Starting phenix.real_space_refine on Sun Aug 24 13:12:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fhh_29085/08_2025/8fhh_29085_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fhh_29085/08_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_29085/08_2025/8fhh_29085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fhh_29085/08_2025/8fhh_29085.map" model { file = "/net/cci-nas-00/data/ceres_data/8fhh_29085/08_2025/8fhh_29085_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fhh_29085/08_2025/8fhh_29085_neut.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.044 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D Time building chain proxies: 5.03, per 1000 atoms: 0.25 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: 1.80 Conformation dependent library (CDL) restraints added in 941.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.68 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: 3.78 Time building geometry restraints manager: 2.43 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.960 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG A 363 TYR 0.010 0.002 TYR D 467 PHE 0.014 0.002 PHE B 537 TRP 0.018 0.002 TRP D 268 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00552 (20292) covalent geometry : angle 0.83068 (27572) hydrogen bonds : bond 0.16716 ( 1109) hydrogen bonds : angle 6.07477 ( 3147) *********************** 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 : 0.864 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: 0.1852 time to fit residues: 121.7918 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 : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** A 635 ASN 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** C 635 ASN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.094405 restraints weight = 24592.319| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.54 r_work: 0.2822 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1723 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= 0.103 Angle : 0.465 5.276 27572 Z= 0.246 Chirality : 0.037 0.176 3140 Planarity : 0.005 0.049 3436 Dihedral : 8.868 100.613 3324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.34 % Allowed : 6.77 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.16), residues: 2408 helix: 0.65 (0.13), residues: 1504 sheet: -2.38 (0.37), residues: 124 loop : -0.34 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 139 TYR 0.010 0.001 TYR D 555 PHE 0.010 0.001 PHE C 574 TRP 0.018 0.001 TRP C 593 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00217 (20292) covalent geometry : angle 0.46515 (27572) hydrogen bonds : bond 0.03586 ( 1109) hydrogen bonds : angle 3.91119 ( 3147) *********************** 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 352 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 0.768 Fit side-chains REVERT: A 31 GLN cc_start: 0.7518 (mt0) cc_final: 0.6585 (tt0) REVERT: A 176 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7575 (mp0) REVERT: A 233 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 318 SER cc_start: 0.8914 (t) cc_final: 0.8448 (m) REVERT: A 414 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7569 (ttt90) REVERT: A 442 MET cc_start: 0.8776 (mtp) cc_final: 0.8386 (mtp) REVERT: A 445 THR cc_start: 0.8995 (t) cc_final: 0.8725 (p) REVERT: B 31 GLN cc_start: 0.7495 (mt0) cc_final: 0.6570 (tt0) REVERT: B 176 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7593 (mp0) REVERT: B 233 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 318 SER cc_start: 0.8917 (t) cc_final: 0.8453 (m) REVERT: B 414 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7564 (ttt90) REVERT: B 442 MET cc_start: 0.8781 (mtp) cc_final: 0.8386 (mtp) REVERT: B 445 THR cc_start: 0.8977 (t) cc_final: 0.8698 (p) REVERT: C 31 GLN cc_start: 0.7483 (mt0) cc_final: 0.6556 (tt0) REVERT: C 176 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7567 (mp0) REVERT: C 233 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 318 SER cc_start: 0.8914 (t) cc_final: 0.8448 (m) REVERT: C 414 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7568 (ttt90) REVERT: C 442 MET cc_start: 0.8783 (mtp) cc_final: 0.8386 (mtp) REVERT: C 445 THR cc_start: 0.8982 (t) cc_final: 0.8705 (p) REVERT: D 31 GLN cc_start: 0.7495 (mt0) cc_final: 0.6569 (tt0) REVERT: D 176 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7569 (mp0) REVERT: D 233 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8163 (mt-10) REVERT: D 318 SER cc_start: 0.8916 (t) cc_final: 0.8448 (m) REVERT: D 414 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7568 (ttt90) REVERT: D 442 MET cc_start: 0.8779 (mtp) cc_final: 0.8386 (mtp) REVERT: D 445 THR cc_start: 0.8987 (t) cc_final: 0.8709 (p) outliers start: 28 outliers final: 11 residues processed: 335 average time/residue: 0.1669 time to fit residues: 84.7131 Evaluate side-chains 300 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 289 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU 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 189 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095204 restraints weight = 24368.467| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.46 r_work: 0.2827 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20292 Z= 0.131 Angle : 0.465 5.387 27572 Z= 0.244 Chirality : 0.039 0.208 3140 Planarity : 0.004 0.051 3436 Dihedral : 8.380 101.292 3324 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.34 % Allowed : 7.54 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2408 helix: 1.29 (0.13), residues: 1500 sheet: -1.53 (0.50), residues: 84 loop : -0.30 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 302 TYR 0.010 0.001 TYR B 216 PHE 0.011 0.001 PHE C 468 TRP 0.015 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00315 (20292) covalent geometry : angle 0.46467 (27572) hydrogen bonds : bond 0.03512 ( 1109) hydrogen bonds : angle 3.70844 ( 3147) *********************** 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 340 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 312 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7518 (mt0) cc_final: 0.6602 (tt0) REVERT: A 176 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7487 (mp0) REVERT: A 233 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 314 LYS cc_start: 0.8541 (tttt) cc_final: 0.8228 (ttmp) REVERT: A 318 SER cc_start: 0.8951 (t) cc_final: 0.8459 (m) REVERT: A 409 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7646 (ttt90) REVERT: A 414 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7494 (ttt90) REVERT: A 444 LEU cc_start: 0.9212 (mt) cc_final: 0.9003 (mt) REVERT: B 31 GLN cc_start: 0.7505 (mt0) cc_final: 0.6578 (tt0) REVERT: B 176 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7497 (mp0) REVERT: B 314 LYS cc_start: 0.8547 (tttt) cc_final: 0.8239 (ttmp) REVERT: B 318 SER cc_start: 0.8952 (t) cc_final: 0.8470 (m) REVERT: B 409 ARG cc_start: 0.8021 (ttt90) cc_final: 0.7625 (ttt90) REVERT: B 414 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7500 (ttt90) REVERT: B 444 LEU cc_start: 0.9211 (mt) cc_final: 0.8998 (mt) REVERT: C 31 GLN cc_start: 0.7501 (mt0) cc_final: 0.6575 (tt0) REVERT: C 176 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7497 (mp0) REVERT: C 318 SER cc_start: 0.8964 (t) cc_final: 0.8463 (m) REVERT: C 409 ARG cc_start: 0.8032 (ttt90) cc_final: 0.7639 (ttt90) REVERT: C 414 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7510 (ttt90) REVERT: C 444 LEU cc_start: 0.9212 (mt) cc_final: 0.8998 (mt) REVERT: D 31 GLN cc_start: 0.7499 (mt0) cc_final: 0.6571 (tt0) REVERT: D 176 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7484 (mp0) REVERT: D 314 LYS cc_start: 0.8539 (tttt) cc_final: 0.8232 (ttmp) REVERT: D 318 SER cc_start: 0.8950 (t) cc_final: 0.8465 (m) REVERT: D 409 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7642 (ttt90) REVERT: D 414 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7495 (ttt90) REVERT: D 444 LEU cc_start: 0.9211 (mt) cc_final: 0.9001 (mt) outliers start: 28 outliers final: 24 residues processed: 328 average time/residue: 0.1601 time to fit residues: 80.1384 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 : 0.802 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 87 optimal weight: 0.7980 chunk 179 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 139 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.123605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.094353 restraints weight = 24691.932| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.44 r_work: 0.2824 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2202 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= 0.089 Angle : 0.427 5.227 27572 Z= 0.225 Chirality : 0.037 0.209 3140 Planarity : 0.004 0.052 3436 Dihedral : 7.946 82.340 3324 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.15 % Allowed : 9.21 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.17), residues: 2408 helix: 1.78 (0.13), residues: 1504 sheet: -2.29 (0.38), residues: 124 loop : -0.08 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 302 TYR 0.010 0.001 TYR A 555 PHE 0.019 0.001 PHE A 574 TRP 0.015 0.001 TRP A 593 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00195 (20292) covalent geometry : angle 0.42713 (27572) hydrogen bonds : bond 0.03072 ( 1109) hydrogen bonds : angle 3.59331 ( 3147) *********************** 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: 24 poor density : 312 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7403 (mt0) cc_final: 0.6540 (tt0) REVERT: A 176 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7579 (mp0) REVERT: A 233 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 314 LYS cc_start: 0.8549 (tttt) cc_final: 0.8259 (tttp) REVERT: A 318 SER cc_start: 0.8955 (t) cc_final: 0.8472 (m) REVERT: A 409 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7648 (ttt90) REVERT: A 414 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7559 (ttt90) REVERT: A 442 MET cc_start: 0.8766 (mtp) cc_final: 0.8370 (mtp) REVERT: B 31 GLN cc_start: 0.7388 (mt0) cc_final: 0.6511 (tt0) REVERT: B 176 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7583 (mp0) REVERT: B 314 LYS cc_start: 0.8554 (tttt) cc_final: 0.8265 (tttp) REVERT: B 318 SER cc_start: 0.8961 (t) cc_final: 0.8481 (m) REVERT: B 409 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7645 (ttt90) REVERT: B 414 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7576 (ttt90) REVERT: B 442 MET cc_start: 0.8780 (mtp) cc_final: 0.8373 (mtp) REVERT: C 31 GLN cc_start: 0.7395 (mt0) cc_final: 0.6515 (tt0) REVERT: C 176 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7590 (mp0) REVERT: C 318 SER cc_start: 0.8956 (t) cc_final: 0.8456 (m) REVERT: C 409 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7639 (ttt90) REVERT: C 414 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7562 (ttt90) REVERT: C 442 MET cc_start: 0.8761 (mtp) cc_final: 0.8353 (mtp) REVERT: D 31 GLN cc_start: 0.7400 (mt0) cc_final: 0.6519 (tt0) REVERT: D 176 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7574 (mp0) REVERT: D 314 LYS cc_start: 0.8545 (tttt) cc_final: 0.8254 (tttp) REVERT: D 318 SER cc_start: 0.8949 (t) cc_final: 0.8466 (m) REVERT: D 409 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7653 (ttt90) REVERT: D 414 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7597 (ttt90) REVERT: D 442 MET cc_start: 0.8753 (mtp) cc_final: 0.8360 (mtp) outliers start: 24 outliers final: 24 residues processed: 324 average time/residue: 0.1718 time to fit residues: 83.6132 Evaluate side-chains 318 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU 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 A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU 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 B residue 474 MET Chi-restraints excluded: chain C residue 111 LEU 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 C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU 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 Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9980 chunk 231 optimal weight: 0.0670 chunk 33 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.123509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093965 restraints weight = 24409.355| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.45 r_work: 0.2815 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2317 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= 0.097 Angle : 0.434 5.241 27572 Z= 0.228 Chirality : 0.037 0.202 3140 Planarity : 0.004 0.052 3436 Dihedral : 7.658 69.210 3324 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.00 % Allowed : 10.88 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.17), residues: 2408 helix: 2.05 (0.13), residues: 1480 sheet: -2.25 (0.39), residues: 124 loop : -0.05 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 302 TYR 0.009 0.001 TYR B 555 PHE 0.020 0.001 PHE A 574 TRP 0.014 0.001 TRP A 593 HIS 0.002 0.000 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00219 (20292) covalent geometry : angle 0.43421 (27572) hydrogen bonds : bond 0.03108 ( 