" N ILE F 297 " pdb=" C ILE F 297 " pdb=" CB ILE F 297 " both_signs ideal model delta sigma weight residual False 2.43 0.35 2.09 2.00e-01 2.50e+01 1.09e+02 ... (remaining 4629 not shown) Planarity restraints: 5320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 7ID H 2 " 0.160 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG 7ID H 2 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 7ID H 2 " 0.114 2.00e-02 2.50e+03 pdb=" CA2 7ID H 2 " 0.348 2.00e-02 2.50e+03 pdb=" N2 7ID H 2 " -0.526 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB 7ID G 2 " -0.159 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG 7ID G 2 " 0.095 2.00e-02 2.50e+03 pdb=" OD1 7ID G 2 " -0.114 2.00e-02 2.50e+03 pdb=" CA2 7ID G 2 " -0.348 2.00e-02 2.50e+03 pdb=" N2 7ID G 2 " 0.526 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD2 7ID H 2 " -0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" NE2 7ID H 2 " 0.505 2.00e-02 2.50e+03 pdb=" CZ2 7ID H 2 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 7ID H 2 " -0.173 2.00e-02 2.50e+03 pdb=" NH2 7ID H 2 " -0.086 2.00e-02 2.50e+03 ... (remaining 5317 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 57 2.42 - 3.04: 18087 3.04 - 3.66: 37982 3.66 - 4.28: 55974 4.28 - 4.90: 98665 Nonbonded interactions: 210765 Sorted by model distance: nonbonded pdb=" N THR A 385 " pdb=" O THR A 385 " model vdw 1.801 2.496 nonbonded pdb=" N THR F 385 " pdb=" O THR F 385 " model vdw 1.802 2.496 nonbonded pdb=" N GLU F 292 " pdb=" O GLU F 292 " model vdw 1.808 2.496 nonbonded pdb=" N GLU A 292 " pdb=" O GLU A 292 " model vdw 1.808 2.496 nonbonded pdb=" O GLU A 363 " pdb=" CB GLU A 363 " model vdw 1.931 2.752 ... (remaining 210760 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = (chain 'C' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = (chain 'D' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = (chain 'E' and (resid 10 through 236 or resid 240 through 250 or resid 252 throu \ gh 254 or resid 278 through 285 or resid 292 through 636)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.860 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.700 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.013 0.992 30230 Z= 0.843 Angle : 2.097 58.334 41025 Z= 1.421 Chirality : 0.123 2.274 4632 Planarity : 0.016 0.298 5320 Dihedral : 13.643 138.679 11327 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.07 % Favored : 92.08 % Rotamer: Outliers : 3.12 % Allowed : 7.30 % Favored : 89.58 % Cbeta Deviations : 2.68 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.18 (0.14), residues: 3650 helix: 0.79 (0.17), residues: 1056 sheet: 0.47 (0.22), residues: 664 loop : -2.27 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 506 TYR 0.018 0.002 TYR E 252 PHE 0.014 0.002 PHE D 445 TRP 0.008 0.001 TRP E 182 HIS 0.005 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.01304 / 0.84 (30230) covalent geometry : angle 2.09693 / 1.42 (41025) hydrogen bonds : bond 0.18077 / 11.73 ( 1042) hydrogen bonds : angle 5.32182 / 3.63 ( 2832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 398 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.1720 (OUTLIER) cc_final: 0.1495 (mtp85) REVERT: A 113 ILE cc_start: 0.5568 (pt) cc_final: 0.5311 (mm) REVERT: A 217 LYS cc_start: 0.5172 (mttt) cc_final: 0.4840 (mmtt) REVERT: A 315 ARG cc_start: 0.5450 (mmm160) cc_final: 0.5168 (mmt180) REVERT: A 461 LYS cc_start: 0.5329 (tptt) cc_final: 0.4951 (pptt) REVERT: A 476 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6013 (tm-30) REVERT: A 483 LYS cc_start: 0.7061 (tttp) cc_final: 0.6858 (ptmm) REVERT: A 494 ARG cc_start: 0.5726 (ttp80) cc_final: 0.5342 (tpt90) REVERT: A 496 SER cc_start: 0.6115 (m) cc_final: 0.5860 (p) REVERT: A 546 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.4760 (tpt-90) REVERT: A 556 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: A 570 HIS cc_start: 0.6454 (t-90) cc_final: 0.5938 (t-170) REVERT: A 585 MET cc_start: 0.6943 (ttm) cc_final: 0.6741 (tpp) REVERT: B 152 GLN cc_start: 0.5997 (tp40) cc_final: 0.5618 (mm110) REVERT: B 173 GLU cc_start: 0.5825 (tt0) cc_final: 0.5600 (mt-10) REVERT: B 216 GLN cc_start: 0.6218 (mt0) cc_final: 0.5885 (mt0) REVERT: B 218 ASP cc_start: 0.7725 (m-30) cc_final: 0.7095 (t0) REVERT: B 227 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4785 (pp) REVERT: B 389 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.6021 (ptp-110) REVERT: B 405 ASN cc_start: 0.7737 (m-40) cc_final: 0.7330 (m-40) REVERT: B 473 ARG cc_start: 0.5686 (mmm160) cc_final: 0.5067 (mmp80) REVERT: B 480 GLU cc_start: 0.7018 (tt0) cc_final: 0.6501 (mp0) REVERT: B 483 LYS cc_start: 0.7755 (mttt) cc_final: 0.7168 (mmtp) REVERT: B 498 ARG cc_start: 0.5298 (ttt90) cc_final: 0.5095 (mpp-170) REVERT: B 501 GLN cc_start: 0.5808 (mt0) cc_final: 0.5571 (mt0) REVERT: B 502 LYS cc_start: 0.5641 (mmmm) cc_final: 0.5071 (mtpt) REVERT: B 505 ASP cc_start: 0.6003 (m-30) cc_final: 0.5536 (m-30) REVERT: B 535 ARG cc_start: 0.7129 (mmm160) cc_final: 0.6762 (tmm160) REVERT: B 582 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6701 (tp30) REVERT: B 594 ASP cc_start: 0.6387 (t70) cc_final: 0.6152 (p0) REVERT: B 603 ARG cc_start: 0.6381 (mtt180) cc_final: 0.6049 (tpt170) REVERT: B 604 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5721 (mm-30) REVERT: B 614 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7171 (tt0) REVERT: B 615 GLN cc_start: 0.8223 (tt0) cc_final: 0.7990 (tt0) REVERT: B 619 GLU cc_start: 0.4878 (mt-10) cc_final: 0.4647 (pm20) REVERT: B 626 GLN cc_start: 0.7049 (mt0) cc_final: 0.6572 (mp10) REVERT: C 119 ARG cc_start: 0.5839 (ttm170) cc_final: 0.5149 (mtm-85) REVERT: C 123 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6245 (mm-30) REVERT: C 139 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7029 (mt-10) REVERT: C 216 GLN cc_start: 0.6553 (mt0) cc_final: 0.6100 (mt0) REVERT: C 222 LYS cc_start: 0.6363 (tttp) cc_final: 0.6127 (tttp) REVERT: C 466 GLU cc_start: 0.6874 (mt-10) cc_final: 0.5964 (pm20) REVERT: C 483 LYS cc_start: 0.7388 (mttt) cc_final: 0.6645 (tppt) REVERT: C 494 ARG cc_start: 0.7023 (ttm110) cc_final: 0.5654 (tpm170) REVERT: C 498 ARG cc_start: 0.6339 (mmm-85) cc_final: 0.5565 (ttp-110) REVERT: C 502 LYS cc_start: 0.6216 (ttmm) cc_final: 0.5558 (ttpp) REVERT: C 535 ARG cc_start: 0.6445 (mtp85) cc_final: 0.6048 (ptm160) REVERT: C 549 LYS cc_start: 0.7747 (mtpm) cc_final: 0.7068 (mttm) REVERT: C 567 MET cc_start: 0.8601 (mtm) cc_final: 0.8389 (mtp) REVERT: C 582 GLU cc_start: 0.7640 (tp30) cc_final: 0.6921 (tm-30) REVERT: C 604 GLU cc_start: 0.6365 (mm-30) cc_final: 0.5665 (mm-30) REVERT: C 610 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6590 (mttm) REVERT: C 614 GLU cc_start: 0.7105 (tt0) cc_final: 0.6708 (tt0) REVERT: C 617 GLU cc_start: 0.7034 (tt0) cc_final: 0.6686 (tt0) REVERT: C 626 GLN cc_start: 0.6248 (mm-40) cc_final: 0.6022 (mt0) REVERT: D 119 ARG cc_start: 0.5808 (ttm170) cc_final: 0.5123 (mtm-85) REVERT: D 123 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6292 (mm-30) REVERT: D 139 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7031 (mt-10) REVERT: D 216 GLN cc_start: 0.6547 (mt0) cc_final: 0.6089 (mt0) REVERT: D 222 LYS cc_start: 0.6359 (tttp) cc_final: 0.6123 (tttp) REVERT: D 466 GLU cc_start: 0.6877 (mt-10) cc_final: 0.5958 (pm20) REVERT: D 483 LYS cc_start: 0.7390 (mttt) cc_final: 0.6627 (tppt) REVERT: D 494 ARG cc_start: 0.7028 (ttm110) cc_final: 0.5672 (tpm170) REVERT: D 498 ARG cc_start: 0.6320 (mmm-85) cc_final: 0.5547 (ttp-110) REVERT: D 502 LYS cc_start: 0.6232 (ttmm) cc_final: 0.5573 (ttpp) REVERT: D 535 ARG cc_start: 0.6438 (mtp85) cc_final: 0.6045 (ptm160) REVERT: D 549 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7084 (mttm) REVERT: D 567 MET cc_start: 0.8603 (mtm) cc_final: 0.8391 (mtp) REVERT: D 582 GLU cc_start: 0.7640 (tp30) cc_final: 0.6924 (tm-30) REVERT: D 604 GLU cc_start: 0.6369 (mm-30) cc_final: 0.5672 (mm-30) REVERT: D 610 LYS cc_start: 0.7053 (mtmt) cc_final: 0.6567 (mttm) REVERT: D 614 GLU cc_start: 0.7106 (tt0) cc_final: 0.6622 (tt0) REVERT: D 617 GLU cc_start: 0.7023 (tt0) cc_final: 0.6669 (tt0) REVERT: D 626 GLN cc_start: 0.6243 (mm-40) cc_final: 0.6010 (mt0) REVERT: E 152 GLN cc_start: 0.6022 (tp40) cc_final: 0.5559 (mm110) REVERT: E 173 GLU cc_start: 0.5839 (tt0) cc_final: 0.5621 (mt-10) REVERT: E 216 GLN cc_start: 0.6159 (mt0) cc_final: 0.5834 (mt0) REVERT: E 218 ASP cc_start: 0.7746 (m-30) cc_final: 0.7100 (t0) REVERT: E 227 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4802 (pp) REVERT: E 389 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.6038 (ptp-110) REVERT: E 405 ASN cc_start: 0.7734 (m-40) cc_final: 0.7327 (m-40) REVERT: E 473 ARG cc_start: 0.5713 (mmm160) cc_final: 0.5100 (mmp80) REVERT: E 480 GLU cc_start: 0.7028 (tt0) cc_final: 0.6496 (mp0) REVERT: E 483 LYS cc_start: 0.7753 (mttt) cc_final: 0.7182 (mmmm) REVERT: E 501 GLN cc_start: 0.5723 (mt0) cc_final: 0.5499 (mt0) REVERT: E 502 LYS cc_start: 0.5691 (mmmm) cc_final: 0.5120 (mtpt) REVERT: E 505 ASP cc_start: 0.6000 (m-30) cc_final: 0.5550 (m-30) REVERT: E 535 ARG cc_start: 0.7131 (mmm160) cc_final: 0.6759 (tmm160) REVERT: E 582 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6695 (tp30) REVERT: E 594 ASP cc_start: 0.6372 (t70) cc_final: 0.6148 (p0) REVERT: E 603 ARG cc_start: 0.6431 (mtt180) cc_final: 0.6019 (tpt170) REVERT: E 604 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5751 (mm-30) REVERT: E 614 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7137 (tt0) REVERT: E 615 GLN cc_start: 0.8259 (tt0) cc_final: 0.7958 (tt0) REVERT: E 619 GLU cc_start: 0.4902 (mt-10) cc_final: 0.4657 (pm20) REVERT: E 626 GLN cc_start: 0.7074 (mt0) cc_final: 0.6551 (mp10) REVERT: F 11 ARG cc_start: 0.1811 (OUTLIER) cc_final: 0.1583 (mtp85) REVERT: F 113 ILE cc_start: 0.5617 (pt) cc_final: 0.5352 (mm) REVERT: F 217 LYS cc_start: 0.5230 (mttt) cc_final: 0.4853 (mmtt) REVERT: F 315 ARG cc_start: 0.5460 (mmm160) cc_final: 0.5182 (mmt180) REVERT: F 461 LYS cc_start: 0.5268 (tptt) cc_final: 0.4902 (pptt) REVERT: F 476 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6011 (tm-30) REVERT: F 483 LYS cc_start: 0.7033 (tttp) cc_final: 0.6818 (ptmm) REVERT: F 494 ARG cc_start: 0.5706 (ttp80) cc_final: 0.5319 (tpt90) REVERT: F 496 SER cc_start: 0.6120 (m) cc_final: 0.5873 (p) REVERT: F 546 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.4652 (mmm160) REVERT: F 556 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.5871 (tm-30) REVERT: F 570 HIS cc_start: 0.6452 (t-90) cc_final: 0.5952 (t-170) REVERT: F 585 MET cc_start: 0.6947 (ttm) cc_final: 0.6744 (tpp) outliers start: 100 outliers final: 28 residues processed: 492 average time/residue: 0.6961 time to fit residues: 395.0834 Evaluate side-chains 306 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 289 PRO Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 289 PRO Chi-restraints excluded: chain E residue 389 ARG Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 399 PHE Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 300 ASN A 366 HIS B 89 ASN B 372 GLN B 416 GLN C 416 GLN C 501 GLN D 416 GLN D 501 GLN E 89 ASN E 300 ASN E 372 GLN E 416 GLN F 300 ASN F 366 HIS F 434 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.227221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174142 restraints weight = 31103.669| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.44 r_work: 0.3724 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30230 Z= 0.132 Angle : 0.626 10.278 41025 Z= 0.336 Chirality : 0.047 0.248 4632 Planarity : 0.005 0.052 5320 Dihedral : 11.935 154.680 4285 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 2.59 % Allowed : 11.30 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: -0.94 (0.14), residues: 3650 helix: 0.88 (0.17), residues: 1100 sheet: 0.48 (0.22), residues: 710 loop : -2.12 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.021 0.001 TYR D 332 PHE 0.012 0.001 PHE D 422 TRP 0.006 0.001 TRP E 182 HIS 0.004 0.001 HIS F 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (30230) covalent geometry : angle 0.62567 / 0.34 (41025) hydrogen bonds : bond 0.04543 / 2.96 ( 1042) hydrogen bonds : angle 4.26403 / 2.95 ( 2832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 546 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6836 (mmm160) REVERT: A 556 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: B 194 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7876 (mm-40) REVERT: B 216 GLN cc_start: 0.7386 (mt0) cc_final: 0.7166 (mt0) REVERT: B 227 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7040 (pp) REVERT: B 502 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7542 (mtpt) REVERT: B 505 ASP cc_start: 0.7889 (m-30) cc_final: 0.7676 (t0) REVERT: B 626 GLN cc_start: 0.8276 (mt0) cc_final: 0.8025 (mp10) REVERT: C 216 GLN cc_start: 0.6968 (mt0) cc_final: 0.6673 (mm-40) REVERT: C 297 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7503 (pp) REVERT: C 494 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7916 (tpm170) REVERT: C 502 