Starting phenix.real_space_refine on Thu Mar 5 10:18:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k4b_22663/03_2026/7k4b_22663_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k4b_22663/03_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_22663/03_2026/7k4b_22663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k4b_22663/03_2026/7k4b_22663.map" model { file = "/net/cci-nas-00/data/ceres_data/7k4b_22663/03_2026/7k4b_22663_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k4b_22663/03_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-5986/lib/python3.9/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, 408 Unusual residues: {' CA': 1, 'PCW': 12, 'VUG': 2, 'Y01': 2} 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: "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: 4.66, 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.59 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: 3.38 Time building geometry restraints manager: 2.22 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.920 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 covalent geometry : bond 0.01344 (21560) covalent geometry : angle 1.53428 (28994) hydrogen bonds : bond 0.32473 ( 718) hydrogen bonds : angle 9.96106 ( 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 : 0.719 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: 0.1589 time to fit residues: 116.9054 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 : 0.572 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 165 HIS A 201 HIS A 206 GLN A 252 ASN A 261 GLN A 267 GLN A 426 HIS A 582 HIS B 201 HIS B 206 GLN B 252 ASN B 261 GLN B 267 GLN B 426 HIS C 201 HIS C 206 GLN C 252 ASN C 261 GLN C 267 GLN C 426 HIS C 572 ASN 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130218 restraints weight = 25023.479| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.58 r_work: 0.3306 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21560 Z= 0.128 Angle : 0.677 7.573 28994 Z= 0.342 Chirality : 0.041 0.164 3166 Planarity : 0.006 0.067 3538 Dihedral : 18.217 145.583 4273 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.98 % Allowed : 10.16 % Favored : 87.85 % 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: -4.22 (0.15), residues: 2412 helix: -2.56 (0.11), residues: 1380 sheet: -4.68 (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 0.029 0.002 PHE C 531 TRP 0.010 0.001 TRP A 593 HIS 0.003 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00281 (21560) covalent geometry : angle 0.67730 (28994) hydrogen bonds : bond 0.04386 ( 718) hydrogen bonds : angle 5.01056 ( 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 410 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 368 time to evaluate : 0.748 Fit side-chains REVERT: A 90 ASP cc_start: 0.8403 (p0) cc_final: 0.7813 (m-30) REVERT: A 230 GLN cc_start: 0.7952 (pm20) cc_final: 0.7681 (pt0) REVERT: A 306 GLN cc_start: 0.8593 (mt0) cc_final: 0.8293 (mm-40) REVERT: A 338 LEU cc_start: 0.8609 (tt) cc_final: 0.8353 (mp) REVERT: A 378 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8020 (pmm) REVERT: B 90 ASP cc_start: 0.8405 (p0) cc_final: 0.7804 (m-30) REVERT: B 130 MET cc_start: 0.6067 (mmm) cc_final: 0.5734 (mmm) REVERT: B 230 GLN cc_start: 0.7893 (pm20) cc_final: 0.7608 (pt0) REVERT: B 306 GLN cc_start: 0.8599 (mt0) cc_final: 0.8286 (mm-40) REVERT: B 338 LEU cc_start: 0.8618 (tt) cc_final: 0.8373 (mp) REVERT: B 381 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7104 (mtmm) REVERT: C 90 ASP cc_start: 0.8407 (p0) cc_final: 0.7805 (m-30) REVERT: C 130 MET cc_start: 0.6138 (mmm) cc_final: 0.5802 (mmm) REVERT: C 230 GLN cc_start: 0.7832 (pm20) cc_final: 0.7548 (pt0) REVERT: C 306 GLN cc_start: 0.8583 (mt0) cc_final: 0.8297 (mm-40) REVERT: C 338 LEU cc_start: 0.8626 (tt) cc_final: 0.8387 (mp) REVERT: C 381 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7055 (mtmm) REVERT: D 73 HIS cc_start: 0.7970 (m90) cc_final: 0.7759 (m-70) REVERT: D 90 ASP cc_start: 0.8309 (p0) cc_final: 0.7893 (m-30) REVERT: D 222 TYR cc_start: 0.8497 (m-80) cc_final: 0.8237 (m-80) REVERT: D 230 GLN cc_start: 0.7950 (pm20) cc_final: 0.7633 (pt0) REVERT: D 306 GLN cc_start: 0.8581 (mt0) cc_final: 0.8278 (mm-40) outliers start: 42 outliers final: 18 residues processed: 398 average time/residue: 0.1455 time to fit residues: 88.4554 Evaluate side-chains 325 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 B residue 582 HIS 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: 