Starting phenix.real_space_refine on Sat Jul 4 14:31:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4b_22663/07_2026/7k4b_22663_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4b_22663/07_2026/7k4b_22663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k4b_22663/07_2026/7k4b_22663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4b_22663/07_2026/7k4b_22663.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4b_22663/07_2026/7k4b_22663_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4b_22663/07_2026/7k4b_22663_neut.cif" } resolution = 3.1 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= 0.040 sd= 0.167 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 Ca 1 9.91 5 P 16 5.49 5 S 160 5.16 5 C 13982 2.51 5 N 3351 2.21 5 O 3608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s 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: 21118 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "B" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "C" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "D" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "A" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 407 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PCW': 12, 'VUG': 2, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain breaks: 1 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-3': 8, 'PCW:plan-4': 9, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 442 Unusual residues: {'PCW': 12, 'VUG': 2, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-3': 8, 'PCW:plan-4': 9, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 347 Unusual residues: {'PCW': 12, 'VUG': 1, 'Y01': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-3': 8, 'PCW:plan-4': 9, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 357 Unusual residues: {'PCW': 12, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-3': 8, 'PCW:plan-4': 9, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 21118 At special positions: 0 Unit cell: (143.59, 143.59, 122.84, 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) Ca 1 19.99 S 160 16.00 P 16 15.00 O 3608 8.00 N 3351 7.00 C 13982 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: 1.53 Conformation dependent library (CDL) restraints added in 654.0 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 58.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 removed outlier: 3.656A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 4.040A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.765A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.851A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.751A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.549A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.529A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 203' Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.807A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.551A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.876A pdb=" N LYS A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.680A pdb=" N SER A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.502A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 removed outlier: 3.767A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.861A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.024A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 575 removed outlier: 3.514A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.803A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 583' Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 608 Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.656A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.039A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.765A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.851A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.751A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.550A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.529A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 203' Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.806A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.551A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.877A pdb=" N LYS B 262 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 3.680A pdb=" N SER B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.503A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 398 removed outlier: 3.766A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.863A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.024A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 539 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.514A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.803A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 583' Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 593 through 608 Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.656A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.040A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 101 removed outlier: 3.764A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 removed outlier: 3.851A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.751A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.549A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.529A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.806A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.550A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.876A pdb=" N LYS C 262 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 318 removed outlier: 3.681A pdb=" N SER C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 331 through 340 removed outlier: 3.503A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 398 