Starting phenix.real_space_refine on Tue Jun 17 14:49:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fhh_29085/06_2025/8fhh_29085_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fhh_29085/06_2025/8fhh_29085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fhh_29085/06_2025/8fhh_29085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fhh_29085/06_2025/8fhh_29085.map" model { file = "/net/cci-nas-00/data/ceres_data/8fhh_29085/06_2025/8fhh_29085_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fhh_29085/06_2025/8fhh_29085_neut.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 140 5.16 5 C 12912 2.51 5 N 3288 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'ERG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Restraints were copied for chains: C, B, D Time building chain proxies: 11.06, per 1000 atoms: 0.56 Number of scatterers: 19824 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 4 15.00 O 3480 8.00 N 3288 7.00 C 12912 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: 4.64 Conformation dependent library (CDL) restraints added in 2.7 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.882A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.606A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.790A pdb=" N ARG A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.037A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.861A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.701A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.931A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.886A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.220A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.748A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.716A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 removed outlier: 3.549A pdb=" N HIS A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.761A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.959A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.571A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.575A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.805A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 3.716A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.882A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.606A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.790A pdb=" N ARG B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.037A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.860A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.701A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.931A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.886A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.220A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.748A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.716A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 3.549A pdb=" N HIS B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.760A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.959A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.571A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.575A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 3.805A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 608 removed outlier: 3.716A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.882A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.606A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.790A pdb=" N ARG C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.037A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.861A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.701A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.930A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.886A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.220A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.748A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.716A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 removed outlier: 3.549A pdb=" N HIS C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.761A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.959A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.571A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.575A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 removed outlier: 3.805A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 3.716A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 601 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.882A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.606A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.790A pdb=" N ARG D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 221 removed outlier: 4.037A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.861A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.701A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 307 removed outlier: 3.931A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.886A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.220A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.747A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.716A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 