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8355 (ttpp) REVERT: C 549 LYS cc_start: 0.8791 (mtpm) cc_final: 0.8533 (mttm) REVERT: D 216 GLN cc_start: 0.6986 (mt0) cc_final: 0.6679 (mm-40) REVERT: D 297 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7500 (pp) REVERT: D 502 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8361 (ttpp) REVERT: D 549 LYS cc_start: 0.8786 (mtpm) cc_final: 0.8530 (mttm) REVERT: E 194 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7918 (mm-40) REVERT: E 216 GLN cc_start: 0.7370 (mt0) cc_final: 0.7146 (mt0) REVERT: E 227 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7062 (pp) REVERT: E 405 ASN cc_start: 0.8298 (m-40) cc_final: 0.8076 (m-40) REVERT: E 502 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7580 (mtpt) REVERT: E 505 ASP cc_start: 0.7884 (m-30) cc_final: 0.7647 (t0) REVERT: E 626 GLN cc_start: 0.8313 (mt0) cc_final: 0.8053 (mp10) REVERT: F 546 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6798 (mmm160) REVERT: F 556 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: F 590 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6555 (m-30) outliers start: 83 outliers final: 33 residues processed: 352 average time/residue: 0.7610 time to fit residues: 308.2286 Evaluate side-chains 260 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 609 ARG Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 94 optimal weight: 9.9990 chunk 318 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 0.0370 chunk 283 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 333 optimal weight: 0.9980 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.224186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164130 restraints weight = 30910.291| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.40 r_work: 0.3448 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30230 Z= 0.146 Angle : 0.633 10.101 41025 Z= 0.337 Chirality : 0.048 0.265 4632 Planarity : 0.005 0.051 5320 Dihedral : 11.200 156.677 4255 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 2.72 % Allowed : 14.17 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: -0.94 (0.14), residues: 3650 helix: 0.76 (0.16), residues: 1126 sheet: 0.69 (0.22), residues: 698 loop : -2.17 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 11 TYR 0.020 0.002 TYR D 628 PHE 0.017 0.002 PHE D 445 TRP 0.007 0.001 TRP E 182 HIS 0.005 0.001 HIS E 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (30230) covalent geometry : angle 0.63325 / 0.34 (41025) hydrogen bonds : bond 0.05463 / 3.63 ( 1042) hydrogen bonds : angle 4.21213 / 2.94 ( 2832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6603 (mmtt) cc_final: 0.6360 (mtpm) REVERT: A 37 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: A 413 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6416 (mp) REVERT: A 546 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6602 (mmm160) REVERT: A 556 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: A 570 HIS cc_start: 0.7557 (t70) cc_final: 0.7162 (t-170) REVERT: B 44 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6477 (t80) REVERT: B 222 LYS cc_start: 0.7636 (mttm) cc_final: 0.7038 (mtpp) REVERT: B 227 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6529 (pp) REVERT: B 502 LYS cc_start: 0.7474 (mmmm) cc_final: 0.6875 (mtpt) REVERT: B 505 ASP cc_start: 0.7578 (m-30) cc_final: 0.7178 (m-30) REVERT: B 626 GLN cc_start: 0.8207 (mt0) cc_final: 0.7696 (mp10) REVERT: C 216 GLN cc_start: 0.7050 (mt0) cc_final: 0.6463 (mm-40) REVERT: C 297 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6465 (pp) REVERT: C 494 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7595 (tpm170) REVERT: C 502 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7820 (ttpp) REVERT: C 549 LYS cc_start: 0.8955 (mtpm) cc_final: 0.8597 (mttm) REVERT: C 604 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7038 (tt0) REVERT: C 614 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: D 216 GLN cc_start: 0.7053 (mt0) cc_final: 0.6468 (mm-40) REVERT: D 297 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6449 (pp) REVERT: D 502 LYS cc_start: 0.8401 (ttmm) cc_final: 0.7833 (ttpp) REVERT: D 549 LYS cc_start: 0.8954 (mtpm) cc_final: 0.8595 (mttm) REVERT: D 604 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7036 (tt0) REVERT: D 614 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: E 44 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6456 (t80) REVERT: E 222 LYS cc_start: 0.7662 (mttm) cc_final: 0.7041 (mtpp) REVERT: E 227 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6553 (pp) REVERT: E 405 ASN cc_start: 0.8294 (m-40) cc_final: 0.7968 (m-40) REVERT: E 502 LYS cc_start: 0.7492 (mmmm) cc_final: 0.6903 (mtpt) REVERT: E 505 ASP cc_start: 0.7604 (m-30) cc_final: 0.7225 (m-30) REVERT: E 626 GLN cc_start: 0.8222 (mt0) cc_final: 0.7705 (mp10) REVERT: F 26 LYS cc_start: 0.6583 (mmtt) cc_final: 0.6343 (mtpm) REVERT: F 413 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6417 (mp) REVERT: F 481 THR cc_start: 0.7071 (p) cc_final: 0.6833 (t) REVERT: F 546 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6577 (mmm160) REVERT: F 556 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: F 590 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6042 (m-30) outliers start: 87 outliers final: 34 residues processed: 292 average time/residue: 0.7071 time to fit residues: 239.0758 Evaluate side-chains 249 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 609 ARG Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 590 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 141 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN B 37 GLN E 300 ASN F 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.222485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166707 restraints weight = 30751.290| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.26 r_work: 0.3642 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30230 Z= 0.178 Angle : 0.668 9.990 41025 Z= 0.356 Chirality : 0.050 0.260 4632 Planarity : 0.005 0.053 5320 Dihedral : 10.820 173.724 4243 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.85 % Favored : 93.04 % Rotamer: Outliers : 3.59 % Allowed : 13.89 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.09 (0.14), residues: 3650 helix: 0.61 (0.16), residues: 1142 sheet: 0.62 (0.22), residues: 698 loop : -2.27 (0.12), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 528 TYR 0.023 0.002 TYR C 165 PHE 0.023 0.002 PHE D 445 TRP 0.008 0.001 TRP C 182 HIS 0.006 0.001 