2.9990 chunk 83 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 0.0000 chunk 140 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 370 GLN B 118 GLN B 267 GLN B 572 ASN C 582 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 370 GLN D 426 HIS D 582 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128920 restraints weight = 25234.189| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.60 r_work: 0.3290 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21560 Z= 0.125 Angle : 0.619 9.256 28994 Z= 0.311 Chirality : 0.041 0.161 3166 Planarity : 0.005 0.065 3538 Dihedral : 16.833 137.274 4273 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.31 % Allowed : 11.44 % Favored : 85.26 % 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: -3.18 (0.16), residues: 2412 helix: -1.57 (0.13), residues: 1372 sheet: -4.22 (0.33), residues: 76 loop : -2.60 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 628 TYR 0.011 0.001 TYR B 324 PHE 0.013 0.001 PHE B 531 TRP 0.008 0.001 TRP C 593 HIS 0.014 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00287 (21560) covalent geometry : angle 0.61868 (28994) hydrogen bonds : bond 0.03943 ( 718) hydrogen bonds : angle 4.57343 ( 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 404 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 334 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8330 (p0) cc_final: 0.7825 (m-30) REVERT: A 130 MET cc_start: 0.5814 (mmm) cc_final: 0.5295 (mmm) REVERT: A 230 GLN cc_start: 0.8080 (pm20) cc_final: 0.7836 (pt0) REVERT: A 306 GLN cc_start: 0.8603 (mt0) cc_final: 0.8286 (mm-40) REVERT: A 338 LEU cc_start: 0.8603 (tt) cc_final: 0.8391 (mp) REVERT: B 90 ASP cc_start: 0.8343 (p0) cc_final: 0.7784 (m-30) REVERT: B 130 MET cc_start: 0.5824 (mmm) cc_final: 0.5553 (mmm) REVERT: B 230 GLN cc_start: 0.8000 (pm20) cc_final: 0.7767 (pt0) REVERT: B 306 GLN cc_start: 0.8615 (mt0) cc_final: 0.8294 (mm-40) REVERT: B 338 LEU cc_start: 0.8619 (tt) cc_final: 0.8407 (mp) REVERT: B 378 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8088 (pmm) REVERT: B 448 SER cc_start: 0.8823 (t) cc_final: 0.8601 (m) REVERT: C 90 ASP cc_start: 0.8368 (p0) cc_final: 0.7822 (m-30) REVERT: C 130 MET cc_start: 0.5839 (mmm) cc_final: 0.5536 (mmm) REVERT: C 222 TYR cc_start: 0.8560 (m-80) cc_final: 0.8221 (m-80) REVERT: C 230 GLN cc_start: 0.7918 (pm20) cc_final: 0.7703 (pt0) REVERT: C 306 GLN cc_start: 0.8599 (mt0) cc_final: 0.8288 (mm-40) REVERT: C 338 LEU cc_start: 0.8629 (tt) cc_final: 0.8417 (mp) REVERT: C 381 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7023 (mtmm) REVERT: D 90 ASP cc_start: 0.8310 (p0) cc_final: 0.7930 (m-30) REVERT: D 130 MET cc_start: 0.5769 (mmm) cc_final: 0.5388 (tpt) REVERT: D 222 TYR cc_start: 0.8574 (m-80) cc_final: 0.8331 (m-80) REVERT: D 230 GLN cc_start: 0.8019 (pm20) cc_final: 0.7776 (pt0) REVERT: D 306 GLN cc_start: 0.8566 (mt0) cc_final: 0.8233 (mm-40) outliers start: 70 outliers final: 47 residues processed: 381 average time/residue: 0.1394 time to fit residues: 82.2304 Evaluate side-chains 360 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 312 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 347 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 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 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP 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 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 C residue 590 ASP 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 276 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 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: 0.8980 chunk 158 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 165 HIS B 370 GLN B 582 HIS C 118 GLN C 370 GLN C 582 HIS D 267 GLN D 572 ASN D 582 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123019 restraints weight = 25295.486| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.65 r_work: 0.3240 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21560 Z= 0.172 Angle : 0.634 6.872 28994 Z= 0.318 Chirality : 0.043 0.185 3166 Planarity : 0.005 0.066 3538 Dihedral : 16.389 132.845 4273 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.92 % Allowed : 12.71 % Favored : 83.36 % 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: -2.54 (0.17), residues: 2412 helix: -1.02 (0.14), residues: 1364 sheet: -3.99 (0.37), residues: 76 loop : -2.36 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 628 TYR 0.018 0.002 TYR C 