removed outlier: 3.549A pdb=" N HIS D 426 " --> pdb=" O GLY D 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.761A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 Processing helix chain 'D' and resid 475 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.959A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.571A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.575A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 585 removed outlier: 3.805A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 608 removed outlier: 3.716A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 601 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.754A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.754A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.754A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.754A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1109 hydrogen bonds defined for protein. 3147 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: 6.05 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3291 1.32 - 1.44: 5291 1.44 - 1.57: 11466 1.57 - 1.69: 16 1.69 - 1.81: 228 Bond restraints: 20292 Sorted by residual: bond pdb=" CA ALA D 595 " pdb=" CB ALA D 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" CA ALA B 595 " pdb=" CB ALA B 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" CA ALA C 595 " pdb=" CB ALA C 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" CA ALA A 595 " pdb=" CB ALA A 595 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" N VAL D 597 " pdb=" CA VAL D 597 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.29e-02 6.01e+03 1.10e+01 ... (remaining 20287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 25813 1.53 - 3.06: 1446 3.06 - 4.58: 221 4.58 - 6.11: 48 6.11 - 7.64: 44 Bond angle restraints: 27572 Sorted by residual: angle pdb=" O ARG B 589 " pdb=" C ARG B 589 " pdb=" N ASP B 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" O ARG C 589 " pdb=" C ARG C 589 " pdb=" N ASP C 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" O ARG D 589 " pdb=" C ARG D 589 " pdb=" N ASP D 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" O ARG A 589 " pdb=" C ARG A 589 " pdb=" N ASP A 590 " ideal model delta sigma weight residual 122.22 114.99 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" N GLN D 513 " pdb=" CA GLN D 513 " pdb=" C GLN D 513 " ideal model delta sigma weight residual 113.28 106.63 6.65 1.22e+00 6.72e-01 2.97e+01 ... (remaining 27567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 12041 24.77 - 49.53: 399 49.53 - 74.30: 40 74.30 - 99.07: 4 99.07 - 123.83: 8 Dihedral angle restraints: 12492 sinusoidal: 5412 harmonic: 7080 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2510 0.054 - 0.107: 489 0.107 - 0.161: 109 0.161 - 0.214: 28 0.214 - 0.268: 4 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CB VAL D 499 " pdb=" CA VAL D 499 " pdb=" CG1 VAL D 499 " pdb=" CG2 VAL D 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A 499 " pdb=" CA VAL A 499 " pdb=" CG1 VAL A 499 " pdb=" CG2 VAL A 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL C 499 " pdb=" CA VAL C 499 " pdb=" CG1 VAL C 499 " pdb=" CG2 VAL C 499 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3137 not shown) Planarity restraints: 3436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 801 " -0.077 2.00e-02 2.50e+03 7.60e-02 5.78e+01 pdb=" C29 POV C 801 " 0.084 2.00e-02 2.50e+03 pdb="C210 POV C 801 " 0.067 2.00e-02 2.50e+03 pdb="C211 POV C 801 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 801 " -0.077 2.00e-02 2.50e+03 7.60e-02 5.77e+01 pdb=" C29 POV D 801 " 0.084 2.00e-02 2.50e+03 pdb="C210 POV D 801 " 0.067 2.00e-02 2.50e+03 pdb="C211 POV D 801 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 801 " 0.077 2.00e-02 2.50e+03 7.59e-02 5.76e+01 pdb=" C29 POV B 801 " -0.084 2.00e-02 2.50e+03 pdb="C210 POV B 801 " -0.067 2.00e-02 2.50e+03 pdb="C211 POV B 801 " 0.074 2.00e-02 2.50e+03 ... (remaining 3433 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5611 2.81 - 3.34: 18198 3.34 - 3.86: 34414 3.86 - 4.38: 40766 4.38 - 4.90: 69454 Nonbonded interactions: 168443 Sorted by model distance: nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.292 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.313 3.040 ... (remaining 168438 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 42.520 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 : 0.006 0.055 20292 Z= 0.317 Angle : 0.831 7.638 27572 Z= 0.524 Chirality : 0.049 0.268 3140 Planarity : 0.007 0.076 3436 Dihedral : 12.506 123.832 7916 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 2408 helix: -1.27 (0.11), residues: 1496 sheet: -2.50 (0.37), residues: 124 loop : -1.11 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 268 HIS 0.005 0.001 HIS B 201 PHE 0.014 0.002 PHE B 537 TYR 0.010 0.002 TYR D 467 ARG 0.003 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.16716 ( 1109) hydrogen bonds : angle 6.07477 ( 3147) covalent geometry : bond 0.00552 (20292) covalent geometry : angle 0.83068 (27572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 452 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7699 (mt0) cc_final: 0.6789 (tt0) REVERT: A 176 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 219 LEU cc_start: 0.8665 (mt) cc_final: 0.8454 (mp) REVERT: A 318 SER cc_start: 0.9124 (t) cc_final: 0.8745 (m) REVERT: A 322 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8600 (mttm) REVERT: A 358 ASN cc_start: 0.8132 (m-40) cc_final: 0.7899 (m-40) REVERT: A 419 THR cc_start: 0.8755 (m) cc_final: 0.8428 (m) REVERT: A 444 LEU cc_start: 0.9315 (mt) cc_final: 0.9105 (mt) REVERT: B 31 GLN cc_start: 0.7699 (mt0) cc_final: 0.6786 (tt0) REVERT: B 176 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7555 (mp0) REVERT: B 219 LEU cc_start: 0.8665 (mt) cc_final: 0.8451 (mp) REVERT: B 318 SER cc_start: 0.9123 (t) cc_final: 0.8744 (m) REVERT: B 322 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8604 (mttm) REVERT: B 358 ASN cc_start: 0.8120 (m-40) cc_final: 0.7890 (m-40) REVERT: B 419 THR cc_start: 0.8750 (m) cc_final: 0.8423 (m) REVERT: B 444 LEU cc_start: 0.9314 (mt) cc_final: 0.9102 (mt) REVERT: C 31 GLN cc_start: 0.7700 (mt0) cc_final: 0.6791 (tt0) REVERT: C 176 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7554 (mp0) REVERT: C 219 LEU cc_start: 0.8668 (mt) cc_final: 0.8453 (mp) REVERT: C 318 SER cc_start: 0.9116 (t) cc_final: 0.8736 (m) REVERT: C 322 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8598 (mttm) REVERT: C 358 ASN cc_start: 0.8121 (m-40) cc_final: 0.7890 (m-40) REVERT: C 419 THR cc_start: 0.8750 (m) cc_final: 0.8425 (m) REVERT: C 444 LEU cc_start: 0.9314 (mt) cc_final: 0.9100 (mt) REVERT: D 31 GLN cc_start: 0.7699 (mt0) cc_final: 0.6790 (tt0) REVERT: D 176 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7554 (mp0) REVERT: D 219 LEU cc_start: 0.8666 (mt) cc_final: 0.8457 (mp) REVERT: D 318 SER cc_start: 0.9118 (t) cc_final: 0.8739 (m) REVERT: D 322 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8601 (mttm) REVERT: D 358 ASN cc_start: 0.8118 (m-40) cc_final: 0.7878 (m-40) REVERT: D 419 THR cc_start: 0.8754 (m) cc_final: 0.8426 (m) REVERT: D 444 LEU cc_start: 0.9315 (mt) cc_final: 0.9101 (mt) outliers start: 4 outliers final: 0 residues processed: 456 average time/residue: 0.4208 time to fit residues: 280.7616 Evaluate side-chains 302 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 122 HIS A 185 HIS A 192 GLN A 267 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 122 HIS B 185 HIS B 192 GLN B 267 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN C 31 GLN C 122 HIS C 185 HIS C 192 GLN C 267 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 122 HIS D 185 HIS D 192 GLN D 267 GLN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.089415 restraints weight = 24721.263| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.53 r_work: 0.2752 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20292 Z= 0.175 Angle : 0.516 5.396 27572 Z= 0.270 Chirality : 0.040 0.185 3140 Planarity : 0.005 0.045 3436 Dihedral : 8.941 111.111 3324 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.05 % Allowed : 6.11 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2408 helix: 0.56 (0.13), residues: 1504 sheet: -1.85 (0.48), residues: 84 loop : -0.47 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 593 HIS 0.004 0.001 HIS C 201 PHE 0.013 0.001 PHE B 468 TYR 0.010 0.001 TYR A 526 ARG 0.004 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1109) hydrogen bonds : angle 4.00348 ( 3147) covalent geometry : bond 0.00422 (20292) covalent geometry : angle 0.51564 (27572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 3.001 Fit side-chains REVERT: A 31 GLN cc_start: 0.7610 (mt0) cc_final: 0.6671 (tt0) REVERT: A 64 LEU cc_start: 0.7782 (mt) cc_final: 0.7404 (mt) REVERT: A 176 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7612 (mp0) REVERT: A 233 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8184 (mt-10) REVERT: A 314 LYS cc_start: 0.8589 (tttt) cc_final: 0.8268 (tttp) REVERT: A 318 SER cc_start: 0.9040 (t) cc_final: 0.8488 (m) REVERT: A 409 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7577 (ttt90) REVERT: A 414 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7565 (ttt180) REVERT: A 442 MET cc_start: 0.8854 (mtp) cc_final: 0.8596 (mtp) REVERT: A 445 THR cc_start: 0.9007 (t) cc_final: 0.8733 (p) REVERT: B 31 GLN cc_start: 0.7594 (mt0) cc_final: 0.6643 (tt0) REVERT: B 64 LEU cc_start: 0.7753 (mt) cc_final: 0.7375 (mt) REVERT: B 176 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7611 (mp0) REVERT: B 233 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8192 (mt-10) REVERT: B 314 LYS cc_start: 0.8591 (tttt) cc_final: 0.8268 (tttp) REVERT: B 318 SER cc_start: 0.9043 (t) cc_final: 0.8494 (m) REVERT: B 409 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7568 (ttt90) REVERT: B 414 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7563 (ttt180) REVERT: B 442 MET cc_start: 0.8853 (mtp) cc_final: 0.8596 (mtp) REVERT: B 445 THR cc_start: 0.9003 (t) cc_final: 0.8724 (p) REVERT: C 31 GLN cc_start: 0.7590 (mt0) cc_final: 