1109) hydrogen bonds : angle 3.57917 ( 3147) *********************** 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 334 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 313 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7385 (mt0) cc_final: 0.6534 (tt0) REVERT: A 233 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 261 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8312 (mm-40) REVERT: A 300 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8107 (mmtm) REVERT: A 314 LYS cc_start: 0.8565 (tttt) cc_final: 0.8264 (tttp) REVERT: A 318 SER cc_start: 0.8967 (t) cc_final: 0.8474 (m) REVERT: A 409 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7781 (ttt90) REVERT: A 414 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7581 (mtt90) REVERT: A 442 MET cc_start: 0.8759 (mtp) cc_final: 0.8512 (mtp) REVERT: B 31 GLN cc_start: 0.7374 (mt0) cc_final: 0.6528 (tt0) REVERT: B 261 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8303 (mm-40) REVERT: B 300 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8110 (mmtm) REVERT: B 314 LYS cc_start: 0.8569 (tttt) cc_final: 0.8268 (tttp) REVERT: B 318 SER cc_start: 0.8957 (t) cc_final: 0.8481 (m) REVERT: B 409 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7800 (ttt90) REVERT: B 414 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7619 (mtt90) REVERT: B 442 MET cc_start: 0.8773 (mtp) cc_final: 0.8522 (mtp) REVERT: C 31 GLN cc_start: 0.7380 (mt0) cc_final: 0.6530 (tt0) REVERT: C 261 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8315 (mm-40) REVERT: C 300 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8102 (mmtm) REVERT: C 314 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8239 (tttp) REVERT: C 318 SER cc_start: 0.8965 (t) cc_final: 0.8451 (m) REVERT: C 409 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7660 (ttt90) REVERT: C 414 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7592 (mtt90) REVERT: C 442 MET cc_start: 0.8764 (mtp) cc_final: 0.8514 (mtp) REVERT: D 31 GLN cc_start: 0.7384 (mt0) cc_final: 0.6534 (tt0) REVERT: D 261 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8310 (mm-40) REVERT: D 300 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8110 (mmtm) REVERT: D 314 LYS cc_start: 0.8560 (tttt) cc_final: 0.8258 (tttp) REVERT: D 318 SER cc_start: 0.8948 (t) cc_final: 0.8470 (m) REVERT: D 409 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7668 (ttt90) REVERT: D 414 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7592 (mtt90) REVERT: D 442 MET cc_start: 0.8757 (mtp) cc_final: 0.8510 (mtp) outliers start: 21 outliers final: 21 residues processed: 325 average time/residue: 0.1613 time to fit residues: 79.4333 Evaluate side-chains 315 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 294 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU 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 A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 175 SER 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 175 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.118505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.088708 restraints weight = 24778.759| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.43 r_work: 0.2757 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20292 Z= 0.217 Angle : 0.538 9.948 27572 Z= 0.275 Chirality : 0.041 0.215 3140 Planarity : 0.004 0.051 3436 Dihedral : 8.035 75.718 3324 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.38 % Allowed : 11.26 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.17), residues: 2408 helix: 1.85 (0.13), residues: 1476 sheet: -1.49 (0.52), residues: 84 loop : -0.21 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 302 TYR 0.014 0.002 TYR C 526 PHE 0.016 0.002 PHE A 468 TRP 0.011 0.001 TRP A 593 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00536 (20292) covalent geometry : angle 0.53800 (27572) hydrogen bonds : bond 0.03974 ( 1109) hydrogen bonds : angle 3.83754 ( 3147) *********************** 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 330 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7656 (mt0) cc_final: 0.6755 (tt0) REVERT: A 233 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 300 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8068 (mttt) REVERT: A 314 LYS cc_start: 0.8652 (tttt) cc_final: 0.8395 (tttp) REVERT: A 318 SER cc_start: 0.9021 (t) cc_final: 0.8416 (m) REVERT: A 414 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7481 (ttt180) REVERT: B 31 GLN cc_start: 0.7645 (mt0) cc_final: 0.6753 (tt0) REVERT: B 300 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8063 (mttt) REVERT: B 314 LYS cc_start: 0.8642 (tttt) cc_final: 0.8384 (tttp) REVERT: B 318 SER cc_start: 0.9017 (t) cc_final: 0.8413 (m) REVERT: B 414 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7499 (ttt180) REVERT: C 31 GLN cc_start: 0.7648 (mt0) cc_final: 0.6753 (tt0) REVERT: C 300 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8062 (mttt) REVERT: C 314 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8249 (tttp) REVERT: C 318 SER cc_start: 0.9018 (t) cc_final: 0.8402 (m) REVERT: C 414 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7472 (ttt180) REVERT: D 31 GLN cc_start: 0.7643 (mt0) cc_final: 0.6749 (tt0) REVERT: D 300 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8064 (mttt) REVERT: D 314 LYS cc_start: 0.8635 (tttt) cc_final: 0.8376 (tttp) REVERT: D 318 SER cc_start: 0.9009 (t) cc_final: 0.8404 (m) REVERT: D 414 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7463 (ttt180) outliers start: 29 outliers final: 25 residues processed: 321 average time/residue: 0.1621 time to fit residues: 78.9508 Evaluate side-chains 322 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 297 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 274 THR 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 274 THR 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 274 THR 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 274 THR Chi-restraints excluded: chain D residue 354 LEU 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 216 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 109 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.122308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.092751 restraints weight = 24733.052| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.43 r_work: 0.2829 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20292 Z= 0.100 Angle : 0.442 5.161 27572 Z= 0.235 Chirality : 0.038 0.192 3140 Planarity : 0.004 0.052 3436 Dihedral : 7.627 69.326 3324 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.00 % Allowed : 12.02 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.17), residues: 2408 helix: 2.03 (0.13), residues: 1496 sheet: -1.37 (0.52), residues: 84 loop : -0.04 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 302 TYR 0.011 0.001 TYR D 555 PHE 0.008 0.001 PHE C 244 TRP 0.015 0.001 TRP A 593 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00226 (20292) covalent geometry : angle 0.44205 (27572) hydrogen bonds : bond 0.03248 ( 1109) hydrogen bonds : angle 3.69834 ( 3147) *********************** 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 333 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 312 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7536 (mt0) cc_final: 0.6673 (tt0) REVERT: A 60 LEU cc_start: 0.8092 (tp) cc_final: 0.7629 (mm) REVERT: A 233 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 314 LYS cc_start: 0.8618 (tttt) cc_final: 0.8413 (tttp) REVERT: A 318 SER cc_start: 0.8994 (t) cc_final: 0.8463 (m) REVERT: A 409 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7814 (ttt90) REVERT: A 414 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7582 (mtt90) REVERT: A 450 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 31 GLN cc_start: 0.7501 (mt0) cc_final: 0.6621 (tt0) REVERT: B 60 LEU cc_start: 0.8088 (tp) cc_final: 0.7624 (mm) REVERT: B 314 LYS cc_start: 0.8617 (tttt) cc_final: 0.8413 (tttp) REVERT: B 318 SER cc_start: 0.8994 (t) cc_final: 0.8464 (m) REVERT: B 409 ARG cc_start: 0.8055 (ttt90) cc_final: 0.7802 (ttt90) REVERT: B 414 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7595 (mtt90) REVERT: B 442 MET cc_start: 0.8772 (mtp) cc_final: 0.8568 (mtm) REVERT: B 450 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 31 GLN cc_start: 0.7493 (mt0) cc_final: 0.6610 (tt0) REVERT: C 60 LEU cc_start: 0.8099 (tp) cc_final: 0.7627 (mm) REVERT: C 314 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8183 (tttp) REVERT: C 318 SER cc_start: 0.8982 (t) cc_final: 0.8457 (m) REVERT: C 409 ARG cc_start: 0.8055 (ttt90) cc_final: 0.7807 (ttt90) REVERT: C 414 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7588 (mtt90) REVERT: C 442 MET cc_start: 0.8773 (mtp) cc_final: 0.8569 (mtm) REVERT: C 450 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7829 (mt-10) REVERT: D 31 GLN cc_start: 0.7501 (mt0) cc_final: 0.6622 (tt0) REVERT: D 60 LEU cc_start: 0.8089 (tp) cc_final: 0.7624 (mm) REVERT: D 314 LYS cc_start: 0.8608 (tttt) cc_final: 0.8400 (tttp) REVERT: D 318 SER cc_start: 0.8986 (t) cc_final: 0.8455 (m) REVERT: D 409 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7809 (ttt90) REVERT: D 414 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7584 (mtt90) REVERT: D 450 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7841 (mt-10) outliers start: 21 outliers final: 21 residues processed: 324 average time/residue: 0.1428 time to fit residues: 70.1051 Evaluate side-chains 313 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 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 354 LEU Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 201 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 191 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.125037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.095598 restraints weight = 24474.768| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.43 r_work: 0.2855 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20292 Z= 0.087 Angle : 0.429 5.532 27572 Z= 0.227 Chirality : 0.037 0.162 3140 Planarity : 0.004 0.052 3436 Dihedral : 7.017 69.844 3324 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.00 % Allowed : 12.83 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.17), residues: 2408 helix: 2.23 (0.13), residues: 1476 sheet: -2.17 (0.39), residues: 124 loop : 0.00 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 302 TYR 0.011 0.001 TYR D 555 PHE 0.025 0.001 PHE D 574 TRP 0.016 0.001 TRP A 593 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00188 (20292) covalent geometry : angle 0.42949 (27572) hydrogen bonds : bond 0.02990 ( 1109) hydrogen bonds : angle 3.62855 ( 3147) *********************** 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 310 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 289 time to evaluate : 0.866 Fit side-chains REVERT: A 31 GLN cc_start: 0.7430 (mt0) cc_final: 0.6564 (tt0) REVERT: A 60 LEU cc_start: 0.8050 (tp) cc_final: 0.7592 (mm) REVERT: A 175 SER cc_start: 0.7357 (OUTLIER) cc_final: 0.6726 (t) REVERT: A 233 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 302 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8133 (mtp-110) REVERT: A 314 LYS cc_start: 0.8605 (tttt) cc_final: 0.8320 (tttp) REVERT: A 318 SER cc_start: 0.8968 (t) cc_final: 0.8492 (m) REVERT: A 409 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7775 (ttt90) REVERT: A 414 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7633 (ttt90) REVERT: B 31 GLN cc_start: 0.7410 (mt0) cc_final: 0.6564 (tt0) REVERT: B 60 LEU cc_start: 0.8051 (tp) cc_final: 0.7590 (mm) REVERT: B 175 SER cc_start: 0.7300 (OUTLIER) cc_final: 0.6676 (t) REVERT: B 302 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8124 (mtp-110) REVERT: B 314 LYS cc_start: 0.8614 (tttt) cc_final: 0.8330 (tttp) REVERT: B 318 SER cc_start: 0.8967 (t) cc_final: 0.8493 (m) REVERT: B 409 ARG cc_start: 0.8035 (ttt90) cc_final: 0.7775 (ttt90) REVERT: B 414 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7608 (mtt90) REVERT: B 442 MET cc_start: 0.8743 (mtp) cc_final: 0.8450 (mtp) REVERT: B 450 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 31 GLN cc_start: 0.7386 (mt0) cc_final: 0.6534 (tt0) REVERT: C 60 LEU cc_start: 0.8058 (tp) cc_final: 0.7593 (mm) REVERT: C 175 SER cc_start: 0.7291 (OUTLIER) cc_final: 0.6673 (t) REVERT: C 302 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.8147 (mtp-110) REVERT: C 314 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8208 (tttp) REVERT: C 318 SER cc_start: 0.8968 (t) cc_final: 0.8467 (m) REVERT: C 409 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7753 (ttt90) REVERT: C 414 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7639 (ttt90) REVERT: C 442 MET cc_start: 0.8745 (mtp) cc_final: 0.8458 (mtp) REVERT: C 450 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7777 (mt-10) REVERT: D 31 GLN cc_start: 0.7420 (mt0) cc_final: 0.6578 (tt0) REVERT: D 60 LEU cc_start: 0.8051 (tp) cc_final: 0.7592 (mm) REVERT: D 175 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6672 (t) REVERT: D 302 