324 PHE 0.013 0.001 PHE A 468 TRP 0.007 0.001 TRP D 593 HIS 0.014 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00418 (21560) covalent geometry : angle 0.63356 (28994) hydrogen bonds : bond 0.03854 ( 718) hydrogen bonds : angle 4.46835 ( 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 395 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 312 time to evaluate : 0.730 Fit side-chains REVERT: A 90 ASP cc_start: 0.8326 (p0) cc_final: 0.7917 (m-30) REVERT: A 130 MET cc_start: 0.5762 (mmm) cc_final: 0.5517 (mmm) REVERT: A 230 GLN cc_start: 0.8092 (pm20) cc_final: 0.7803 (pt0) REVERT: A 306 GLN cc_start: 0.8650 (mt0) cc_final: 0.8258 (mm-40) REVERT: B 90 ASP cc_start: 0.8383 (p0) cc_final: 0.7870 (m-30) REVERT: B 130 MET cc_start: 0.5874 (mmm) cc_final: 0.5454 (mmm) REVERT: B 230 GLN cc_start: 0.8030 (pm20) cc_final: 0.7755 (pt0) REVERT: B 306 GLN cc_start: 0.8653 (mt0) cc_final: 0.8271 (mm-40) REVERT: B 378 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8109 (pmm) REVERT: C 90 ASP cc_start: 0.8376 (p0) cc_final: 0.7875 (m-30) REVERT: C 130 MET cc_start: 0.5800 (mmm) cc_final: 0.5515 (mmm) REVERT: C 230 GLN cc_start: 0.7913 (pm20) cc_final: 0.7678 (pt0) REVERT: C 306 GLN cc_start: 0.8673 (mt0) cc_final: 0.8279 (mm-40) REVERT: C 381 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6916 (mtmm) REVERT: C 481 MET cc_start: 0.8511 (ptt) cc_final: 0.8300 (ptp) REVERT: D 90 ASP cc_start: 0.8323 (p0) cc_final: 0.7918 (m-30) REVERT: D 130 MET cc_start: 0.5931 (mmm) cc_final: 0.5577 (tpt) REVERT: D 140 ARG cc_start: 0.7748 (ptp90) cc_final: 0.7410 (mtm-85) REVERT: D 222 TYR cc_start: 0.8666 (m-80) cc_final: 0.8334 (m-80) REVERT: D 306 GLN cc_start: 0.8625 (mt0) cc_final: 0.8215 (mm-40) REVERT: D 481 MET cc_start: 0.8410 (ptp) cc_final: 0.8118 (ptp) outliers start: 83 outliers final: 54 residues processed: 380 average time/residue: 0.1392 time to fit residues: 81.7761 Evaluate side-chains 356 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 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 590 ASP Chi-restraints excluded: chain B residue 592 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 314 LYS Chi-restraints excluded: chain C residue 315 GLU 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 62 ASN 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 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: 1.9990 chunk 230 optimal weight: 0.3980 chunk 197 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS 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 D 258 HIS D 546 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122023 restraints weight = 24432.167| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.71 r_work: 0.3186 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21560 Z= 0.117 Angle : 0.592 7.607 28994 Z= 0.296 Chirality : 0.041 0.176 3166 Planarity : 0.005 0.065 3538 Dihedral : 15.791 127.591 4273 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.97 % Allowed : 13.09 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.02 (0.17), residues: 2412 helix: -0.55 (0.14), residues: 1364 sheet: -3.90 (0.39), residues: 76 loop : -2.21 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 628 TYR 0.021 0.001 TYR D 324 PHE 0.014 0.001 PHE B 211 TRP 0.008 0.001 TRP C 495 HIS 0.019 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00275 (21560) covalent geometry : angle 0.59169 (28994) hydrogen bonds : bond 0.03424 ( 718) hydrogen bonds : angle 4.29728 ( 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 403 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 319 time to evaluate : 0.700 Fit side-chains REVERT: A 90 ASP cc_start: 0.8172 (p0) cc_final: 0.7712 (m-30) REVERT: A 130 MET cc_start: 0.5537 (mmm) cc_final: 0.5230 (tpt) REVERT: A 222 TYR cc_start: 0.8174 (m-80) cc_final: 0.7973 (m-80) REVERT: A 230 GLN cc_start: 0.7929 (pm20) cc_final: 0.7624 (pt0) REVERT: A 306 GLN cc_start: 0.8633 (mt0) cc_final: 0.8025 (mm-40) REVERT: A 502 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8452 (mt) REVERT: B 90 ASP cc_start: 0.8205 (p0) cc_final: 0.7733 (m-30) REVERT: B 130 MET cc_start: 0.5216 (mmm) cc_final: 0.4910 (mmm) REVERT: B 306 GLN cc_start: 0.8643 (mt0) cc_final: 0.8118 (mm-40) REVERT: B 378 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8106 (pmm) REVERT: B 481 MET cc_start: 0.8413 (ptt) cc_final: 0.8172 (ptp) REVERT: C 90 ASP cc_start: 0.8233 (p0) cc_final: 0.7724 (m-30) REVERT: C 130 MET cc_start: 0.5271 (mmm) cc_final: 0.4961 (mmm) REVERT: C 306 GLN cc_start: 0.8654 (mt0) cc_final: 0.8124 (mm-40) REVERT: C 474 MET cc_start: 0.8178 (tmm) cc_final: 0.7861 (tmm) REVERT: C 481 MET cc_start: 0.8442 (ptt) cc_final: 0.8208 (ptp) REVERT: D 90 ASP cc_start: 0.8239 (p0) cc_final: 0.7754 (m-30) REVERT: D 130 MET cc_start: 0.5452 (mmm) cc_final: 0.5031 (tpt) REVERT: D 140 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7416 (mtm-85) REVERT: D 174 ASN cc_start: 0.8022 (t0) cc_final: 0.7726 (t0) REVERT: D 222 TYR cc_start: 0.8520 (m-80) cc_final: 0.8158 (m-80) REVERT: D 306 GLN cc_start: 0.8625 (mt0) cc_final: 0.8043 (mm-40) REVERT: D 502 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8474 (mt) outliers start: 84 outliers final: 52 residues processed: 390 average time/residue: 0.1418 time to fit residues: 85.8593 Evaluate side-chains 359 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 502 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 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 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 315 GLU 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 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 62 ASN 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 276 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 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 575 ILE 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: 2.9990 chunk 93 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 125 optimal weight: 0.0470 chunk 116 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 582 HIS C 73 HIS C 118 GLN C 165 HIS C 261 GLN C 546 ASN D 261 GLN D 546 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120275 restraints weight = 24406.925| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.71 r_work: 0.3214 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21560 Z= 0.142 Angle : 0.602 7.676 28994 Z= 0.299 Chirality : 0.042 0.179 3166 Planarity : 0.005 0.064 3538 Dihedral : 15.419 122.624 4273 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.58 % Allowed : 13.14 % Favored : 82.28 % 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: -1.82 (0.17), residues: 2412 helix: -0.33 (0.14), residues: 1384 sheet: -3.79 (0.41), residues: 76 loop : -2.24 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 628 TYR 0.016 0.001 TYR D 324 PHE 0.014 0.001 PHE D 211 TRP 0.007 0.001 TRP B 495 HIS 0.012 0.001 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00345 (21560) covalent geometry : angle 0.60200 (28994) hydrogen bonds : bond 0.03488 ( 718) hydrogen bonds : angle 4.25699 ( 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 407 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 310 time to evaluate : 0.680 Fit side-chains REVERT: A 80 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: A 90 ASP cc_start: 0.8236 (p0) cc_final: 0.7826 (m-30) REVERT: A 96 MET cc_start: 0.8563 (mmt) cc_final: 0.8316 (mmt) REVERT: A 130 MET cc_start: 0.5637 (mmm) cc_final: 0.5336 (tpt) REVERT: A 222 TYR cc_start: 0.8297 (m-80) cc_final: 0.8007 (m-80) REVERT: A 252 ASN cc_start: 0.8917 (t0) cc_final: 0.8716 (t0) REVERT: A 306 GLN cc_start: 0.8658 (mt0) cc_final: 0.8145 (mm-40) REVERT: A 502 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (mt) REVERT: B 90 ASP cc_start: 0.8270 (p0) cc_final: 0.7797 (m-30) REVERT: B 130 MET cc_start: 0.5402 (mmm) cc_final: 0.5148 (tpt) REVERT: B 140 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7334 (mtm-85) REVERT: B 306 GLN cc_start: 0.8667 (mt0) cc_final: 0.8156 (mm-40) REVERT: B 315 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8362 (mp0) REVERT: B 378 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8336 (pmm) REVERT: B 481 MET cc_start: 0.8440 (ptt) cc_final: 0.8219 (ptp) REVERT: B 502 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8458 (mt) REVERT: C 80 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: C 90 ASP cc_start: 0.8297 (p0) cc_final: 0.7820 (m-30) REVERT: C 130 MET cc_start: 0.5465 (mmm) cc_final: 0.5186 (mmm) REVERT: C 140 ARG cc_start: 0.7735 (ptp90) cc_final: 0.7353 (mtm-85) REVERT: C 306 GLN cc_start: 0.8677 (mt0) cc_final: 0.8174 (mm-40) REVERT: C 474 MET cc_start: 0.8180 (tmm) cc_final: 0.7859 (tmm) REVERT: C 481 MET cc_start: 0.8462 (ptt) cc_final: 0.8245 (ptp) REVERT: C 502 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8474 (mt) REVERT: D 90 ASP cc_start: 0.8256 (p0) cc_final: 0.7826 (m-30) REVERT: D 130 MET cc_start: 0.5381 (mmm) cc_final: 0.5013 (tpt) REVERT: D 140 ARG cc_start: 0.7678 (ptp90) cc_final: 0.7389 (mtm-85) REVERT: D 222 TYR cc_start: 0.8543 (m-80) cc_final: 0.8230 (m-80) REVERT: D 306 GLN cc_start: 0.8650 (mt0) cc_final: 0.8078 (mm-40) REVERT: D 502 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8487 (mt) outliers start: 97 outliers final: 61 residues processed: 397 average time/residue: 0.1425 time to fit residues: 87.1253 Evaluate side-chains 369 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 378 MET 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 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 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 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 592 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 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 315 GLU 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 D residue 49 LEU Chi-restraints excluded: chain D residue 62 ASN 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 448 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 161 optimal weight: 0.2980 chunk 229 optimal weight: 0.7980 chunk 192 optimal weight: 0.0270 chunk 206 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 261 GLN A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 261 GLN B 546 ASN C 73 HIS C 261 GLN C 546 ASN D 546 ASN D 582 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122240 restraints weight = 24445.517| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.70 r_work: 0.3220 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3248 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= 0.109 Angle : 0.579 7.444 28994 Z= 0.287 Chirality : 0.041 0.169 3166 Planarity : 0.004 0.064 3538 Dihedral : 14.974 116.898 4273 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.92 % Allowed : 13.85 % Favored : 82.23 % 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: -1.45 (0.17), residues: 2412 helix: -0.01 (0.15), residues: 1364 sheet: -3.76 (0.41), residues: 76 loop : -2.09 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 628 TYR 0.015 0.001 TYR D 324 PHE 0.009 0.001 PHE A 211 TRP 0.009 0.001 TRP A 583 HIS 0.021 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00253 (21560) covalent geometry : angle 0.57856 (28994) hydrogen bonds : bond 0.03227 ( 718) hydrogen bonds : angle 4.18149 ( 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 395 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 312 time to evaluate : 0.701 Fit side-chains REVERT: A 90 ASP cc_start: 0.8246 (p0) cc_final: 0.7857 (m-30) REVERT: A 96 MET cc_start: 0.8598 (mmt) cc_final: 0.8286 (mmt) REVERT: A 130 MET cc_start: 0.5519 (mmm) cc_final: 0.5315 (tpt) REVERT: A 140 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7335 (mtm-85) REVERT: A 222 TYR cc_start: 0.8264 (m-80) cc_final: 0.8015 (m-80) REVERT: A 252 ASN cc_start: 0.8881 (t0) cc_final: 0.8622 (t0) REVERT: A 306 GLN cc_start: 0.8656 (mt0) cc_final: 0.8063 (mm-40) REVERT: B 90 ASP cc_start: 0.8255 (p0) cc_final: 0.7850 (m-30) REVERT: B 130 MET cc_start: 0.5346 (mmm) cc_final: 0.5104 (tpt) REVERT: B 140 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7326 (mtm-85) REVERT: B 252 ASN cc_start: 0.8901 (t0) cc_final: 0.8675 (t0) REVERT: B 306 GLN cc_start: 0.8628 (mt0) cc_final: 0.8073 (mm-40) REVERT: B 315 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8363 (mp0) REVERT: B 378 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8325 (pmm) REVERT: B 502 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 80 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: C 90 ASP cc_start: 0.8273 (p0) cc_final: 0.7857 (m-30) REVERT: C 130 MET cc_start: 0.5346 (mmm) cc_final: 0.5088 (tpt) REVERT: C 140 ARG cc_start: 0.7699 (ptp90) cc_final: 0.7350 (mtm-85) REVERT: C 174 ASN cc_start: 0.8036 (t0) cc_final: 0.7718 (t0) REVERT: C 306 GLN cc_start: 0.8675 (mt0) cc_final: 0.8113 (mm-40) REVERT: C 378 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8282 (pmm) REVERT: C 474 MET cc_start: 0.8098 (tmm) cc_final: 0.7807 (tmm) REVERT: C 481 MET cc_start: 0.8459 (ptt) cc_final: 0.8249 (ptp) REVERT: C 502 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8522 (mt) REVERT: D 90 ASP cc_start: 0.8244 (p0) cc_final: 0.7899 (m-30) REVERT: D 130 MET cc_start: 0.5234 (mmm) cc_final: 0.4943 (tpt) REVERT: D 140 ARG cc_start: 0.7701 (ptp90) cc_final: 0.7421 (mtm-85) REVERT: D 222 TYR cc_start: 0.8525 (m-80) cc_final: 0.8234 (m-80) REVERT: D 306 GLN cc_start: 0.8638 (mt0) cc_final: 0.8090 (mm-40) REVERT: D 481 MET cc_start: 0.8034 (ptp) cc_final: 0.7587 (tpt) REVERT: D 502 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8528 (mt) outliers start: 83 outliers final: 61 residues processed: 384 average time/residue: 0.1409 time to fit residues: 82.6386 Evaluate side-chains 372 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 305 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 311 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 378 MET Chi-restraints excluded: chain A residue 499 VAL 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 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 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 523 PHE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 GLU 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 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 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 49 LEU Chi-restraints excluded: chain D residue 62 ASN 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS B 73 HIS C 73 HIS D 261 GLN D 546 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118594 restraints weight = 24482.411| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.69 r_work: 0.3168 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21560 Z= 0.175 Angle : 0.632 7.980 28994 Z= 0.312 Chirality : 0.043 0.173 3166 Planarity : 0.005 0.063 3538 Dihedral : 14.990 112.180 4273 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.25 % Allowed : 13.94 % Favored : 81.81 % 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: -1.48 (0.17), residues: 2412 helix: -0.03 (0.15), residues: 1384 sheet: -3.77 (0.42), residues: 76 loop : -2.13 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 594 TYR 0.014 0.001 TYR D 324 PHE 0.013 0.001 PHE A 468 TRP 0.020 0.001 TRP D 583 HIS 0.007 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00432 (21560) covalent geometry : angle 0.63241 (28994) hydrogen bonds : bond 0.03596 ( 718) hydrogen bonds : angle 4.23255 ( 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 388 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 298 time to evaluate : 0.683 Fit side-chains REVERT: A 90 ASP cc_start: 0.8286 (p0) cc_final: 0.7910 (m-30) REVERT: A 130 MET cc_start: 0.5727 (mmm) cc_final: 0.5465 (tpt) REVERT: A 140 ARG cc_start: 0.7720 (ptp90) cc_final: 0.7387 (mtm-85) REVERT: A 306 GLN cc_start: 0.8662 (mt0) cc_final: 0.8179 (mm-40) REVERT: A 315 GLU cc_start: 0.8495 (mp0) cc_final: 0.8166 (mp0) REVERT: B 90 ASP cc_start: 0.8249 (p0) cc_final: 0.7884 (m-30) REVERT: B 130 MET cc_start: 0.5502 (mmm) cc_final: 0.5219 (tpt) REVERT: B 306 GLN cc_start: 0.8677 (mt0) cc_final: 0.8212 (mm-40) REVERT: B 378 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8301 (pmm) REVERT: B 474 MET cc_start: 0.7750 (tmm) cc_final: 0.6996 (tpp) REVERT: B 502 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (mt) REVERT: C 90 ASP cc_start: 0.8286 (p0) cc_final: 0.7876 (m-30) REVERT: C 130 MET cc_start: 0.5510 (mmm) cc_final: 0.5226 (tpt) REVERT: C 140 ARG cc_start: 0.7754 (ptp90) cc_final: 0.7424 (mtm-85) REVERT: C 306 GLN cc_start: 0.8722 (mt0) cc_final: 0.8224 (mm-40) REVERT: C 474 MET cc_start: 0.8237 (tmm) cc_final: 0.7905 (tmm) REVERT: C 502 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8518 (mt) REVERT: D 90 ASP cc_start: 0.8266 (p0) cc_final: 0.7896 (m-30) REVERT: D 96 MET cc_start: 0.8577 (mmt) cc_final: 0.8373 (mmt) REVERT: D 140 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7421 (mtm-85) REVERT: D 222 TYR cc_start: 0.8552 (m-80) cc_final: 0.8208 (m-80) REVERT: D 306 GLN cc_start: 0.8640 (mt0) cc_final: 0.8076 (mm-40) REVERT: D 502 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8518 (mt) outliers start: 90 outliers final: 72 residues processed: 382 average time/residue: 0.1482 time to fit residues: 86.3439 Evaluate side-chains 363 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 287 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 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 311 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 378 MET Chi-restraints excluded: chain A residue 499 VAL 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 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 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 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 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 62 ASN 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 448 