0.6634 (tt0) REVERT: C 64 LEU cc_start: 0.7753 (mt) cc_final: 0.7377 (mt) REVERT: C 176 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7613 (mp0) REVERT: C 233 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8196 (mt-10) REVERT: C 314 LYS cc_start: 0.8578 (tttt) cc_final: 0.8254 (tttp) REVERT: C 318 SER cc_start: 0.9039 (t) cc_final: 0.8490 (m) REVERT: C 409 ARG cc_start: 0.8048 (ttt90) cc_final: 0.7568 (ttt90) REVERT: C 414 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7567 (ttt180) REVERT: C 442 MET cc_start: 0.8848 (mtp) cc_final: 0.8591 (mtp) REVERT: C 445 THR cc_start: 0.9001 (t) cc_final: 0.8723 (p) REVERT: D 31 GLN cc_start: 0.7605 (mt0) cc_final: 0.6653 (tt0) REVERT: D 64 LEU cc_start: 0.7759 (mt) cc_final: 0.7384 (mt) REVERT: D 176 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7606 (mp0) REVERT: D 233 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 314 LYS cc_start: 0.8577 (tttt) cc_final: 0.8252 (tttp) REVERT: D 318 SER cc_start: 0.9035 (t) cc_final: 0.8484 (m) REVERT: D 409 ARG cc_start: 0.8051 (ttt90) cc_final: 0.7574 (ttt90) REVERT: D 414 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7566 (ttt180) REVERT: D 442 MET cc_start: 0.8850 (mtp) cc_final: 0.8592 (mtp) REVERT: D 445 THR cc_start: 0.9005 (t) cc_final: 0.8726 (p) outliers start: 43 outliers final: 28 residues processed: 355 average time/residue: 0.4144 time to fit residues: 228.6686 Evaluate side-chains 313 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 616 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 147 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN A 635 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN C 635 ASN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099873 restraints weight = 23658.873| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.43 r_work: 0.2870 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20292 Z= 0.095 Angle : 0.446 5.278 27572 Z= 0.235 Chirality : 0.037 0.217 3140 Planarity : 0.004 0.050 3436 Dihedral : 8.408 99.735 3324 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.86 % Allowed : 8.64 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2408 helix: 1.29 (0.13), residues: 1500 sheet: -1.52 (0.51), residues: 84 loop : -0.31 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 593 HIS 0.002 0.000 HIS A 185 PHE 0.016 0.001 PHE D 574 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 1109) hydrogen bonds : angle 3.70980 ( 3147) covalent geometry : bond 0.00213 (20292) covalent geometry : angle 0.44639 (27572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 300 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7478 (mt0) cc_final: 0.6563 (tt0) REVERT: A 176 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7628 (mp0) REVERT: A 233 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 314 LYS cc_start: 0.8488 (tttt) cc_final: 0.8168 (ttmp) REVERT: A 318 SER cc_start: 0.8921 (t) cc_final: 0.8420 (m) REVERT: A 409 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7551 (ttt90) REVERT: A 414 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7509 (ttt180) REVERT: A 442 MET cc_start: 0.8755 (mtp) cc_final: 0.8472 (mtp) REVERT: B 31 GLN cc_start: 0.7453 (mt0) cc_final: 0.6542 (tt0) REVERT: B 176 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7639 (mp0) REVERT: B 314 LYS cc_start: 0.8501 (tttt) cc_final: 0.8181 (ttmp) REVERT: B 318 SER cc_start: 0.8926 (t) cc_final: 0.8427 (m) REVERT: B 409 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7537 (ttt90) REVERT: B 414 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7506 (ttt180) REVERT: B 442 MET cc_start: 0.8764 (mtp) cc_final: 0.8480 (mtp) REVERT: C 31 GLN cc_start: 0.7445 (mt0) cc_final: 0.6532 (tt0) REVERT: C 176 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7633 (mp0) REVERT: C 314 LYS cc_start: 0.8497 (tttt) cc_final: 0.8175 (ttmp) REVERT: C 318 SER cc_start: 0.8925 (t) cc_final: 0.8424 (m) REVERT: C 409 ARG cc_start: 0.8003 (ttt90) cc_final: 0.7549 (ttt90) REVERT: C 414 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7521 (ttt180) REVERT: C 442 MET cc_start: 0.8758 (mtp) cc_final: 0.8474 (mtp) REVERT: D 31 GLN cc_start: 0.7448 (mt0) cc_final: 0.6534 (tt0) REVERT: D 176 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7619 (mp0) REVERT: D 314 LYS cc_start: 0.8488 (tttt) cc_final: 0.8167 (ttmp) REVERT: D 318 SER cc_start: 0.8923 (t) cc_final: 0.8423 (m) REVERT: D 409 ARG cc_start: 0.8008 (ttt90) cc_final: 0.7553 (ttt90) REVERT: D 414 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7524 (ttt180) outliers start: 18 outliers final: 16 residues processed: 304 average time/residue: 0.3456 time to fit residues: 158.8044 Evaluate side-chains 308 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 292 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.086217 restraints weight = 25078.768| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.56 r_work: 0.2736 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20292 Z= 0.235 Angle : 0.545 6.585 27572 Z= 0.280 Chirality : 0.042 0.248 3140 Planarity : 0.004 0.049 3436 Dihedral : 8.529 99.558 