Starting phenix.real_space_refine on Sat Sep 28 18:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/09_2024/8fhh_29085_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/09_2024/8fhh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/09_2024/8fhh_29085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/09_2024/8fhh_29085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/09_2024/8fhh_29085_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhh_29085/09_2024/8fhh_29085_neut.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 140 5.16 5 C 12912 2.51 5 N 3288 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19824 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'ERG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Restraints were copied for chains: C, B, D Time building chain proxies: 11.38, per 1000 atoms: 0.57 Number of scatterers: 19824 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 4 15.00 O 3480 8.00 N 3288 7.00 C 12912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.5 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 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: 7.48 Time building geometry restraints manager: 5.57 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: 0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 44.690 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- 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= 0.347 Angle : 0.831 7.638 27572 Z= 0.524 Chirality : 0.049 0.268 3140 Planarity : 0.007 0.076 3436 Dihedral : 12.506 123.832 7916 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 2408 helix: -1.27 (0.11), residues: 1496 sheet: -2.50 (0.37), residues: 124 loop : -1.11 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 268 HIS 0.005 0.001 HIS B 201 PHE 0.014 0.002 PHE B 537 TYR 0.010 0.002 TYR D 467 ARG 0.003 0.000 ARG A 363 *********************** 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 fitting. rotamer outliers: 4 poor density : 452 time to evaluate : 2.133 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: 0.3636 time to fit residues: 239.5448 Evaluate side-chains 302 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 122 HIS A 185 HIS A 192 GLN A 267 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 122 HIS B 185 HIS B 192 GLN B 267 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN C 31 GLN C 122 HIS C 185 HIS C 192 GLN C 267 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 122 HIS D 185 HIS D 192 GLN D 267 GLN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20292 Z= 0.268 Angle : 0.516 5.396 27572 Z= 0.270 Chirality : 0.040 0.185 3140 Planarity : 0.005 0.045 3436 Dihedral : 8.941 111.117 3324 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.05 % Allowed : 6.11 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2408 helix: 0.56 (0.13), residues: 1504 sheet: -1.85 (0.48), residues: 84 loop : -0.47 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 593 HIS 0.004 0.001 HIS C 201 PHE 0.013 0.001 PHE B 468 TYR 0.010 0.001 TYR A 526 ARG 0.004 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 328 time to evaluate : 2.037 Fit side-chains REVERT: A 31 GLN cc_start: 0.7712 (mt0) cc_final: 0.6827 (tt0) REVERT: A 64 LEU cc_start: 0.7861 (mt) cc_final: 0.7497 (mt) REVERT: A 176 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7526 (mp0) REVERT: A 233 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8173 (mt-10) REVERT: A 314 LYS cc_start: 0.8751 (tttt) cc_final: 0.8476 (tttp) REVERT: A 318 SER cc_start: 0.9198 (t) cc_final: 0.8685 (m) REVERT: A 409 ARG cc_start: 0.8144 (ttt90) cc_final: 0.7698 (ttt90) REVERT: A 414 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7682 (ttt180) REVERT: A 442 MET cc_start: 0.9042 (mtp) cc_final: 0.8800 (mtp) REVERT: A 445 THR cc_start: 0.8972 (t) cc_final: 0.8753 (p) REVERT: B 31 GLN cc_start: 0.7704 (mt0) cc_final: 0.6799 (tt0) REVERT: B 64 LEU cc_start: 0.7862 (mt) cc_final: 0.7500 (mt) REVERT: B 176 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7529 (mp0) REVERT: B 233 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 314 LYS cc_start: 0.8750 (tttt) cc_final: 0.8475 (tttp) REVERT: B 318 SER cc_start: 0.9196 (t) cc_final: 0.8685 (m) REVERT: B 409 ARG cc_start: 0.8142 (ttt90) cc_final: 0.7693 (ttt90) REVERT: B 414 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7684 (ttt180) REVERT: B 442 MET cc_start: 0.9042 (mtp) cc_final: 0.8798 (mtp) REVERT: B 445 THR cc_start: 0.8969 (t) cc_final: 0.8750 (p) REVERT: C 31 GLN cc_start: 0.7701 (mt0) cc_final: 0.6799 (tt0) REVERT: C 64 LEU cc_start: 0.7862 (mt) cc_final: 0.7498 (mt) REVERT: C 176 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7529 (mp0) REVERT: C 233 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 314 LYS cc_start: 0.8750 (tttt) cc_final: 0.8474 (tttp) REVERT: C 318 SER cc_start: 0.9196 (t) cc_final: 0.8683 (m) REVERT: C 409 ARG cc_start: 0.8139 (ttt90) cc_final: 0.7691 (ttt90) REVERT: C 414 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7686 (ttt180) REVERT: C 442 MET cc_start: 0.9045 (mtp) cc_final: 0.8802 (mtp) REVERT: C 445 THR cc_start: 0.8970 (t) cc_final: 0.8748 (p) REVERT: D 31 GLN cc_start: 0.7701 (mt0) cc_final: 0.6797 (tt0) REVERT: D 64 LEU cc_start: 0.7863 (mt) cc_final: 0.7501 (mt) REVERT: D 176 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7527 (mp0) REVERT: D 233 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8177 (mt-10) REVERT: D 314 LYS cc_start: 0.8755 (tttt) cc_final: 0.8480 (tttp) REVERT: D 318 SER cc_start: 0.9199 (t) cc_final: 0.8685 (m) REVERT: D 409 ARG cc_start: 0.8144 (ttt90) cc_final: 0.7697 (ttt90) REVERT: D 414 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7683 (ttt180) REVERT: D 442 MET cc_start: 0.9044 (mtp) cc_final: 0.8801 (mtp) REVERT: D 445 THR cc_start: 0.8972 (t) cc_final: 0.8749 (p) outliers start: 43 outliers final: 28 residues processed: 355 average time/residue: 0.3068 time to fit residues: 166.2841 Evaluate side-chains 313 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 616 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 218 optimal weight: 0.2980 chunk 235 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN A 635 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN C 635 ASN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20292 Z= 0.143 Angle : 0.448 5.291 27572 Z= 0.236 Chirality : 0.037 0.220 3140 Planarity : 0.004 0.049 3436 Dihedral : 8.383 99.471 3324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.95 % Allowed : 8.54 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2408 helix: 1.30 (0.13), residues: 1500 sheet: -1.53 (0.51), residues: 84 loop : -0.31 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.002 0.000 HIS A 185 PHE 0.014 0.001 PHE D 574 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG A 302 *********************** 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 321 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7650 (mt0) cc_final: 0.6796 (tt0) REVERT: A 176 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7560 (mp0) REVERT: A 233 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 314 LYS cc_start: 0.8786 (tttt) cc_final: 0.8502 (ttmp) REVERT: A 318 SER cc_start: 0.9145 (t) cc_final: 0.8689 (m) REVERT: A 409 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7671 (ttt90) REVERT: A 414 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7627 (ttt180) REVERT: A 442 MET cc_start: 0.8993 (mtp) cc_final: 0.8720 (mtp) REVERT: B 31 GLN cc_start: 0.7619 (mt0) cc_final: 0.6775 (tt0) REVERT: B 176 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7559 (mp0) REVERT: B 314 LYS