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 257 GLN B 261 GLN C 261 GLN D 261 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 = 0.3731 r_free = 0.3731 target = 0.153098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120994 restraints weight = 24357.085| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.69 r_work: 0.3200 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3401 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= 0.121 Angle : 0.594 8.230 28994 Z= 0.294 Chirality : 0.041 0.166 3166 Planarity : 0.004 0.064 3538 Dihedral : 14.639 107.078 4273 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.88 % Allowed : 14.51 % Favored : 81.62 % 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: -1.18 (0.18), residues: 2412 helix: 0.18 (0.15), residues: 1376 sheet: -3.82 (0.41), residues: 76 loop : -1.92 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 628 TYR 0.014 0.001 TYR D 324 PHE 0.009 0.001 PHE A 211 TRP 0.007 0.001 TRP C 495 HIS 0.013 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00291 (21560) covalent geometry : angle 0.59410 (28994) hydrogen bonds : bond 0.03278 ( 718) hydrogen bonds : angle 4.16677 ( 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 384 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 302 time to evaluate : 0.753 Fit side-chains REVERT: A 90 ASP cc_start: 0.8255 (p0) cc_final: 0.7968 (m-30) REVERT: A 222 TYR cc_start: 0.8419 (m-80) cc_final: 0.8101 (m-80) REVERT: A 306 GLN cc_start: 0.8640 (mt0) cc_final: 0.8073 (mm-40) REVERT: A 474 MET cc_start: 0.7699 (tmm) cc_final: 0.7007 (tpp) REVERT: B 90 ASP cc_start: 0.8225 (p0) cc_final: 0.7886 (m-30) REVERT: B 130 MET cc_start: 0.5337 (mmm) cc_final: 0.5095 (tpt) REVERT: B 252 ASN cc_start: 0.8944 (t0) cc_final: 0.8730 (t0) REVERT: B 306 GLN cc_start: 0.8648 (mt0) cc_final: 0.8104 (mm-40) REVERT: B 378 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (pmm) REVERT: B 474 MET cc_start: 0.7689 (tmm) cc_final: 0.6879 (tpp) REVERT: B 502 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 57 ASP cc_start: 0.7670 (t70) cc_final: 0.7379 (t70) REVERT: C 90 ASP cc_start: 0.8271 (p0) cc_final: 0.7934 (m-30) REVERT: C 130 MET cc_start: 0.5332 (mmm) cc_final: 0.5104 (tpt) REVERT: C 140 ARG cc_start: 0.7747 (ptp90) cc_final: 0.7425 (mtm-85) REVERT: C 306 GLN cc_start: 0.8691 (mt0) cc_final: 0.8187 (mm-40) REVERT: C 378 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8255 (pmm) REVERT: C 474 MET cc_start: 0.8099 (tmm) cc_final: 0.7835 (tmm) REVERT: C 502 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8530 (mt) REVERT: C 594 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7601 (mpp-170) REVERT: D 90 ASP cc_start: 0.8248 (p0) cc_final: 0.7913 (m-30) REVERT: D 140 ARG cc_start: 0.7727 (ptp90) cc_final: 0.7460 (mtm-85) REVERT: D 222 TYR cc_start: 0.8558 (m-80) cc_final: 0.8280 (m-80) REVERT: D 306 GLN cc_start: 0.8654 (mt0) cc_final: 0.8112 (mm-40) REVERT: D 403 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7779 (mt-10) REVERT: D 502 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8522 (mt) outliers start: 82 outliers final: 70 residues processed: 377 average time/residue: 0.1403 time to fit residues: 81.0281 Evaluate side-chains 375 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 300 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU 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 311 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 378 MET Chi-restraints excluded: chain A residue 499 VAL 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 592 LEU Chi-restraints excluded: chain A residue 611 CYS 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 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 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 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 62 ASN 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 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 448 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS C 257 GLN D 257 GLN D 261 GLN D 582 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121761 restraints weight = 24544.257| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.70 r_work: 0.3179 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3479 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= 0.114 Angle : 0.591 9.072 28994 Z= 0.292 Chirality : 0.041 0.164 3166 Planarity : 0.005 0.065 3538 Dihedral : 14.355 101.889 4273 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.88 % Allowed : 14.89 % 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: -0.99 (0.18), residues: 2412 helix: 0.33 (0.15), residues: 1364 sheet: -3.83 (0.41), residues: 76 loop : -1.79 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 628 TYR 0.013 0.001 TYR D 324 PHE 0.012 0.001 PHE A 211 TRP 0.007 0.001 TRP D 495 HIS 0.009 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00268 (21560) covalent geometry : angle 0.59064 (28994) hydrogen bonds : bond 0.03189 ( 718) hydrogen bonds : angle 4.11789 ( 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 396 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 314 time to evaluate : 0.668 Fit side-chains REVERT: A 90 ASP cc_start: 0.8225 (p0) cc_final: 0.7869 (m-30) REVERT: A 222 TYR cc_start: 0.8350 (m-80) cc_final: 0.8009 (m-80) REVERT: A 306 GLN cc_start: 0.8574 (mt0) cc_final: 0.7975 (mm-40) REVERT: A 474 MET cc_start: 0.7694 (tmm) cc_final: 0.6897 (tpp) REVERT: B 90 ASP cc_start: 0.8161 (p0) cc_final: 0.7809 (m-30) REVERT: B 252 ASN cc_start: 0.8892 (t0) cc_final: 0.8651 (t0) REVERT: B 306 GLN cc_start: 0.8616 (mt0) cc_final: 0.8030 (mm-40) REVERT: B 474 MET cc_start: 0.7687 (tmm) cc_final: 0.6804 (tpp) REVERT: B 481 MET cc_start: 0.8058 (ptp) cc_final: 0.7582 (tpt) REVERT: B 502 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (mt) REVERT: C 57 ASP cc_start: 0.7668 (t70) cc_final: 0.7339 (t70) REVERT: C 90 ASP cc_start: 0.8199 (p0) cc_final: 0.7843 (m-30) REVERT: C 130 MET cc_start: 0.5192 (mmm) cc_final: 0.4925 (tpt) REVERT: C 140 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7423 (mtm-85) REVERT: C 306 GLN cc_start: 0.8610 (mt0) cc_final: 0.7990 (mm-40) REVERT: C 378 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8250 (pmm) REVERT: C 474 MET cc_start: 0.8105 (tmm) cc_final: 0.7871 (tmm) REVERT: C 502 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8488 (mt) REVERT: D 90 ASP cc_start: 0.8195 (p0) cc_final: 0.7900 (m-30) REVERT: D 130 MET cc_start: 0.5119 (mmm) cc_final: 0.4864 (tpt) REVERT: D 140 ARG cc_start: 0.7739 (ptp90) cc_final: 0.7488 (mtm-85) REVERT: D 174 ASN cc_start: 0.8011 (t0) cc_final: 0.7793 (t0) REVERT: D 222 TYR cc_start: 0.8515 (m-80) cc_final: 0.8274 (m-80) REVERT: D 306 GLN cc_start: 0.8578 (mt0) cc_final: 0.7977 (mm-40) REVERT: D 403 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7787 (mt-10) REVERT: D 474 MET cc_start: 0.7578 (tmm) cc_final: 0.6851 (tpp) REVERT: D 502 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8491 (mt) outliers start: 82 outliers final: 72 residues processed: 389 average time/residue: 0.1509 time to fit residues: 90.2692 Evaluate side-chains 376 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 311 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 378 MET 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 592 LEU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain B residue 88 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 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 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 C residue 592 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 62 ASN 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 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 448 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 546 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS C 261 GLN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121334 restraints weight = 24658.567| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.68 r_work: 0.3204 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3526 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= 0.128 Angle : 0.601 8.100 28994 Z= 0.297 Chirality : 0.042 0.171 3166 Planarity : 0.005 0.064 3538 Dihedral : 14.100 96.931 4273 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.06 % Allowed : 14.65 % Favored : 81.29 % 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: -0.96 (0.18), residues: 2412 helix: 0.35 (0.15), residues: 1364 sheet: -3.83 (0.41), residues: 76 loop : -1.77 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 628 TYR 0.013 0.001 TYR D 324 PHE 0.019 0.001 PHE A 211 TRP 0.011 0.001 TRP C 583 HIS 0.011 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00309 (21560) covalent geometry : angle 0.60146 (28994) hydrogen bonds : bond 0.03269 ( 718) hydrogen bonds : angle 4.11847 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5642.84 seconds wall clock time: 96 minutes 58.27 seconds (5818.27 seconds total)