3324 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 9.26 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2408 helix: 1.43 (0.13), residues: 1484 sheet: -1.63 (0.51), residues: 84 loop : -0.32 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 593 HIS 0.004 0.001 HIS A 201 PHE 0.017 0.002 PHE C 468 TYR 0.014 0.002 TYR C 216 ARG 0.005 0.001 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1109) hydrogen bonds : angle 3.87965 ( 3147) covalent geometry : bond 0.00583 (20292) covalent geometry : angle 0.54477 (27572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 2.362 Fit side-chains REVERT: A 31 GLN cc_start: 0.7662 (mt0) cc_final: 0.6742 (tt0) REVERT: A 233 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8215 (mt-10) REVERT: A 300 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8042 (mttt) REVERT: A 314 LYS cc_start: 0.8644 (tttt) cc_final: 0.8423 (tttp) REVERT: A 318 SER cc_start: 0.9039 (t) cc_final: 0.8428 (m) REVERT: A 340 MET cc_start: 0.9116 (mmm) cc_final: 0.8791 (mmp) REVERT: A 414 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7501 (ttt180) REVERT: A 444 LEU cc_start: 0.9241 (mt) cc_final: 0.9026 (mt) REVERT: B 31 GLN cc_start: 0.7670 (mt0) cc_final: 0.6748 (tt0) REVERT: B 300 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8040 (mttt) REVERT: B 314 LYS cc_start: 0.8638 (tttt) cc_final: 0.8417 (tttp) REVERT: B 318 SER cc_start: 0.9037 (t) cc_final: 0.8428 (m) REVERT: B 340 MET cc_start: 0.9105 (mmm) cc_final: 0.8775 (mmp) REVERT: B 414 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7495 (ttt180) REVERT: B 444 LEU cc_start: 0.9244 (mt) cc_final: 0.9026 (mt) REVERT: C 31 GLN cc_start: 0.7669 (mt0) cc_final: 0.6743 (tt0) REVERT: C 300 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8035 (mttt) REVERT: C 314 LYS cc_start: 0.8629 (tttt) cc_final: 0.8406 (tttp) REVERT: C 318 SER cc_start: 0.9031 (t) cc_final: 0.8418 (m) REVERT: C 340 MET cc_start: 0.9111 (mmm) cc_final: 0.8783 (mmp) REVERT: C 414 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7502 (ttt180) REVERT: C 444 LEU cc_start: 0.9245 (mt) cc_final: 0.9028 (mt) REVERT: D 31 GLN cc_start: 0.7669 (mt0) cc_final: 0.6744 (tt0) REVERT: D 300 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8041 (mttt) REVERT: D 314 LYS cc_start: 0.8634 (tttt) cc_final: 0.8411 (tttp) REVERT: D 318 SER cc_start: 0.9034 (t) cc_final: 0.8421 (m) REVERT: D 340 MET cc_start: 0.9115 (mmm) cc_final: 0.8785 (mmp) REVERT: D 414 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7499 (ttt180) REVERT: D 444 LEU cc_start: 0.9240 (mt) cc_final: 0.9029 (mt) outliers start: 37 outliers final: 29 residues processed: 323 average time/residue: 0.3282 time to fit residues: 160.3990 Evaluate side-chains 309 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 160 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 218 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092401 restraints weight = 24795.189| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.47 r_work: 0.2837 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20292 Z= 0.102 Angle : 0.443 5.139 27572 Z= 0.235 Chirality : 0.038 0.239 3140 Planarity : 0.004 0.051 3436 Dihedral : 8.011 73.353 3324 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.34 % Allowed : 10.59 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2408 helix: 1.83 (0.13), residues: 1476 sheet: -1.43 (0.53), residues: 84 loop : -0.17 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 593 HIS 0.002 0.000 HIS A 201 PHE 0.015 0.001 PHE D 574 TYR 0.011 0.001 TYR C 555 ARG 0.005 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 1109) hydrogen bonds : angle 3.67942 ( 3147) covalent geometry : bond 0.00230 (20292) covalent geometry : angle 0.44335 (27572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 328 time to evaluate : 2.132 Fit side-chains REVERT: A 31 GLN cc_start: 0.7746 (mt0) cc_final: 0.6910 (tt0) REVERT: A 233 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8273 (mt-10) REVERT: A 300 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8188 (mmtm) REVERT: A 318 SER cc_start: 0.9116 (t) cc_final: 0.8623 (m) REVERT: A 340 MET cc_start: 0.9021 (mmm) cc_final: 0.8530 (mmp) REVERT: A 409 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7946 (ttt90) REVERT: A 414 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7747 (ttt90) REVERT: B 31 GLN cc_start: 0.7710 (mt0) cc_final: 0.6870 (tt0) REVERT: B 300 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8186 (mmtm) REVERT: B 318 SER cc_start: 0.9117 (t) cc_final: 0.8628 (m) REVERT: B 340 MET cc_start: 0.9006 (mmm) cc_final: 0.8512 (mmp) REVERT: B 409 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7945 (ttt90) REVERT: B 414 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7750 (ttt90) REVERT: C 31 GLN cc_start: 0.7709 (mt0) cc_final: 0.6865 (tt0) REVERT: C 300 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8187 (mmtm) REVERT: C 318 SER cc_start: 0.9111 (t) cc_final: 0.8616 (m) REVERT: C 340 MET cc_start: 0.9011 (mmm) cc_final: 0.8515 (mmp) REVERT: C 409 ARG cc_start: 0.8173 (ttt90) cc_final: 0.7949 (ttt90) REVERT: C 414 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7754 (ttt90) REVERT: D 31 GLN cc_start: 0.7712 (mt0) cc_final: 0.6869 (tt0) REVERT: D 300 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8192 (mmtm) REVERT: D 318 SER cc_start: 0.9112 (t) cc_final: 0.8618 (m) REVERT: D 340 MET cc_start: 0.9019 (mmm) cc_final: 0.8518 (mmp) REVERT: D 409 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7955 (ttt90) REVERT: D 414 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7751 (ttt90) outliers start: 28 outliers final: 24 residues processed: 344 average time/residue: 0.3271 time to fit residues: 171.4059 Evaluate side-chains 320 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.087624 restraints weight = 25063.699| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.45 r_work: 0.2708 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20292 Z= 0.209 Angle : 0.517 7.439 27572 Z= 0.269 Chirality : 0.041 0.246 3140 Planarity : 0.004 0.049 3436 Dihedral : 8.172 75.214 3324 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.96 % Allowed : 11.78 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2408 helix: 1.77 (0.13), residues: 1480 sheet: -1.64 (0.52), residues: 84 loop : -0.19 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 593 HIS 0.004 0.001 HIS A 201 PHE 0.017 0.002 PHE A 574 TYR 0.012 0.002 TYR B 526 ARG 0.006 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1109) hydrogen bonds : angle 3.86904 ( 3147) covalent geometry : bond 0.00514 (20292) covalent geometry : angle 0.51714 (27572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 2.684 Fit side-chains REVERT: A 31 GLN cc_start: 0.7582 (mt0) cc_final: 0.6661 (tt0) REVERT: A 233 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8209 (mt-10) REVERT: A 300 LYS cc_start: 0.8638 (mtpt) cc_final: 0.7957 (mttt) REVERT: A 318 SER cc_start: 0.8944 (t) cc_final: 0.8317 (m) REVERT: A 340 MET cc_start: 0.9100 (mmm) cc_final: 0.8764 (mmp) REVERT: A 409 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7721 (ttt90) REVERT: A 414 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7426 (ttt90) REVERT: B 31 GLN cc_start: 0.7563 (mt0) cc_final: 0.6647 (tt0) REVERT: B 300 LYS cc_start: 0.8636 (mtpt) cc_final: 0.7954 (mttt) REVERT: B 318 SER cc_start: 0.8942 (t) cc_final: 0.8316 (m) REVERT: B 340 MET cc_start: 0.9101 (mmm) cc_final: 0.8760 (mmp) REVERT: B 414 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7417 (ttt90) REVERT: C 31 GLN cc_start: 0.7561 (mt0) cc_final: 0.6644 (tt0) REVERT: C 300 LYS cc_start: 0.8635 (mtpt) cc_final: 0.7955 (mttt) REVERT: C 318 SER cc_start: 0.8939 (t) cc_final: 0.8312 (m) REVERT: C 340 MET cc_start: 0.9103 (mmm) cc_final: 0.8764 (mmp) REVERT: C 414 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7435 (ttt90) REVERT: D 31 GLN cc_start: 0.7568 (mt0) cc_final: 0.6649 (tt0) REVERT: D 300 LYS cc_start: 0.8629 (mtpt) cc_final: 0.7948 (mttt) REVERT: D 318 SER cc_start: 0.8939 (t) cc_final: 0.8311 (m) REVERT: D 340 MET cc_start: 0.9106 (mmm) cc_final: 0.8764 (mmp) REVERT: D 414 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7420 (ttt90) outliers start: 41 outliers final: 25 residues processed: 319 average time/residue: 0.4153 time to fit residues: 205.0136 Evaluate side-chains 305 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 226 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.088329 restraints weight = 24945.268| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.43 r_work: 0.2725 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20292 Z= 0.168 Angle : 0.486 5.457 27572 Z= 0.255 Chirality : 0.040 0.219 3140 Planarity : 0.004 0.050 3436 Dihedral : 7.998 66.837 3324 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.15 % Allowed : 11.64 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2408 helix: 1.83 (0.13), residues: 1480 sheet: -1.65 (0.52), residues: 84 loop : -0.17 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 593 HIS 0.004 0.001 HIS D 201 PHE 0.023 0.001 PHE C 574 TYR 0.010 0.001 TYR B 216 ARG 0.007 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1109) hydrogen bonds : angle 3.86085 ( 3147) covalent geometry : bond 0.00411 (20292) covalent geometry : angle 0.48578 (27572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 2.674 Fit side-chains REVERT: A 31 GLN cc_start: 0.7571 (mt0) cc_final: 0.6659 (tt0) REVERT: A 233 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 300 LYS cc_start: 0.8623 (mtpt) cc_final: 0.7981 (mttt) REVERT: A 318 SER cc_start: 0.8910 (t) cc_final: 0.8299 (m) REVERT: A 414 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7450 (ttt90) REVERT: B 31 GLN cc_start: 0.7541 (mt0) cc_final: 0.6626 (tt0) REVERT: B 300 LYS cc_start: 0.8626 (mtpt) cc_final: 0.7983 (mttt) REVERT: B 318 SER cc_start: 0.8915 (t) cc_final: 0.8305 (m) REVERT: B 409 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7717 (ttt90) REVERT: B 414 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7457 (ttt90) REVERT: C 31 GLN cc_start: 0.7547 (mt0) cc_final: 0.6630 (tt0) REVERT: C 300 LYS cc_start: 0.8627 (mtpt) cc_final: 0.7986 (mttt) REVERT: C 318 SER cc_start: 