removed outlier: 3.766A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.861A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.024A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 539 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.514A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.803A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 578 through 583' Processing helix chain 'C' and resid 587 through 592 Processing helix chain 'C' and resid 593 through 608 Processing helix chain 'D' and resid 29 through 46 removed outlier: 3.655A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 4.039A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.765A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.852A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.752A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.550A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.528A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 203' Processing helix chain 'D' and resid 210 through 222 removed outlier: 3.807A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.550A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.877A pdb=" N LYS D 262 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.680A pdb=" N SER D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 331 through 340 removed outlier: 3.503A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 398 removed outlier: 3.767A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 476 through 487 removed outlier: 3.862A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.023A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 539 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 575 removed outlier: 3.514A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 3.802A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 578 through 583' Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 593 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 277 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 277 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 277 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 277 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2058 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: 3.04 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3185 1.31 - 1.43: 5634 1.43 - 1.56: 12401 1.56 - 1.68: 68 1.68 - 1.81: 272 Bond restraints: 21560 Sorted by residual: bond pdb=" C19 PCW B 708 " pdb=" C20 PCW B 708 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW D 709 " pdb=" C20 PCW D 709 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW A 704 " pdb=" C20 PCW A 704 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW C 706 " pdb=" C20 PCW C 706 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C19 PCW D 706 " pdb=" C20 PCW D 706 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 21555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 28001 3.56 - 7.12: 712 7.12 - 10.68: 224 10.68 - 14.24: 45 14.24 - 17.80: 12 Bond angle restraints: 28994 Sorted by residual: angle pdb=" C19 PCW A 709 " pdb=" C20 PCW A 709 " pdb=" C21 PCW A 709 " ideal model delta sigma weight residual 127.82 110.02 17.80 3.00e+00 1.11e-01 3.52e+01 angle pdb=" C19 PCW D 714 " pdb=" C20 PCW D 714 " pdb=" C21 PCW D 714 " ideal model delta sigma weight residual 127.82 110.25 17.57 3.00e+00 1.11e-01 3.43e+01 angle pdb=" C THR A 360 " pdb=" N SER A 361 " pdb=" CA SER A 361 " ideal model delta sigma weight residual 122.29 130.86 -8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" C THR D 360 " pdb=" N SER D 361 " pdb=" CA SER D 361 " ideal model delta sigma weight residual 122.29 130.82 -8.53 1.48e+00 4.57e-01 3.32e+01 angle pdb=" C THR B 360 " pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta sigma weight residual 122.29 130.79 -8.50 1.48e+00 4.57e-01 3.30e+01 ... (remaining 28989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.07: 12817 29.07 - 58.15: 621 58.15 - 87.22: 114 87.22 - 116.29: 8 116.29 - 145.37: 13 Dihedral angle restraints: 13573 sinusoidal: 6453 harmonic: 7120 Sorted by residual: dihedral pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta harmonic sigma weight residual 180.00 149.05 30.95 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N MET B 130 " pdb=" CA MET B 130 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 149.10 30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 13570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2829 0.101 - 0.201: 297 0.201 - 0.302: 25 0.302 - 0.402: 11 0.402 - 0.503: 4 Chirality restraints: 3166 Sorted by residual: chirality pdb=" CG LEU A 367 " pdb=" CB LEU A 367 " pdb=" CD1 LEU A 367 " pdb=" CD2 LEU A 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CG LEU D 367 " pdb=" CB LEU D 367 " pdb=" CD1 LEU D 367 " pdb=" CD2 LEU D 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CG LEU C 367 " pdb=" CB LEU C 367 " pdb=" CD1 LEU C 367 " pdb=" CD2 LEU C 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 3163 not shown) Planarity restraints: 3538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 703 " 0.147 2.00e-02 2.50e+03 1.34e-01 1.80e+02 pdb=" C19 PCW B 703 " -0.174 2.00e-02 2.50e+03 pdb=" C20 PCW B 703 " -0.086 2.00e-02 2.50e+03 pdb=" C21 PCW B 703 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW C 702 " -0.145 2.00e-02 2.50e+03 1.32e-01 1.75e+02 pdb=" C19 PCW C 702 " 0.171 2.00e-02 2.50e+03 pdb=" C20 PCW C 702 " 0.086 2.00e-02 2.50e+03 pdb=" C21 PCW C 702 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A 716 " 0.145 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C19 PCW A 716 " -0.171 2.00e-02 2.50e+03 pdb=" C20 PCW A 716 " -0.085 2.00e-02 2.50e+03 pdb=" C21 PCW A 716 " 0.111 2.00e-02 2.50e+03 ... (remaining 3535 