HIS E 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (30230) covalent geometry : angle 0.66831 / 0.36 (41025) hydrogen bonds : bond 0.06192 / 4.13 ( 1042) hydrogen bonds : angle 4.25294 / 2.96 ( 2832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 207 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7224 (mp) REVERT: A 546 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.6966 (mmm160) REVERT: A 556 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: B 194 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8312 (mm-40) REVERT: B 222 LYS cc_start: 0.7957 (mttm) cc_final: 0.7682 (mtpp) REVERT: B 227 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7031 (pp) REVERT: B 502 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7612 (mtpt) REVERT: B 505 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: B 582 GLU cc_start: 0.7626 (tp30) cc_final: 0.7080 (tt0) REVERT: B 604 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: B 626 GLN cc_start: 0.8283 (mt0) cc_final: 0.7939 (mp10) REVERT: C 216 GLN cc_start: 0.7262 (mt0) cc_final: 0.6881 (mm-40) REVERT: C 297 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7431 (pp) REVERT: C 494 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8027 (tpm170) REVERT: C 502 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8344 (ttpp) REVERT: C 535 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7378 (ptm160) REVERT: C 549 LYS cc_start: 0.8870 (mtpm) cc_final: 0.8617 (mttm) REVERT: D 216 GLN cc_start: 0.7265 (mt0) cc_final: 0.6906 (mm-40) REVERT: D 297 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (pp) REVERT: D 502 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8352 (ttpp) REVERT: D 535 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7400 (ptm160) REVERT: D 549 LYS cc_start: 0.8872 (mtpm) cc_final: 0.8613 (mttm) REVERT: E 194 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8334 (mm-40) REVERT: E 222 LYS cc_start: 0.7970 (mttm) cc_final: 0.7672 (mtpp) REVERT: E 227 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7029 (pp) REVERT: E 405 ASN cc_start: 0.8366 (m-40) cc_final: 0.8150 (m-40) REVERT: E 502 LYS cc_start: 0.7959 (mmmm) cc_final: 0.7623 (mtpt) REVERT: E 505 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: E 604 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: E 626 GLN cc_start: 0.8265 (mt0) cc_final: 0.7934 (mp10) REVERT: F 413 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7269 (mp) REVERT: F 546 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.6957 (mmm160) REVERT: F 556 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: F 590 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6520 (m-30) outliers start: 115 outliers final: 53 residues processed: 299 average time/residue: 0.7485 time to fit residues: 259.7053 Evaluate side-chains 261 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 189 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 609 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 590 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 327 optimal weight: 1.9990 chunk 272 optimal weight: 30.0000 chunk 158 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 156 ASN E 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.220987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.166542 restraints weight = 30825.816| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.32 r_work: 0.3627 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30230 Z= 0.225 Angle : 0.735 12.087 41025 Z= 0.393 Chirality : 0.052 0.260 4632 Planarity : 0.005 0.054 5320 Dihedral : 10.691 170.615 4229 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.29 % Favored : 92.49 % Rotamer: Outliers : 3.87 % Allowed : 14.76 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.25 (0.14), residues: 3650 helix: 0.54 (0.16), residues: 1114 sheet: 0.43 (0.21), residues: 688 loop : -2.31 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 528 TYR 0.029 0.002 TYR C 165 PHE 0.030 0.003 PHE C 445 TRP 0.011 0.002 TRP C 182 HIS 0.006 0.002 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (30230) covalent geometry : angle 0.73505 / 0.39 (41025) hydrogen bonds : bond 0.07301 / 4.87 ( 1042) hydrogen bonds : angle 4.34528 / 3.03 ( 2832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 194 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: A 413 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7275 (mp) REVERT: A 546 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7021 (mmm160) REVERT: A 556 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: A 590 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6705 (m-30) REVERT: B 227 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7055 (pp) REVERT: B 483 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8176 (mmtp) REVERT: B 502 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7599 (mtpt) REVERT: B 505 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: B 604 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: B 626 GLN cc_start: 0.8334 (mt0) cc_final: 0.7959 (mp10) REVERT: C 141 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5445 (p90) REVERT: C 216 GLN cc_start: 0.7438 (mt0) cc_final: 0.7017 (mm-40) REVERT: C 297 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7446 (pp) REVERT: C 494 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8075 (tpm170) REVERT: C 502 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8371 (ttpp) REVERT: C 535 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: C 549 LYS cc_start: 0.8865 (mtpm) cc_final: 0.8602 (mttm) REVERT: C 604 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: D 141 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5355 (p90) REVERT: D 216 GLN cc_start: 0.7437 (mt0) cc_final: 0.7036 (mm-40) REVERT: D 297 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7438 (pp) REVERT: D 502 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8390 (ttpp) REVERT: D 535 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7429 (ptm160) REVERT: D 549 LYS cc_start: 0.8878 (mtpm) cc_final: 0.8608 (mttm) REVERT: D 604 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: E 227 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7061 (pp) REVERT: E 405 ASN cc_start: 0.8434 (m-40) cc_final: 0.8215 (m-40) REVERT: E 483 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8204 (mmtp) REVERT: E 502 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7609 (mtpt) REVERT: E 505 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: E 604 