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.8144 (mtp-110) REVERT: D 314 LYS cc_start: 0.8600 (tttt) cc_final: 0.8315 (tttp) REVERT: D 318 SER cc_start: 0.8964 (t) cc_final: 0.8490 (m) REVERT: D 409 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7759 (ttt90) REVERT: D 414 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7633 (ttt90) outliers start: 21 outliers final: 13 residues processed: 305 average time/residue: 0.1384 time to fit residues: 64.4367 Evaluate side-chains 303 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 286 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU 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 175 SER 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 175 SER 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 175 SER Chi-restraints excluded: chain D residue 354 LEU 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 222 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 145 optimal weight: 0.0670 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.124621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094804 restraints weight = 24409.414| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.46 r_work: 0.2886 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2649 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= 0.099 Angle : 0.444 8.000 27572 Z= 0.233 Chirality : 0.037 0.158 3140 Planarity : 0.004 0.052 3436 Dihedral : 6.953 70.108 3324 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.81 % Allowed : 13.07 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.17), residues: 2408 helix: 2.27 (0.13), residues: 1488 sheet: -2.18 (0.38), residues: 124 loop : -0.00 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 302 TYR 0.010 0.001 TYR C 555 PHE 0.009 0.001 PHE D 574 TRP 0.014 0.001 TRP C 593 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00227 (20292) covalent geometry : angle 0.44438 (27572) hydrogen bonds : bond 0.03067 ( 1109) hydrogen bonds : angle 3.62183 ( 3147) *********************** 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 306 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 0.671 Fit side-chains REVERT: A 31 GLN cc_start: 0.7613 (mt0) cc_final: 0.6778 (tt0) REVERT: A 60 LEU cc_start: 0.8120 (tp) cc_final: 0.7655 (mm) REVERT: A 175 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7007 (t) REVERT: A 233 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 300 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8211 (mmtm) REVERT: A 314 LYS cc_start: 0.8771 (tttt) cc_final: 0.8525 (tttp) REVERT: A 318 SER cc_start: 0.9063 (t) cc_final: 0.8605 (m) REVERT: A 409 ARG cc_start: 0.8140 (ttt90) cc_final: 0.7875 (ttt90) REVERT: B 31 GLN cc_start: 0.7573 (mt0) cc_final: 0.6748 (tt0) REVERT: B 60 LEU cc_start: 0.8123 (tp) cc_final: 0.7655 (mm) REVERT: B 175 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7005 (t) REVERT: B 300 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8184 (mmtm) REVERT: B 314 LYS cc_start: 0.8778 (tttt) cc_final: 0.8533 (tttp) REVERT: B 318 SER cc_start: 0.9063 (t) cc_final: 0.8606 (m) REVERT: B 409 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7881 (ttt90) REVERT: B 450 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 31 GLN cc_start: 0.7568 (mt0) cc_final: 0.6739 (tt0) REVERT: C 60 LEU cc_start: 0.8126 (tp) cc_final: 0.7654 (mm) REVERT: C 175 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7004 (t) REVERT: C 300 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8189 (mmtm) REVERT: C 318 SER cc_start: 0.9075 (t) cc_final: 0.8576 (m) REVERT: C 409 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7875 (ttt90) REVERT: C 450 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 31 GLN cc_start: 0.7578 (mt0) cc_final: 0.6754 (tt0) REVERT: D 60 LEU cc_start: 0.8120 (tp) cc_final: 0.7656 (mm) REVERT: D 175 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.6995 (t) REVERT: D 300 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8222 (mmtm) REVERT: D 314 LYS cc_start: 0.8770 (tttt) cc_final: 0.8522 (tttp) REVERT: D 318 SER cc_start: 0.9062 (t) cc_final: 0.8603 (m) REVERT: D 409 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7880 (ttt90) outliers start: 17 outliers final: 9 residues processed: 301 average time/residue: 0.1250 time to fit residues: 57.0287 Evaluate side-chains 301 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 