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5690 2.81 - 3.33: 17769 3.33 - 3.85: 32652 3.85 - 4.38: 41664 4.38 - 4.90: 69820 Nonbonded interactions: 167595 Sorted by model distance: nonbonded pdb=" OG SER D 506 " pdb=" OH TYR D 526 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 506 " pdb=" OH TYR B 526 " model vdw 2.287 3.040 nonbonded pdb=" OG SER C 506 " pdb=" OH TYR C 526 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.288 3.040 nonbonded pdb=" NH1 ARG B 632 " pdb=" OD1 ASP C 34 " model vdw 2.328 3.120 ... (remaining 167590 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' and (resid 22 through 638 or (resid 708 through 709 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ )) or (resid 710 and (name C15 or name C16 or name C17 or name C18 or name C19)) \ )) selection = (chain 'B' and (resid 22 through 638 or (resid 708 through 709 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ )) or (resid 710 and (name C15 or name C16 or name C17 or name C18 or name C19)) \ )) selection = (chain 'C' and (resid 22 through 638 or resid 708 through 709 or (resid 710 and \ (name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'D' and (resid 22 through 638 or (resid 708 through 709 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ )) or (resid 710 and (name C15 or name C16 or name C17 or name C18 or name C19)) \ )) } 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: 1.560 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.650 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 0.215 21560 Z= 0.622 Angle : 1.534 17.801 28994 Z= 0.697 Chirality : 0.067 0.503 3166 Planarity : 0.011 0.134 3538 Dihedral : 17.365 145.366 8965 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.91 % Favored : 91.00 % Rotamer: Outliers : 0.95 % Allowed : 5.62 % Favored : 93.43 % 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: -6.09 (0.11), residues: 2412 helix: -4.21 (0.07), residues: 1364 sheet: -5.03 (0.19), residues: 84 loop : -3.42 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 305 TYR 0.030 0.003 TYR A 547 PHE 0.024 0.003 PHE B 169 TRP 0.023 0.003 TRP C 593 HIS 0.009 0.002 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.01344 / 0.62 (21560) covalent geometry : angle 1.53428 / 0.70 (28994) hydrogen bonds : bond 0.32473 / 21.18 ( 718) hydrogen bonds : angle 9.96106 / 6.93 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 480 time to evaluate : 0.776 Fit side-chains REVERT: A 51 LEU cc_start: 0.8078 (tt) cc_final: 0.7796 (tp) REVERT: A 78 MET cc_start: 0.8288 (mmt) cc_final: 0.8018 (mmt) REVERT: A 90 ASP cc_start: 0.7995 (p0) cc_final: 0.7562 (m-30) REVERT: A 130 MET cc_start: 0.6180 (mmm) cc_final: 0.5465 (mmm) REVERT: A 174 ASN cc_start: 0.7626 (t0) cc_final: 0.7345 (t0) REVERT: A 211 PHE cc_start: 0.8673 (m-10) cc_final: 0.8390 (m-10) REVERT: A 306 GLN cc_start: 0.8389 (mt0) cc_final: 0.7831 (mm-40) REVERT: A 324 TYR cc_start: 0.8349 (m-10) cc_final: 0.8144 (m-80) REVERT: A 378 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7779 (pmm) REVERT: A 381 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7082 (mtmm) REVERT: A 495 TRP cc_start: 0.9102 (m100) cc_final: 0.8845 (m100) REVERT: B 51 LEU cc_start: 0.8186 (tt) cc_final: 0.7924 (tp) REVERT: B 78 MET cc_start: 0.8369 (mmt) cc_final: 0.8121 (mmt) REVERT: B 90 ASP cc_start: 0.8036 (p0) cc_final: 0.7653 (m-30) REVERT: B 174 ASN cc_start: 0.7699 (t0) cc_final: 0.7242 (t0) REVERT: B 222 TYR cc_start: 0.8293 (m-80) cc_final: 0.8011 (m-80) REVERT: B 306 GLN cc_start: 0.8390 (mt0) cc_final: 0.7870 (mm-40) REVERT: B 315 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 322 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8165 (mtpp) REVERT: B 381 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7097 (ttpp) REVERT: B 481 MET cc_start: 0.7935 (ptt) cc_final: 0.7494 (ptt) REVERT: B 495 TRP cc_start: 0.9108 (m100) cc_final: 0.8870 (m100) REVERT: C 45 TRP cc_start: 0.7872 (m-10) cc_final: 0.7641 (m-10) REVERT: C 51 LEU cc_start: 0.8171 (tt) cc_final: 0.7938 (tp) REVERT: C 78 MET cc_start: 0.8442 (mmt) cc_final: 0.8201 (mmt) REVERT: C 90 ASP cc_start: 0.8087 (p0) cc_final: 0.7698 (m-30) REVERT: C 174 ASN cc_start: 0.7769 (t0) cc_final: 0.7567 (t0) REVERT: C 222 TYR cc_start: 0.8363 (m-80) cc_final: 0.8061 (m-80) REVERT: C 306 GLN cc_start: 0.8367 (mt0) cc_final: 0.7835 (mm-40) REVERT: C 315 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7736 (mt-10) REVERT: C 381 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7036 (ttpp) REVERT: C 481 MET cc_start: 0.7895 (ptt) cc_final: 0.7659 (ptt) REVERT: C 495 TRP cc_start: 0.9123 (m100) cc_final: 0.8892 (m100) REVERT: D 51 LEU cc_start: 0.8174 (tt) cc_final: 0.7969 (tp) REVERT: D 73 HIS cc_start: 0.7860 (m90) cc_final: 0.7605 (m-70) REVERT: D 90 ASP cc_start: 0.7951 (p0) cc_final: 0.7683 (m-30) REVERT: D 107 PHE cc_start: 0.8397 (m-80) cc_final: 0.8179 (m-80) REVERT: D 222 TYR cc_start: 0.8430 (m-80) cc_final: 0.7702 (m-80) REVERT: D 306 GLN cc_start: 0.8338 (mt0) cc_final: 0.7864 (mm-40) REVERT: D 315 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7830 (mt-10) REVERT: D 481 MET cc_start: 0.7908 (ptt) cc_final: 0.7697 (ptt) outliers start: 20 outliers final: 11 residues processed: 493 average time/residue: 0.1567 time to fit residues: 116.0661 Evaluate side-chains 353 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 341 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 165 HIS A 201 HIS A 206 GLN A 252 ASN A 261 GLN A 267 GLN A 582 HIS B 201 HIS B 206 GLN B 252 ASN B 261 GLN B 267 GLN B 426 HIS C 118 GLN C 201 HIS C 206 GLN C 252 ASN C 261 GLN C 267 GLN C 426 HIS C 582 HIS D 118 GLN D 165 HIS D 201 HIS D 206 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 267 