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: E 626 GLN cc_start: 0.8312 (mt0) cc_final: 0.7957 (mp10) REVERT: F 194 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: F 413 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7283 (mp) REVERT: F 546 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7014 (mmm160) REVERT: F 556 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: F 590 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6879 (m-30) outliers start: 124 outliers final: 48 residues processed: 293 average time/residue: 0.7527 time to fit residues: 255.2756 Evaluate side-chains 257 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 609 ARG Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 609 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 183 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 294 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 362 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.222873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167884 restraints weight = 30777.186| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.29 r_work: 0.3652 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30230 Z= 0.136 Angle : 0.596 8.954 41025 Z= 0.320 Chirality : 0.047 0.262 4632 Planarity : 0.005 0.056 5320 Dihedral : 10.194 158.864 4228 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 3.12 % Allowed : 16.01 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.08 (0.14), residues: 3650 helix: 0.73 (0.16), residues: 1126 sheet: 0.83 (0.22), residues: 654 loop : -2.35 (0.12), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 119 TYR 0.020 0.001 TYR C 165 PHE 0.017 0.002 PHE D 445 TRP 0.009 0.001 TRP C 182 HIS 0.004 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (30230) covalent geometry : angle 0.59641 / 0.32 (41025) hydrogen bonds : bond 0.05162 / 3.44 ( 1042) hydrogen bonds : angle 4.13417 / 2.88 ( 2832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 191 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: A 240 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.3852 (mm) REVERT: A 413 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7150 (mp) REVERT: A 546 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.6869 (mmm160) REVERT: A 556 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: B 222 LYS cc_start: 0.7983 (mttm) cc_final: 0.7669 (mtpp) REVERT: B 227 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7101 (pp) REVERT: B 308 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8260 (tpt170) REVERT: B 483 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8154 (mmtp) REVERT: B 502 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7564 (mtpt) REVERT: B 582 GLU cc_start: 0.7624 (tp30) cc_final: 0.7065 (tt0) REVERT: B 604 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: B 626 GLN cc_start: 0.8365 (mt0) cc_final: 0.7987 (mp10) REVERT: B 631 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: C 216 GLN cc_start: 0.7116 (mt0) cc_final: 0.6773 (mm-40) REVERT: C 297 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7404 (pp) REVERT: C 494 ARG cc_start: 0.8220 (ttm110) cc_final: 0.8014 (tpm170) REVERT: C 502 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8331 (ttpp) REVERT: C 535 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7364 (ptm160) REVERT: C 549 LYS cc_start: 0.8841 (mtpm) cc_final: 0.8582 (mttm) REVERT: C 604 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: C 614 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: D 216 GLN cc_start: 0.7123 (mt0) cc_final: 0.6766 (mm-40) REVERT: D 297 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7418 (pp) REVERT: D 502 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8336 (ttpp) REVERT: D 535 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7367 (ptm160) REVERT: D 549 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8590 (mttm) REVERT: D 604 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: D 614 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: E 222 LYS cc_start: 0.7972 (mttm) cc_final: 0.7650 (mtpp) REVERT: E 227 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7096 (pp) REVERT: E 308 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8257 (tpt170) REVERT: E 483 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8176 (mmtp) REVERT: E 502 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7597 (mtpt) REVERT: E 505 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: E 626 GLN cc_start: 0.8352 (mt0) cc_final: 0.7972 (mp10) REVERT: E 631 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: F 194 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: F 240 LEU cc_start: 0.4425 (OUTLIER) cc_final: 0.3991 (mm) REVERT: F 413 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7150 (mp) REVERT: F 546 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6869 (mmm160) REVERT: F 556 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: F 590 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6838 (m-30) outliers start: 100 outliers final: 46 residues processed: 274 average time/residue: 0.7936 time to fit residues: 251.0143 Evaluate side-chains 258 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 183 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 590 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 306 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 206 optimal weight: 30.0000 chunk 220 optimal weight: 40.0000 chunk 309 optimal weight: 0.5980 chunk 286 optimal weight: 7.9990 chunk 331 optimal weight: 30.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 ASN B 451 ASN E 451 ASN F 573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.219545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.164405 restraints weight = 30668.167| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.34 r_work: 0.3482 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 30230 Z= 0.279 Angle : 0.811 13.275 41025 Z= 0.433 Chirality : 0.056 0.340 4632 Planarity : 0.006 0.053 5320 Dihedral : 10.742 153.241 4227 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.51 % Rotamer: Outliers : 4.06 % Allowed : 15.36 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.41 (0.13), residues: 3650 helix: 0.36 (0.16), residues: 1118 sheet: 0.27 (0.21), residues: 688 loop : -2.34 (0.12), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 315 TYR 0.033 0.003 TYR D 165 PHE 0.036 0.003 PHE C 445 TRP 0.011 0.002 TRP C 182 HIS 0.008 0.002 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.28 (30230) covalent