288 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 175 SER 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 175 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 175 SER 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 57 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3339 r_free = 0.3339 target = 0.124094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.093956 restraints weight = 24505.736| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.47 r_work: 0.2866 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20292 Z= 0.114 Angle : 0.458 8.414 27572 Z= 0.239 Chirality : 0.038 0.158 3140 Planarity : 0.004 0.052 3436 Dihedral : 6.991 70.038 3324 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.67 % Allowed : 13.55 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.17), residues: 2408 helix: 2.29 (0.13), residues: 1464 sheet: -1.33 (0.53), residues: 84 loop : -0.08 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 302 TYR 0.009 0.001 TYR D 555 PHE 0.012 0.001 PHE A 408 TRP 0.012 0.001 TRP B 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00270 (20292) covalent geometry : angle 0.45769 (27572) hydrogen bonds : bond 0.03222 ( 1109) hydrogen bonds : angle 3.67641 ( 3147) ********************** 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 298 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 284 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7678 (mt0) cc_final: 0.6851 (tt0) REVERT: A 175 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7605 (t) REVERT: A 233 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 314 LYS cc_start: 0.8811 (tttt) cc_final: 0.8572 (tttp) REVERT: A 318 SER cc_start: 0.9106 (t) cc_final: 0.8639 (m) REVERT: B 31 GLN cc_start: 0.7642 (mt0) cc_final: 0.6816 (tt0) REVERT: B 175 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7603 (t) REVERT: B 314 LYS cc_start: 0.8817 (tttt) cc_final: 0.8580 (tttp) REVERT: B 318 SER cc_start: 0.9105 (t) cc_final: 0.8640 (m) REVERT: B 409 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7900 (ttt90) REVERT: B 450 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 31 GLN cc_start: 0.7631 (mt0) cc_final: 0.6809 (tt0) REVERT: C 175 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7587 (t) REVERT: C 318 SER cc_start: 0.9134 (t) cc_final: 0.8639 (m) REVERT: C 450 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7889 (mt-10) REVERT: D 31 GLN cc_start: 0.7643 (mt0) cc_final: 0.6825 (tt0) REVERT: D 175 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7596 (t) REVERT: D 314 LYS cc_start: 0.8811 (tttt) cc_final: 0.8572 (tttp) REVERT: D 318 SER cc_start: 0.9103 (t) cc_final: 0.8637 (m) outliers start: 14 outliers final: 10 residues processed: 293 average time/residue: 0.1346 time to fit residues: 59.4542 Evaluate side-chains 298 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 284 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 175 SER 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 175 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 175 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 1.9990 chunk 218 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** ** 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 = 0.3322 r_free = 0.3322 target = 0.123017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.092973 restraints weight = 24388.262| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.43 r_work: 0.2810 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2678 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= 0.112 Angle : 0.447 5.195 27572 Z= 0.237 Chirality : 0.038 0.154 3140 Planarity : 0.004 0.052 3436 Dihedral : 6.998 70.408 3324 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.95 % Allowed : 13.55 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.17), residues: 2408 helix: 2.30 (0.13), residues: 1464 sheet: -1.33 (0.53), residues: 84 loop : -0.07 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 302 TYR 0.009 0.001 TYR D 555 PHE 0.024 0.001 PHE B 574 TRP 0.013 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00264 (20292) covalent geometry : angle 0.44740 (27572) hydrogen bonds : bond 0.03218 ( 1109) hydrogen bonds : angle 3.67077 ( 3147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5062.94 seconds wall clock time: 87 minutes 43.59 seconds (5263.59 seconds total)