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133175 restraints weight = 25017.501| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.43 r_work: 0.3337 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21560 Z= 0.130 Angle : 0.678 7.471 28994 Z= 0.343 Chirality : 0.041 0.163 3166 Planarity : 0.006 0.067 3538 Dihedral : 18.250 145.687 4273 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.94 % Allowed : 10.16 % Favored : 87.90 % 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: -4.23 (0.15), residues: 2412 helix: -2.57 (0.11), residues: 1380 sheet: -4.69 (0.26), residues: 76 loop : -2.80 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 628 TYR 0.013 0.001 TYR B 467 PHE 0.030 0.002 PHE C 531 TRP 0.010 0.001 TRP A 593 HIS 0.002 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21560) covalent geometry : angle 0.67834 / 0.34 (28994) hydrogen bonds : bond 0.04557 / 2.99 ( 718) hydrogen bonds : angle 5.02861 / 3.47 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 368 time to evaluate : 0.481 Fit side-chains REVERT: A 90 ASP cc_start: 0.8377 (p0) cc_final: 0.7833 (m-30) REVERT: A 230 GLN cc_start: 0.7929 (pm20) cc_final: 0.7676 (pt0) REVERT: A 306 GLN cc_start: 0.8542 (mt0) cc_final: 0.8288 (mm-40) REVERT: A 338 LEU cc_start: 0.8584 (tt) cc_final: 0.8330 (mp) REVERT: A 378 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7996 (pmm) REVERT: B 90 ASP cc_start: 0.8376 (p0) cc_final: 0.7815 (m-30) REVERT: B 130 MET cc_start: 0.6063 (mmm) cc_final: 0.5749 (mmm) REVERT: B 230 GLN cc_start: 0.7861 (pm20) cc_final: 0.7595 (pt0) REVERT: B 306 GLN cc_start: 0.8542 (mt0) cc_final: 0.8274 (mm-40) REVERT: B 338 LEU cc_start: 0.8592 (tt) cc_final: 0.8349 (mp) REVERT: B 381 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7154 (mtmm) REVERT: C 90 ASP cc_start: 0.8380 (p0) cc_final: 0.7825 (m-30) REVERT: C 130 MET cc_start: 0.6134 (mmm) cc_final: 0.5837 (mmm) REVERT: C 230 GLN cc_start: 0.7812 (pm20) cc_final: 0.7543 (pt0) REVERT: C 306 GLN cc_start: 0.8515 (mt0) cc_final: 0.8271 (mm-40) REVERT: C 338 LEU cc_start: 0.8603 (tt) cc_final: 0.8366 (mp) REVERT: C 381 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7110 (mtmm) REVERT: D 73 HIS cc_start: 0.7938 (m90) cc_final: 0.7731 (m-70) REVERT: D 90 ASP cc_start: 0.8288 (p0) cc_final: 0.7914 (m-30) REVERT: D 222 TYR cc_start: 0.8494 (m-80) cc_final: 0.8262 (m-80) REVERT: D 230 GLN cc_start: 0.7931 (pm20) cc_final: 0.7624 (pt0) REVERT: D 306 GLN cc_start: 0.8518 (mt0) cc_final: 0.8262 (mm-40) outliers start: 41 outliers final: 18 residues processed: 395 average time/residue: 0.1414 time to fit residues: 85.1045 Evaluate side-chains 324 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 305 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 122 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 239 optimal weight: 0.2980 chunk 140 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN A 370 GLN B 267 GLN B 370 GLN B 572 ASN B 582 HIS C 582 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 370 GLN D 582 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132602 restraints weight = 25210.333| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.48 r_work: 0.3322 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21560 Z= 0.112 Angle : 0.607 9.180 28994 Z= 0.306 Chirality : 0.040 0.150 3166 Planarity : 0.005 0.064 3538 Dihedral : 16.691 136.690 4273 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.07 % Allowed : 11.53 % Favored : 85.40 % 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: -3.16 (0.16), residues: 2412 helix: -1.55 (0.13), residues: 1372 sheet: -4.20 (0.33), residues: 76 loop : -2.61 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 628 TYR 0.011 0.001 TYR B 324 PHE 0.013 0.001 PHE B 531 TRP 0.007 0.001 TRP C 593 HIS 0.014 0.001 HIS C 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21560) covalent geometry : angle 0.60705 / 0.31 (28994) hydrogen bonds : bond 0.03839 / 2.51 ( 718) hydrogen bonds : angle 4.55302 / 3.15 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 344 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8319 (p0) cc_final: 0.7883 (m-30) REVERT: A 130 MET cc_start: 0.5685 (mmm) cc_final: 0.5167 (mmm) REVERT: A 306 GLN cc_start: 0.8555 (mt0) cc_final: 0.8294 (mm-40) REVERT: B 90 ASP cc_start: 0.8324 (p0) cc_final: 0.7814 (m-30) REVERT: B 222 TYR cc_start: 0.8465 (m-80) cc_final: 0.8139 (m-80) REVERT: B 306 GLN cc_start: 0.8584 (mt0) cc_final: 0.8266 (mm-40) REVERT: B 378 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8061 (pmm) REVERT: B 448 SER cc_start: 0.8719 (t) cc_final: 0.8507 (m) REVERT: C 90 ASP cc_start: 0.8356 (p0) cc_final: 0.7865 (m-30) REVERT: C 130 MET cc_start: 0.5648 (mmm) cc_final: 0.5401 (mmm) REVERT: C 222 TYR cc_start: 0.8492 (m-80) cc_final: 0.8200 (m-80) REVERT: C 306 GLN cc_start: 0.8562 (mt0) cc_final: 0.8261 (mm-40) REVERT: C 381 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7137 (mtmm) REVERT: D 90 ASP cc_start: 0.8309 (p0) cc_final: 0.7973 (m-30) REVERT: D 130 MET cc_start: 0.5662 (mmm) cc_final: 0.5338 (tpt) REVERT: D 230 GLN cc_start: 0.7988 (pm20) cc_final: 0.7771 (pt0) REVERT: D 306 GLN cc_start: 0.8505 (mt0) cc_final: 0.8249 (mm-40) outliers start: 65 outliers final: 45 residues processed: 386 average time/residue: 0.1438 time to fit residues: 85.7442 Evaluate side-chains 357 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 5.9990 chunk 158 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 118 GLN B 165 HIS B 572 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 426 HIS ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124168 restraints weight = 25307.454| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.63 r_work: 0.3194 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21560 