geometry : angle 0.81144 / 0.43 (41025) hydrogen bonds : bond 0.08341 / 5.56 ( 1042) hydrogen bonds : angle 4.43500 / 3.10 ( 2832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 196 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: A 240 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4243 (mm) REVERT: A 413 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7180 (mp) REVERT: A 546 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7053 (mmm160) REVERT: A 590 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: B 194 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8535 (mm-40) REVERT: B 222 LYS cc_start: 0.8227 (mttm) cc_final: 0.7780 (mtpp) REVERT: B 308 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8514 (tpt170) REVERT: B 483 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8325 (mmtp) REVERT: B 502 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7662 (mtpt) REVERT: B 505 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: B 582 GLU cc_start: 0.7813 (tp30) cc_final: 0.7276 (tt0) REVERT: B 604 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: B 626 GLN cc_start: 0.8579 (mt0) cc_final: 0.8086 (mp10) REVERT: B 631 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: B 635 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6838 (pp) REVERT: C 141 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5764 (p90) REVERT: C 297 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7328 (pp) REVERT: C 494 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8070 (tpm170) REVERT: C 502 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8418 (ttpp) REVERT: C 535 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7422 (ptm160) REVERT: C 549 LYS cc_start: 0.8940 (mtpm) cc_final: 0.8638 (mttm) REVERT: C 604 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: D 141 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.5761 (p90) REVERT: D 297 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7273 (pp) REVERT: D 502 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8432 (ttpp) REVERT: D 535 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7437 (ptm160) REVERT: D 549 LYS cc_start: 0.8952 (mtpm) cc_final: 0.8647 (mttm) REVERT: D 604 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: D 614 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: E 194 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8594 (mm-40) REVERT: E 222 LYS cc_start: 0.8218 (mttm) cc_final: 0.7770 (mtpp) REVERT: E 308 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8515 (tpt170) REVERT: E 483 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8349 (mmtp) REVERT: E 502 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7668 (mtpt) REVERT: E 505 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: E 582 GLU cc_start: 0.7802 (tp30) cc_final: 0.7283 (tt0) REVERT: E 604 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: E 626 GLN cc_start: 0.8580 (mt0) cc_final: 0.8091 (mp10) REVERT: E 631 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: E 635 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6857 (pp) REVERT: F 194 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: F 240 LEU cc_start: 0.4681 (OUTLIER) cc_final: 0.4404 (mm) REVERT: F 413 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7183 (mp) REVERT: F 546 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7045 (mmm160) outliers start: 130 outliers final: 57 residues processed: 306 average time/residue: 0.7991 time to fit residues: 281.2317 Evaluate side-chains 269 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 180 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain E residue 46 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 604 GLU Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 570 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 44 optimal weight: 0.0050 chunk 352 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 258 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 499 GLN E 499 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.223905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170282 restraints weight = 31030.628| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.36 r_work: 0.3686 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30230 Z= 0.114 Angle : 0.555 8.468 41025 Z= 0.299 Chirality : 0.046 0.313 4632 Planarity : 0.004 0.061 5320 Dihedral : 9.863 143.741 4221 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % Rotamer: Outliers : 2.65 % Allowed : 16.85 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.00 (0.14), residues: 3650 helix: 0.81 (0.17), residues: 1122 sheet: 0.87 (0.22), residues: 658 loop : -2.30 (0.12), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 119 TYR 0.014 0.001 TYR C 165 PHE 0.012 0.001 PHE C 492 TRP 0.006 0.001 TRP B 182 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (30230) covalent geometry : angle 0.55530 / 0.30 (41025) hydrogen bonds : bond 0.04191 / 2.80 ( 1042) hydrogen bonds : angle 4.02444 / 2.80 ( 2832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 188 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: A 240 LEU cc_start: 0.4104 (OUTLIER) cc_final: 0.3819 (mm) REVERT: A 546 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6951 (mmm160) REVERT: B 222 LYS cc_start: 0.7920 (mttm) cc_final: 0.7644 (mtpp) REVERT: B 227 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7118 (pp) REVERT: B 308 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8197 (tpt170) REVERT: B 406 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7550 (ptt90) REVERT: B 483 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8115 (mmtp) REVERT: B 502 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7557 (mtpt) REVERT: B 505 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: B 535 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.6042 (mtm-85) REVERT: B 582 GLU cc_start: 0.7713 (tp30) cc_final: 0.7243 (tt0) REVERT: B 626 GLN cc_start: 0.8349 (mt0) cc_final: 0.7958 (mp10) REVERT: B 631 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: C 216 GLN cc_start: 0.6948 (mt0) cc_final: 0.6650 (mm-40) REVERT: C 297 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7417 (pp) REVERT: C 442 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: C 494 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7995 (tpm170) REVERT: C 502 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8303 (ttpp) REVERT: C 535 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7369 (ptm160) REVERT: C 549 LYS cc_start: 0.8808 (mtpm) cc_final: 0.8553 (mttm) REVERT: C 604 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: C 614 GLU cc_start: 0.7797 (tt0) cc_final: 0.7306 (mp0) REVERT: D 216 GLN cc_start: 0.6949 (mt0) cc_final: 0.6653 (mm-40) REVERT: D 297 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7422 (pp) REVERT: D 442 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: D 502 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8308 (ttpp) REVERT: D 535 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7399 (ptm160) REVERT: D 549 LYS cc_start: 0.8821 (mtpm) cc_final: 0.8562 (mttm) REVERT: D 604 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: E 222 LYS cc_start: 0.7910 (mttm) cc_final: 0.7634 (mtpp) REVERT: E 227 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7117 (pp) REVERT: E 308 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8179 (tpt170) REVERT: E 406 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7540 (ptt90) REVERT: E 483 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8124 (mmtp) REVERT: E 502 LYS cc_start: 0.7863 (mmmm) cc_final: 0.7533 (mtpt) REVERT: E 535 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6027 (mtm-85) REVERT: E 582 GLU cc_start: 0.7620 (tp30) cc_final: 0.7201 (tt0) REVERT: E 626 GLN cc_start: 0.8317 (mt0) cc_final: 0.7936 (mp10) REVERT: E 631 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: F 194 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: F 315 ARG cc_start: 0.7240 (mmt180) cc_final: 0.6965 (mmt180) REVERT: F 546 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6944 (mmm160) outliers start: 85 outliers final: 35 residues processed: 255 average time/residue: 0.8067 time to fit residues: 237.3870 Evaluate side-chains 243 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 535 ARG Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 546 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 352 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 271 optimal weight: 0.5980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.221670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160817 restraints weight = 30622.034| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.90 r_work: 0.3372 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30230 Z= 0.171 Angle : 0.639 9.951 41025 Z= 0.343 Chirality : 0.049 0.295 4632 Planarity : 0.005 0.056 5320 Dihedral : 9.964 139.888 4221 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.77 % Favored : 93.01 % Rotamer: Outliers : 2.90 % Allowed : 16.79 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.06 (0.14), residues: 3650 helix: 0.74 (0.16), residues: 1118 sheet: 0.82 (0.22), residues: 636 loop : -2.28 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 315 TYR 0.025 0.002 TYR D 165 PHE 0.023 0.002 PHE C 445 TRP 0.008 0.001 TRP E 182 HIS 0.004 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (30230) covalent geometry : angle 0.63929 / 0.34 (41025) hydrogen bonds : bond 0.05962 / 3.98 ( 1042) hydrogen bonds : angle 4.14087 / 2.88 ( 2832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 183 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: A 240 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4727 (mm) REVERT: A 546 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6712 (mmm160) REVERT: B 194 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8734 (mm-40) REVERT: B 222 LYS cc_start: 0.7656 (mttm) cc_final: 0.7072 (mtpp) REVERT: B 227 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6635 (pp) REVERT: B 308 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7995 (tpt170) REVERT: B 406 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7330 (ptt90) REVERT: B 483 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8298 (mmtp) REVERT: B 502 LYS cc_start: 0.7596 (mmmm) cc_final: 0.7023 (mtpt) REVERT: B 505 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: B 535 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5965 (mtm-85) REVERT: B 626 GLN cc_start: 0.8380 (mt0) cc_final: 0.7721 (mp10) REVERT: B 631 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: C 216 GLN cc_start: 0.7274 (mt0) cc_final: 0.6676 (mm-40) REVERT: C 297 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6504 (pp) REVERT: C 442 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: C 494 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7746 (tpm170) REVERT: C 502 LYS cc_start: 0.8497 (ttmm) cc_final: 0.7966 (ttpp) REVERT: C 535 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7170 (ptm160) REVERT: C 549 LYS cc_start: 0.8984 (mtpm) cc_final: 0.8642 (mttm) REVERT: D 216 GLN cc_start: 0.7237 (mt0) cc_final: 0.6673 (mm-40) REVERT: D 442 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: D 502 LYS cc_start: 0.8502 (ttmm) cc_final: 0.7977 (ttpp) REVERT: D 535 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7179 (ptm160) REVERT: D 549 LYS cc_start: 0.8986 (mtpm) cc_final: 0.8645 (mttm) REVERT: D 614 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: E 194 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8738 (mm-40) REVERT: E 222 LYS cc_start: 0.7636 (mttm) cc_final: 0.7050 (mtpp) REVERT: E 227 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6629 (pp) REVERT: E 308 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7990 (tpt170) REVERT: E 406 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7345 (ptt90) REVERT: E 483 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8302 (mmtp) REVERT: E 502 LYS cc_start: 0.7628 (mmmm) cc_final: 0.7012 (mtpt) REVERT: E 505 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: E 535 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.6006 (mtm-85) REVERT: E 582 GLU cc_start: 0.7686 (tp30) cc_final: 0.7088 (tt0) REVERT: E 626 GLN cc_start: 0.8381 (mt0) cc_final: 0.7721 (mp10) REVERT: E 631 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: F 194 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: F 546 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6717 (mmm160) REVERT: F 556 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7554 (tm-30) outliers start: 93 outliers final: 46 residues processed: 262 average time/residue: 0.8162 time to fit residues: 246.2526 Evaluate side-chains 245 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 535 ARG Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 546 ARG Chi-restraints excluded: chain F residue 556 GLU Chi-restraints excluded: chain F residue 570 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 351 optimal