0.8908 (t) cc_final: 0.8297 (m) REVERT: C 409 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7730 (ttt90) REVERT: C 414 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7458 (ttt90) REVERT: D 31 GLN cc_start: 0.7549 (mt0) cc_final: 0.6632 (tt0) REVERT: D 300 LYS cc_start: 0.8626 (mtpt) cc_final: 0.7983 (mttt) REVERT: D 318 SER cc_start: 0.8912 (t) cc_final: 0.8302 (m) REVERT: D 409 ARG cc_start: 0.8048 (ttt90) cc_final: 0.7719 (ttt90) REVERT: D 414 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7476 (ttt90) outliers start: 45 outliers final: 39 residues processed: 318 average time/residue: 0.4119 time to fit residues: 201.9782 Evaluate side-chains 318 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 153 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 168 optimal weight: 0.0870 chunk 188 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.122034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.092165 restraints weight = 24879.149| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.47 r_work: 0.2780 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20292 Z= 0.098 Angle : 0.437 6.957 27572 Z= 0.231 Chirality : 0.037 0.182 3140 Planarity : 0.004 0.050 3436 Dihedral : 7.368 68.721 3324 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.53 % Allowed : 12.55 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.17), residues: 2408 helix: 2.05 (0.13), residues: 1500 sheet: -1.49 (0.53), residues: 84 loop : -0.04 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.002 0.000 HIS A 201 PHE 0.027 0.001 PHE D 574 TYR 0.012 0.001 TYR A 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 1109) hydrogen bonds : angle 3.73765 ( 3147) covalent geometry : bond 0.00222 (20292) covalent geometry : angle 0.43675 (27572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7516 (mt0) cc_final: 0.6634 (tt0) REVERT: A 60 LEU cc_start: 0.8090 (tp) cc_final: 0.7637 (mm) REVERT: A 233 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8198 (mt-10) REVERT: A 318 SER cc_start: 0.8970 (t) cc_final: 0.8427 (m) REVERT: A 414 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7619 (mtt90) REVERT: B 31 GLN cc_start: 0.7468 (mt0) cc_final: 0.6602 (tt0) REVERT: B 60 LEU cc_start: 0.8091 (tp) cc_final: 0.7638 (mm) REVERT: B 318 SER cc_start: 0.8975 (t) cc_final: 0.8435 (m) REVERT: B 414 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7621 (mtt90) REVERT: B 578 MET cc_start: 0.8087 (mtt) cc_final: 0.7803 (mtt) REVERT: C 31 GLN cc_start: 0.7479 (mt0) cc_final: 0.6609 (tt0) REVERT: C 60 LEU cc_start: 0.8088 (tp) cc_final: 0.7639 (mm) REVERT: C 318 SER cc_start: 0.8966 (t) cc_final: 0.8423 (m) REVERT: C 414 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7630 (mtt90) REVERT: C 578 MET cc_start: 0.8117 (mtt) cc_final: 0.7834 (mtt) REVERT: D 31 GLN cc_start: 0.7489 (mt0) cc_final: 0.6617 (tt0) REVERT: D 60 LEU cc_start: 0.8089 (tp) cc_final: 0.7638 (mm) REVERT: D 318 SER cc_start: 0.8969 (t) cc_final: 0.8435 (m) REVERT: D 414 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7613 (mtt90) REVERT: D 442 MET cc_start: 0.8312 (mtm) cc_final: 0.8058 (mtp) outliers start: 32 outliers final: 32 residues processed: 307 average time/residue: 0.5420 time to fit residues: 256.1922 Evaluate side-chains 305 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 73 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.091568 restraints weight = 24690.679| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.46 r_work: 0.2793 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20292 Z= 0.111 Angle : 0.449 8.874 27572 Z= 0.236 Chirality : 0.037 0.168 3140 Planarity : 0.004 0.050 3436 Dihedral : 7.263 68.637 3324 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.34 % Allowed : 13.02 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2408 helix: 2.16 (0.13), residues: 1496 sheet: -1.51 (0.53), residues: 84 loop : -0.07 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE D 408 TYR 0.010 0.001 TYR A 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 1109) hydrogen bonds : angle 3.72914 ( 3147) covalent geometry : bond 0.00259 (20292) covalent geometry : angle 0.44852 (27572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 281 time to evaluate : 3.230 Fit side-chains REVERT: A 31 GLN cc_start: 0.7509 (mt0) cc_final: 0.6639 (tt0) REVERT: A 60 LEU cc_start: 0.8091 (tp) cc_final: 0.7640 (mm) REVERT: A 233 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 300 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8129 (mmtm) REVERT: A 302 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8161 (mtp-110) REVERT: A 318 SER cc_start: 0.8980 (t) cc_final: 0.8439 (m) REVERT: A 414 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7618 (mtt90) REVERT: B 31 GLN cc_start: 0.7466 (mt0) cc_final: 0.6604 (tt0) REVERT: B 300 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8134 (mmtm) REVERT: B 302 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8159 (mtp-110) REVERT: B 318 SER cc_start: 0.8983 (t) cc_final: 0.8448 (m) REVERT: B 414 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7620 (mtt90) REVERT: B 578 MET cc_start: 0.8244 (mtt) cc_final: 0.7984 (mtt) REVERT: C 31 GLN cc_start: 0.7482 (mt0) cc_final: 0.6618 (tt0) REVERT: C 300 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8125 (mmtm) REVERT: C 302 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8173 (mtp-110) REVERT: C 318 SER cc_start: 0.8977 (t) cc_final: 0.8439 (m) REVERT: C 414 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7632 (mtt90) REVERT: C 578 MET cc_start: 0.8257 (mtt) cc_final: 0.7995 (mtt) REVERT: D 31 GLN cc_start: 0.7481 (mt0) cc_final: 0.6618 (tt0) REVERT: D 300 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8131 (mmtm) REVERT: D 302 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8160 (mtp-110) REVERT: D 318 SER cc_start: 0.8979 (t) cc_final: 0.8441 (m) REVERT: D 414 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7619 (mtt90) outliers start: 28 outliers final: 26 residues processed: 303 average time/residue: 0.4853 time to fit residues: 234.9031 Evaluate side-chains 298 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092448 restraints weight = 24631.877| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.46 r_work: 0.2806 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20292 Z= 0.102 Angle : 0.445 8.627 27572 Z= 0.236 Chirality : 0.038 0.189 3140 Planarity : 0.004 0.051 3436 Dihedral : 7.185 69.457 3324 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.43 % Allowed : 12.93 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.17), residues: 2408 helix: 2.15 (0.13), residues: 1488 sheet: -1.46 (0.53), residues: 84 loop : -0.08 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.001 PHE A 574 TYR 0.010 0.001 TYR C 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 1109) hydrogen bonds : angle 3.71529 ( 3147) covalent geometry : bond 0.00232 (20292) covalent geometry : angle 0.44486 (27572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 3.193 Fit side-chains REVERT: A 31 GLN cc_start: 0.7487 (mt0) cc_final: 0.6634 (tt0) REVERT: A 60 LEU cc_start: 0.8094 (tp) cc_final: 0.7636 (mm) REVERT: A 175 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 233 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8209 (mt-10) REVERT: A 302 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8181 (mtp-110) REVERT: A 318 SER cc_start: 0.8956 (t) cc_final: 0.8422 (m) REVERT: A 414 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7584 (mtt90) REVERT: B 31 GLN cc_start: 0.7460 (mt0) cc_final: 0.6637 (tt0) REVERT: B 300 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8129 (mmtm) REVERT: B 302 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8162 (mtp-110) REVERT: B 318 SER cc_start: 0.8959 (t) cc_final: 0.8431 (m) REVERT: B 414 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7588 (mtt90) REVERT: B 578 MET cc_start: 0.8244 (mtt) cc_final: 0.8029 (mtt) REVERT: C 31 GLN cc_start: 0.7472 (mt0) cc_final: 0.6647 (tt0) REVERT: C 175 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7544 (t) REVERT: C 300 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8127 (mmtm) REVERT: C 302 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8184 (mtp-110) REVERT: C 318 SER cc_start: 0.8955 (t) cc_final: 0.8422 (m) REVERT: C 414 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7600 (mtt90) REVERT: C 578 MET cc_start: 0.8258 (mtt) cc_final: 0.8043 (mtt) REVERT: D 31 GLN cc_start: 0.7476 (mt0) cc_final: 0.6652 (tt0) REVERT: D 175 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7536 (t) REVERT: D 300 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8127 (mmtm) REVERT: D 302 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8168 (mtp-110) REVERT: D 318 SER cc_start: 0.8963 (t) cc_final: 0.8429 (m) REVERT: D 414 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7585 (mtt90) REVERT: D 442 MET cc_start: 0.8281 (mtm) cc_final: 0.8022 (mtp) outliers start: 30 outliers final: 27 residues processed: 289 average time/residue: 0.3393 time to fit residues: 151.3852 Evaluate side-chains 295 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 189 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 193 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.092389 restraints weight = 24863.030| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.43 r_work: 0.2784 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20292 Z= 0.103 Angle : 0.437 5.046 27572 Z= 0.233 Chirality : 0.038 0.181 3140 Planarity : 0.004 0.051 3436 Dihedral : 7.124 70.078 3324 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.67 % Allowed : 12.74 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2408 helix: 2.16 (0.13), residues: 1488 sheet: -1.46 (0.53), residues: 84 loop : -0.06 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.002 0.001 HIS A 201 PHE 0.027 0.001 PHE D 574 TYR 0.010 0.001 TYR B 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1109) hydrogen bonds : angle 3.69667 ( 3147) covalent geometry : bond 0.00238 (20292) covalent geometry : angle 0.43701 (27572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13135.76 seconds wall clock time: 238 minutes 18.70 seconds (14298.70 seconds total)