Z= 0.203 Angle : 0.658 8.145 28994 Z= 0.329 Chirality : 0.044 0.190 3166 Planarity : 0.005 0.065 3538 Dihedral : 16.484 133.077 4273 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.73 % Allowed : 12.52 % Favored : 83.74 % 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: -2.58 (0.17), residues: 2412 helix: -1.05 (0.14), residues: 1368 sheet: -3.94 (0.37), residues: 76 loop : -2.39 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 628 TYR 0.019 0.002 TYR C 324 PHE 0.015 0.002 PHE D 468 TRP 0.007 0.001 TRP D 593 HIS 0.016 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 (21560) covalent geometry : angle 0.65834 / 0.33 (28994) hydrogen bonds : bond 0.04029 / 2.63 ( 718) hydrogen bonds : angle 4.50553 / 3.13 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 311 time to evaluate : 0.743 Fit side-chains REVERT: A 90 ASP cc_start: 0.8338 (p0) cc_final: 0.7962 (m-30) REVERT: A 130 MET cc_start: 0.5916 (mmm) cc_final: 0.5677 (mmm) REVERT: A 306 GLN cc_start: 0.8680 (mt0) cc_final: 0.8302 (mm-40) REVERT: B 90 ASP cc_start: 0.8369 (p0) cc_final: 0.7969 (m-30) REVERT: B 130 MET cc_start: 0.5817 (mmm) cc_final: 0.5595 (mmm) REVERT: B 306 GLN cc_start: 0.8681 (mt0) cc_final: 0.8311 (mm-40) REVERT: C 90 ASP cc_start: 0.8392 (p0) cc_final: 0.7914 (m-30) REVERT: C 130 MET cc_start: 0.5878 (mmm) cc_final: 0.5623 (mmm) REVERT: C 306 GLN cc_start: 0.8676 (mt0) cc_final: 0.8299 (mm-40) REVERT: C 381 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7001 (mtmm) REVERT: C 481 MET cc_start: 0.8325 (ptp) cc_final: 0.8108 (ptp) REVERT: D 62 ASN cc_start: 0.7043 (m110) cc_final: 0.6835 (m110) REVERT: D 90 ASP cc_start: 0.8348 (p0) cc_final: 0.7969 (m-30) REVERT: D 130 MET cc_start: 0.5969 (mmm) cc_final: 0.5629 (tpt) REVERT: D 140 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7410 (mtm-85) REVERT: D 306 GLN cc_start: 0.8646 (mt0) cc_final: 0.8260 (mm-40) outliers start: 79 outliers final: 52 residues processed: 376 average time/residue: 0.1478 time to fit residues: 85.4986 Evaluate side-chains 349 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 195 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 258 HIS B 261 GLN B 582 HIS C 73 HIS C 258 HIS C 261 GLN C 370 GLN C 572 ASN D 258 HIS D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122346 restraints weight = 24428.200| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.71 r_work: 0.3173 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21560 Z= 0.112 Angle : 0.582 6.881 28994 Z= 0.293 Chirality : 0.041 0.166 3166 Planarity : 0.005 0.065 3538 Dihedral : 15.727 127.422 4270 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.30 % Allowed : 12.85 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.05 (0.17), residues: 2412 helix: -0.55 (0.14), residues: 1368 sheet: -3.83 (0.40), residues: 76 loop : -2.27 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.021 0.001 TYR D 324 PHE 0.015 0.001 PHE D 211 TRP 0.008 0.001 TRP B 495 HIS 0.026 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (21560) covalent geometry : angle 0.58247 / 0.29 (28994) hydrogen bonds : bond 0.03423 / 2.23 ( 718) hydrogen bonds : angle 4.29844 / 2.98 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 313 time to evaluate : 0.589 Fit side-chains REVERT: A 90 ASP cc_start: 0.8190 (p0) cc_final: 0.7736 (m-30) REVERT: A 130 MET cc_start: 0.5584 (mmm) cc_final: 0.5319 (tpt) REVERT: A 222 TYR cc_start: 0.8201 (m-80) cc_final: 0.7992 (m-80) REVERT: A 306 GLN cc_start: 0.8635 (mt0) cc_final: 0.8022 (mm-40) REVERT: A 315 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: B 90 ASP cc_start: 0.8160 (p0) cc_final: 0.7680 (m-30) REVERT: B 130 MET cc_start: 0.5402 (mmm) cc_final: 0.4927 (tpt) REVERT: B 306 GLN cc_start: 0.8647 (mt0) cc_final: 0.8036 (mm-40) REVERT: B 378 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8335 (pmm) REVERT: B 481 MET cc_start: 0.8262 (ptp) cc_final: 0.8048 (ptp) REVERT: C 90 ASP cc_start: 0.8220 (p0) cc_final: 0.7717 (m-30) REVERT: C 130 MET cc_start: 0.5315 (mmm) cc_final: 0.4983 (mmm) REVERT: C 306 GLN cc_start: 0.8637 (mt0) cc_final: 0.8020 (mm-40) REVERT: C 474 MET cc_start: 0.8175 (tmm) cc_final: 0.7864 (tmm) REVERT: C 481 MET cc_start: 0.8346 (ptp) cc_final: 0.8111 (ptp) REVERT: D 62 ASN cc_start: 0.6995 (m110) cc_final: 0.6727 (m110) REVERT: D 90 ASP cc_start: 0.8231 (p0) cc_final: 0.7752 (m-30) REVERT: D 130 MET cc_start: 0.5476 (mmm) cc_final: 0.5051 (tpt) REVERT: D 140 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7428 (mtm-85) REVERT: D 174 ASN cc_start: 0.7995 (t0) cc_final: 0.7734 (t0) REVERT: D 306 GLN cc_start: 0.8616 (mt0) cc_final: 0.8032 (mm-40) REVERT: D 502 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8471 (mt) outliers start: 91 outliers final: 58 residues processed: 388 average time/residue: 0.1383 time to fit residues: 83.5407 Evaluate side-chains 363 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS A 258 HIS A 261 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 73 HIS B 261 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 73 HIS C 165 HIS C 261 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119858 restraints weight = 24472.359| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.71 r_work: 0.3132 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21560 Z= 0.157 Angle : 0.607 7.594 28994 Z= 0.302 Chirality : 0.042 0.172 3166 Planarity : 0.005 0.064 3538 Dihedral : 15.490 122.916 4270 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.58 % Allowed : 12.81 % Favored : 82.61 % 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: -1.84 (0.17), residues: 2412 helix: -0.36 (0.14), residues: 1384 sheet: -3.77 (0.41), residues: 76 loop : -2.24 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.017 