weight: 0.7980 chunk 110 optimal weight: 0.0270 chunk 266 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 365 optimal weight: 1.9990 chunk 314 optimal weight: 0.9990 chunk 201 optimal weight: 0.3980 chunk 361 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN F 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.223630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168417 restraints weight = 30835.038| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.21 r_work: 0.3679 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30230 Z= 0.115 Angle : 0.559 9.128 41025 Z= 0.301 Chirality : 0.046 0.299 4632 Planarity : 0.004 0.056 5320 Dihedral : 9.596 135.838 4221 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.56 % Favored : 94.22 % Rotamer: Outliers : 2.18 % Allowed : 17.57 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.90 (0.14), residues: 3650 helix: 0.91 (0.17), residues: 1118 sheet: 0.91 (0.22), residues: 654 loop : -2.23 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 119 TYR 0.017 0.001 TYR C 165 PHE 0.013 0.001 PHE D 445 TRP 0.006 0.001 TRP E 182 HIS 0.003 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (30230) covalent geometry : angle 0.55880 / 0.30 (41025) hydrogen bonds : bond 0.04339 / 2.91 ( 1042) hydrogen bonds : angle 3.98940 / 2.78 ( 2832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7300 Ramachandran restraints generated. 3650 Oldfield, 0 Emsley, 3650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 183 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: A 546 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.6987 (mmm160) REVERT: A 556 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: B 222 LYS cc_start: 0.7935 (mttm) cc_final: 0.7643 (mtpp) REVERT: B 227 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7071 (pp) REVERT: B 308 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8147 (tpt170) REVERT: B 406 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7531 (ptt90) REVERT: B 483 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7984 (mmtp) REVERT: B 502 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7549 (mtpt) REVERT: B 505 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: B 530 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: B 535 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6079 (mtm-85) REVERT: B 626 GLN cc_start: 0.8296 (mt0) cc_final: 0.7897 (mp10) REVERT: B 631 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: C 216 GLN cc_start: 0.6984 (mt0) cc_final: 0.6689 (mm-40) REVERT: C 297 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7405 (pp) REVERT: C 442 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7983 (pt0) REVERT: C 494 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7980 (tpm170) REVERT: C 502 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8321 (ttpp) REVERT: C 535 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7333 (ptm160) REVERT: C 549 LYS cc_start: 0.8804 (mtpm) cc_final: 0.8552 (mttm) REVERT: C 604 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: C 614 GLU cc_start: 0.7784 (tt0) cc_final: 0.7332 (mp0) REVERT: D 216 GLN cc_start: 0.6979 (mt0) cc_final: 0.6701 (mm-40) REVERT: D 442 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: D 502 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8314 (ttpp) REVERT: D 535 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7350 (ptm160) REVERT: D 549 LYS cc_start: 0.8814 (mtpm) cc_final: 0.8550 (mttm) REVERT: D 604 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: D 614 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: E 222 LYS cc_start: 0.7918 (mttm) cc_final: 0.7625 (mtpp) REVERT: E 227 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7066 (pp) REVERT: E 308 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8133 (tpt170) REVERT: E 406 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7531 (ptt90) REVERT: E 483 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8005 (mmtp) REVERT: E 502 LYS cc_start: 0.7876 (mmmm) cc_final: 0.7518 (mtpt) REVERT: E 530 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: E 535 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6073 (mtm-85) REVERT: E 582 GLU cc_start: 0.7634 (tp30) cc_final: 0.7267 (tt0) REVERT: E 626 GLN cc_start: 0.8291 (mt0) cc_final: 0.7898 (mp10) REVERT: E 631 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: F 194 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: F 546 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6985 (mmm160) outliers start: 70 outliers final: 36 residues processed: 238 average time/residue: 0.8460 time to fit residues: 230.3712 Evaluate side-chains 241 residues out of total 3204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 483 LYS Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 535 ARG Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 614 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 406 ARG Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain E residue 530 GLU Chi-restraints excluded: chain E residue 535 ARG Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 546 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 11 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 320 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 248 optimal weight: 0.3980 chunk 307 optimal weight: 50.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.222411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168191 restraints weight = 30988.164| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.28 r_work: 0.3660 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30230 Z= 0.143 Angle : 0.596 9.155 41025 Z= 0.321 Chirality : 0.048 0.286 4632 Planarity : 0.005 0.054 5320 Dihedral : 9.609 133.418 4221 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.27 % Favored : 93.51 % Rotamer: Outliers : 2.50 % Allowed : 17.42 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.93 (0.14), residues: 3650 helix: 0.86 (0.16), residues: 1118 sheet: 0.86 (0.22), residues: 654 loop : -2.22 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 11 TYR 0.022 0.001 TYR C 165 PHE 0.020 0.002 PHE D 445 TRP 0.007 0.001 TRP E 182 HIS 0.004 0.001 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (30230) covalent geometry : angle 0.59632 / 0.32 (41025) hydrogen bonds : bond 0.05235 / 3.51 ( 1042) hydrogen bonds : angle 4.04145 / 2.82 ( 2832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11937.12 seconds wall clock time: 203 minutes 26.52 seconds (12206.52 seconds total)