0.001 TYR D 324 PHE 0.014 0.001 PHE B 211 TRP 0.006 0.001 TRP B 495 HIS 0.013 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (21560) covalent geometry : angle 0.60729 / 0.30 (28994) hydrogen bonds : bond 0.03591 / 2.33 ( 718) hydrogen bonds : angle 4.26679 / 2.96 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 303 time to evaluate : 0.566 Fit side-chains REVERT: A 80 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: A 90 ASP cc_start: 0.8245 (p0) cc_final: 0.7772 (m-30) REVERT: A 96 MET cc_start: 0.8572 (mmt) cc_final: 0.8314 (mmt) REVERT: A 130 MET cc_start: 0.5726 (mmm) cc_final: 0.5421 (tpt) REVERT: A 222 TYR cc_start: 0.8302 (m-80) cc_final: 0.7994 (m-80) REVERT: A 306 GLN cc_start: 0.8644 (mt0) cc_final: 0.8097 (mm-40) REVERT: A 315 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: A 502 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 80 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: B 90 ASP cc_start: 0.8238 (p0) cc_final: 0.7744 (m-30) REVERT: B 130 MET cc_start: 0.5531 (mmm) cc_final: 0.5179 (tpt) REVERT: B 140 ARG cc_start: 0.7675 (ptp90) cc_final: 0.7349 (mtm-85) REVERT: B 306 GLN cc_start: 0.8645 (mt0) cc_final: 0.8097 (mm-40) REVERT: B 378 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8330 (pmm) REVERT: B 502 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 90 ASP cc_start: 0.8216 (p0) cc_final: 0.7734 (m-30) REVERT: C 130 MET cc_start: 0.5573 (mmm) cc_final: 0.5255 (mmm) REVERT: C 140 ARG cc_start: 0.7650 (ptp90) cc_final: 0.7317 (mtm-85) REVERT: C 306 GLN cc_start: 0.8635 (mt0) cc_final: 0.8102 (mm-40) REVERT: C 315 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8346 (mp0) REVERT: C 474 MET cc_start: 0.8260 (tmm) cc_final: 0.7916 (tmm) REVERT: C 502 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8439 (mt) REVERT: D 62 ASN cc_start: 0.7011 (m110) cc_final: 0.6735 (m110) REVERT: D 90 ASP cc_start: 0.8234 (p0) cc_final: 0.7786 (m-30) REVERT: D 130 MET cc_start: 0.5551 (mmm) cc_final: 0.5167 (tpt) REVERT: D 140 ARG cc_start: 0.7689 (ptp90) cc_final: 0.7401 (mtm-85) REVERT: D 306 GLN cc_start: 0.8615 (mt0) cc_final: 0.8013 (mm-40) REVERT: D 315 GLU cc_start: 0.8486 (mp0) cc_final: 0.8241 (pm20) REVERT: D 502 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8448 (mt) outliers start: 97 outliers final: 67 residues processed: 392 average time/residue: 0.1358 time to fit residues: 82.3727 Evaluate side-chains 372 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 297 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS A 261 GLN A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 73 HIS B 261 GLN B 546 ASN B 582 HIS C 73 HIS C 261 GLN C 546 ASN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.152689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120292 restraints weight = 24506.354| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.72 r_work: 0.3204 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21560 Z= 0.138 Angle : 0.598 7.675 28994 Z= 0.297 Chirality : 0.042 0.179 3166 Planarity : 0.005 0.064 3538 Dihedral : 15.228 118.847 4270 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.35 % Allowed : 13.61 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.57 (0.17), residues: 2412 helix: -0.18 (0.14), residues: 1380 sheet: -3.76 (0.41), residues: 76 loop : -2.05 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 628 TYR 0.015 0.001 TYR D 324 PHE 0.011 0.001 PHE A 211 TRP 0.007 0.001 TRP C 495 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (21560) covalent geometry : angle 0.59768 / 0.30 (28994) hydrogen bonds : bond 0.03441 / 2.24 ( 718) hydrogen bonds : angle 4.23056 / 2.93 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 305 time to evaluate : 0.665 Fit side-chains REVERT: A 90 ASP cc_start: 0.8269 (p0) cc_final: 0.7855 (m-30) REVERT: A 130 MET cc_start: 0.5745 (mmm) cc_final: 0.5498 (tpt) REVERT: A 140 ARG cc_start: 0.7679 (ptp90) cc_final: 0.7308 (mtm-85) REVERT: A 222 TYR cc_start: 0.8414 (m-80) cc_final: 0.8065 (m-80) REVERT: A 306 GLN cc_start: 0.8695 (mt0) cc_final: 0.8200 (mm-40) REVERT: A 502 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8510 (mt) REVERT: A 594 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7556 (mpp-170) REVERT: B 80 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: B 90 ASP cc_start: 0.8224 (p0) cc_final: 0.7830 (m-30) REVERT: B 130 MET cc_start: 0.5495 (mmm) cc_final: 0.5163 (tpt) REVERT: B 140 ARG cc_start: 0.7713 (ptp90) cc_final: 0.7361 (mtm-85) REVERT: B 306 GLN cc_start: 0.8708 (mt0) cc_final: 0.8223 (mm-40) REVERT: B 378 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8331 (pmm) REVERT: B 481 MET cc_start: 0.8068 (ptp) cc_final: 0.7748 (tpt) REVERT: B 502 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8522 (mt) REVERT: C 90 ASP cc_start: 0.8281 (p0) cc_final: 0.7881 (m-30) REVERT: C 130 MET cc_start: 0.5522 (mmm) cc_final: 0.5214 (tpt) REVERT: C 140 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7365 (mtm-85) REVERT: C 306 GLN cc_start: 0.8698 (mt0) cc_final: 0.8213 (mm-40) REVERT: C 315 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8347 (mp0) REVERT: C 378 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8286 (pmm) REVERT: C 474 MET cc_start: 0.8184 (tmm) cc_final: 0.7866 (tmm) REVERT: C 502 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8525 (mt) REVERT: D 62 ASN cc_start: 0.6999 (m110) cc_final: 0.6748 (m110) REVERT: D 90 ASP cc_start: 0.8270 (p0) cc_final: 0.7896 (m-30) REVERT: D 130 MET cc_start: 0.5404 (mmm) cc_final: 0.5074 (tpt) REVERT: D 140 ARG cc_start: 0.7695 (ptp90) cc_final: 0.7401 (mtm-85) REVERT: D 306 GLN cc_start: 0.8648 (mt0) cc_final: 0.8099 (mm-40) REVERT: D 502 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8532 (mt) REVERT: D 594 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7591 (mpp-170) outliers start: 92 outliers final: 66 residues processed: 389 average time/residue: 0.1407 time to fit residues: 84.0266 Evaluate side-chains 372 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 73 HIS B 546 ASN B 582 HIS C 73 HIS C 546 ASN D 261 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.152562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120246 restraints weight = 24349.128| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.71 r_work: 0.3206 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21560 Z= 0.137 Angle : 0.596 7.782 28994 Z= 0.295 Chirality : 0.042 0.168 3166 Planarity : 0.005 0.064 3538 Dihedral : 15.000 114.672 4270 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.35 % Allowed : 13.89 % Favored : 81.76 % 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: -1.41 (0.17), residues: 2412 helix: -0.04 (0.15), residues: 1376 sheet: -3.77 (0.41), residues: 76 loop : -1.96 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 355 TYR 0.015 0.001 TYR D 324 PHE 0.010 0.001 PHE A 211 TRP 0.007 0.001 TRP C 495 HIS 0.009 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (21560) covalent geometry : angle 0.59595 / 0.30 (28994) hydrogen bonds : bond 0.03401 / 2.21 ( 718) hydrogen bonds : angle 4.21470 / 2.92 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 302 time to evaluate : 0.824 Fit side-chains REVERT: A 90 ASP cc_start: 0.8251 (p0) cc_final: 0.7887 (m-30) REVERT: A 130 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.5362 (tpt) REVERT: A 140 ARG cc_start: 0.7667 (ptp90) cc_final: 0.7335 (mtm-85) REVERT: A 222 TYR cc_start: 0.8427 (m-80) cc_final: 0.8117 (m-80) REVERT: A 306 GLN cc_start: 0.8674 (mt0) cc_final: 0.8182 (mm-40) REVERT: A 315 GLU cc_start: 0.8437 (mp0) cc_final: 0.8224 (pm20) REVERT: A 502 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 90 ASP cc_start: 0.8226 (p0) cc_final: 0.7839 (m-30) REVERT: B 130 MET cc_start: 0.5431 (mmm) cc_final: 0.5119 (tpt) REVERT: B 140 ARG cc_start: 0.7727 (ptp90) cc_final: 0.7394 (mtm-85) REVERT: B 306 GLN cc_start: 0.8678 (mt0) cc_final: 0.8192 (mm-40) REVERT: B 378 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8319 (pmm) REVERT: B 481 MET cc_start: 0.7995 (ptp) cc_final: 0.7743 (tpt) REVERT: B 502 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8512 (mt) REVERT: C 90 ASP cc_start: 0.8271 (p0) cc_final: 0.7881 (m-30) REVERT: C 130 MET cc_start: 0.5459 (mmm) cc_final: 0.5191 (tpt) REVERT: C 174 ASN cc_start: 0.8059 (t0) cc_final: 0.7729 (t0) REVERT: C 306 GLN cc_start: 0.8687 (mt0) cc_final: 0.8195 (mm-40) REVERT: C 378 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (pmm) REVERT: C 474 MET cc_start: 0.8135 (tmm) cc_final: 0.7824 (tmm) REVERT: C 502 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8525 (mt) REVERT: C 594 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7571 (mpp-170) REVERT: D 62 ASN cc_start: 0.7003 (m110) cc_final: 0.6750 (m110) REVERT: D 90 ASP cc_start: 0.8245 (p0) cc_final: 0.7877 (m-30) REVERT: D 140 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7404 (mtm-85) REVERT: D 306 GLN cc_start: 0.8634 (mt0) cc_final: 0.8080 (mm-40) REVERT: D 502 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8525 (mt) REVERT: D 594 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7626 (mpp-170) outliers start: 92 outliers final: 75 residues processed: 386 average time/residue: 0.1366 time to fit residues: 80.9611 Evaluate side-chains 377 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 295 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 159 optimal weight: 0.4980 chunk 177 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS A 261 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 261 GLN B 582 HIS C 261 GLN D 261 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119297 restraints weight = 24396.218| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.70 r_work: 0.3192 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21560 Z= 0.159 Angle : 0.612 7.966 28994 Z= 0.303 Chirality : 0.043 0.176 3166 Planarity : 0.005 0.064 3538 Dihedral : 14.906 111.031 4270 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.30 % Allowed : 14.46 % Favored : 81.24 % 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: -1.37 (0.17), residues: 2412 helix: 0.00 (0.15), residues: 1372 sheet: -3.76 (0.41), residues: 76 loop : -1.95 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 628 TYR 0.015 0.001 TYR D 324 PHE 0.015 0.001 PHE A 211 TRP 0.006 0.001 TRP A 583 HIS 0.006 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (21560) covalent geometry : angle 0.61208 / 0.30 (28994) hydrogen bonds : bond 0.03485 / 2.27 ( 718) hydrogen bonds : angle 4.22084 / 2.93 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 299 time to evaluate : 0.732 Fit side-chains REVERT: A 90 ASP cc_start: 0.8249 (p0) cc_final: 0.7904 (m-30) REVERT: A 130 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.5416 (tpt) REVERT: A 222 TYR cc_start: 0.8463 (m-80) cc_final: 0.8136 (m-80) REVERT: A 306 GLN cc_start: 0.8676 (mt0) cc_final: 0.8181 (mm-40) REVERT: A 315 GLU cc_start: 0.8460 (mp0) cc_final: 0.8250 (pm20) REVERT: A 502 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8508 (mt) REVERT: B 90 ASP cc_start: 0.8219 (p0) cc_final: 0.7856 (m-30) REVERT: B 130 MET cc_start: 0.5502 (mmm) cc_final: 0.5243 (tpt) REVERT: B 306 GLN cc_start: 0.8692 (mt0) cc_final: 0.8211 (mm-40) REVERT: B 378 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (pmm) REVERT: B 474 MET cc_start: 0.7719 (tmm) cc_final: 0.6971 (tpp) REVERT: B 481 MET cc_start: 0.8017 (ptp) cc_final: 0.7734 (tpt) REVERT: B 502 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8529 (mt) REVERT: C 90 ASP cc_start: 0.8253 (p0) cc_final: 0.7880 (m-30) REVERT: C 130 MET cc_start: 0.5500 (mmm) cc_final: 0.5208 (tpt) REVERT: C 174 ASN cc_start: 0.8087 (t0) cc_final: 0.7776 (t0) REVERT: C 306 GLN cc_start: 0.8731 (mt0) cc_final: 0.8231 (mm-40) REVERT: C 315 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8422 (mp0) REVERT: C 378 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8252 (pmm) REVERT: C 502 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8530 (mt) REVERT: C 594 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7604 (mpp-170) REVERT: C 610 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8272 (tpp-160) REVERT: D 62 ASN cc_start: 0.7067 (m110) cc_final: 0.6800 (m110) REVERT: D 90 ASP cc_start: 0.8270 (p0) cc_final: 0.7887 (m-30) REVERT: D 140 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7420 (mtm-85) REVERT: D 306 GLN cc_start: 0.8673 (mt0) cc_final: 0.8110 (mm-40) REVERT: D 502 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8541 (mt) outliers start: 91 outliers final: 73 residues processed: 384 average time/residue: 0.1409 time to fit residues: 83.4424 Evaluate side-chains 376 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 296 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 582 HIS D 257 GLN D 261 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120952 restraints weight = 24571.219| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.70 r_work: 0.3215 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21560 Z= 0.122 Angle : 0.590 8.311 28994 Z= 0.293 Chirality : 0.041 0.164 3166 Planarity : 0.005 0.064 3538 Dihedral : 14.582 105.734 4270 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.02 % Allowed : 14.74 % Favored : 81.24 % 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: -1.20 (0.18), residues: 2412 helix: 0.15 (0.15), residues: 1376 sheet: -3.75 (0.41), residues: 76 loop : -1.90 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 628 TYR 0.015 0.001 TYR D 324 PHE 0.014 0.001 PHE D 211 TRP 0.010 0.001 TRP A 583 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (21560) covalent geometry : angle 0.58987 / 0.29 (28994) hydrogen bonds : bond 0.03278 / 2.13 ( 718) hydrogen bonds : angle 4.16655 / 2.88 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 0.606 Fit side-chains REVERT: A 90 ASP cc_start: 0.8213 (p0) cc_final: 0.7884 (m-30) REVERT: A 130 MET cc_start: 0.5490 (mmm) cc_final: 0.5261 (tpt) REVERT: A 222 TYR cc_start: 0.8436 (m-80) cc_final: 0.8119 (m-80) REVERT: A 306 GLN cc_start: 0.8613 (mt0) cc_final: 0.8037 (mm-40) REVERT: A 315 GLU cc_start: 0.8482 (mp0) cc_final: 0.8271 (pm20) REVERT: A 474 MET cc_start: 0.7668 (tmm) cc_final: 0.6906 (tpp) REVERT: A 502 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 90 ASP cc_start: 0.8195 (p0) cc_final: 0.7858 (m-30) REVERT: B 130 MET cc_start: 0.5300 (mmm) cc_final: 0.5064 (tpt) REVERT: B 306 GLN cc_start: 0.8651 (mt0) cc_final: 0.8098 (mm-40) REVERT: B 378 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8299 (pmm) REVERT: B 474 MET cc_start: 0.7694 (tmm) cc_final: 0.6851 (tpp) REVERT: B 502 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8517 (mt) REVERT: C 57 ASP cc_start: 0.7649 (t70) cc_final: 0.7355 (t70) REVERT: C 90 ASP cc_start: 0.8219 (p0) cc_final: 0.7873 (m-30) REVERT: C 174 ASN cc_start: 0.8043 (t0) cc_final: 0.7768 (t0) REVERT: C 306 GLN cc_start: 0.8641 (mt0) cc_final: 0.8056 (mm-40) REVERT: C 315 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8449 (mp0) REVERT: C 378 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8257 (pmm) REVERT: C 474 MET cc_start: 0.7938 (tmm) cc_final: 0.7737 (tmm) REVERT: C 502 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8518 (mt) REVERT: C 610 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.8251 (tpp-160) REVERT: D 62 ASN cc_start: 0.7031 (m110) cc_final: 0.6782 (m110) REVERT: D 90 ASP cc_start: 0.8237 (p0) cc_final: 0.7907 (m-30) REVERT: D 140 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7463 (mtm-85) REVERT: D 306 GLN cc_start: 0.8642 (mt0) cc_final: 0.8085 (mm-40) REVERT: D 474 MET cc_start: 0.7621 (tmm) cc_final: 0.6913 (tpp) REVERT: D 502 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8530 (mt) outliers start: 85 outliers final: 72 residues processed: 383 average time/residue: 0.1446 time to fit residues: 84.6373 Evaluate side-chains 377 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 299 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 611 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS A 261 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 261 GLN B 582 HIS C 261 GLN D 261 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122995 restraints weight = 24661.234| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.77 r_work: 0.3171 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21560 Z= 0.108 Angle : 0.583 8.761 28994 Z= 0.289 Chirality : 0.041 0.164 3166 Planarity : 0.005 0.065 3538 Dihedral : 14.280 100.599 4270 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.92 % Allowed : 15.17 % Favored : 80.91 % 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: -0.98 (0.18), residues: 2412 helix: 0.34 (0.15), residues: 1352 sheet: -3.76 (0.41), residues: 76 loop : -1.77 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 628 TYR 0.014 0.001 TYR D 324 PHE 0.013 0.001 PHE D 211 TRP 0.009 0.001 TRP A 583 HIS 0.008 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21560) covalent geometry : angle 0.58268 / 0.29 (28994) hydrogen bonds : bond 0.03157 / 2.04 ( 718) hydrogen bonds : angle 4.12046 / 2.84 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5342.80 seconds wall clock time: 91 minutes 58.58 seconds (5518.58 seconds total)