cc_start: 0.8785 (tttt) cc_final: 0.8507 (ttmp) REVERT: B 318 SER cc_start: 0.9146 (t) cc_final: 0.8695 (m) REVERT: B 409 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7667 (ttt90) REVERT: B 414 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7676 (ttt90) REVERT: B 442 MET cc_start: 0.8994 (mtp) cc_final: 0.8721 (mtp) REVERT: C 31 GLN cc_start: 0.7622 (mt0) cc_final: 0.6781 (tt0) REVERT: C 176 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7560 (mp0) REVERT: C 314 LYS cc_start: 0.8785 (tttt) cc_final: 0.8508 (ttmp) REVERT: C 318 SER cc_start: 0.9144 (t) cc_final: 0.8693 (m) REVERT: C 409 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7665 (ttt90) REVERT: C 414 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7677 (ttt90) REVERT: C 442 MET cc_start: 0.8998 (mtp) cc_final: 0.8725 (mtp) REVERT: D 31 GLN cc_start: 0.7620 (mt0) cc_final: 0.6776 (tt0) REVERT: D 176 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7560 (mp0) REVERT: D 314 LYS cc_start: 0.8786 (tttt) cc_final: 0.8510 (ttmp) REVERT: D 318 SER cc_start: 0.9145 (t) cc_final: 0.8693 (m) REVERT: D 409 ARG cc_start: 0.8089 (ttt90) cc_final: 0.7670 (ttt90) REVERT: D 414 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7643 (ttt180) outliers start: 20 outliers final: 16 residues processed: 305 average time/residue: 0.3293 time to fit residues: 151.5442 Evaluate side-chains 311 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 295 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20292 Z= 0.386 Angle : 0.560 6.192 27572 Z= 0.287 Chirality : 0.043 0.252 3140 Planarity : 0.004 0.047 3436 Dihedral : 8.583 99.912 3324 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 9.30 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2408 helix: 1.40 (0.13), residues: 1484 sheet: -1.67 (0.51), residues: 84 loop : -0.33 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 593 HIS 0.004 0.001 HIS B 201 PHE 0.018 0.002 PHE C 468 TYR 0.015 0.002 TYR A 526 ARG 0.005 0.001 ARG B 302 *********************** 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 326 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 289 time to evaluate : 2.195 Fit side-chains REVERT: A 31 GLN cc_start: 0.7757 (mt0) cc_final: 0.6890 (tt0) REVERT: A 233 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 300 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8036 (mttt) REVERT: A 318 SER cc_start: 0.9169 (t) cc_final: 0.8589 (m) REVERT: A 340 MET cc_start: 0.9224 (mmm) cc_final: 0.8937 (mmp) REVERT: A 414 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7607 (mtt90) REVERT: A 444 LEU cc_start: 0.9276 (mt) cc_final: 0.9072 (mt) REVERT: B 31 GLN cc_start: 0.7730 (mt0) cc_final: 0.6873 (tt0) REVERT: B 300 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8027 (mttt) REVERT: B 314 LYS cc_start: 0.8781 (tttt) cc_final: 0.8581 (tttp) REVERT: B 318 SER cc_start: 0.9171 (t) cc_final: 0.8591 (m) REVERT: B 340 MET cc_start: 0.9225 (mmm) cc_final: 0.8938 (mmp) REVERT: B 414 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7601 (ttt180) REVERT: B 444 LEU cc_start: 0.9275 (mt) cc_final: 0.9069 (mt) REVERT: C 31 GLN cc_start: 0.7730 (mt0) cc_final: 0.6875 (tt0) REVERT: C 300 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8028 (mttt) REVERT: C 314 LYS cc_start: 0.8781 (tttt) cc_final: 0.8580 (tttp) REVERT: C 318 SER cc_start: 0.9170 (t) cc_final: 0.8588 (m) REVERT: C 340 MET cc_start: 0.9223 (mmm) cc_final: 0.8937 (mmp) REVERT: C 414 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7599 (ttt180) REVERT: C 444 LEU cc_start: 0.9276 (mt) cc_final: 0.9069 (mt) REVERT: D 31 GLN cc_start: 0.7728 (mt0) cc_final: 0.6870 (tt0) REVERT: D 300 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8029 (mttt) REVERT: D 318 SER cc_start: 0.9169 (t) cc_final: 0.8588 (m) REVERT: D 340 MET cc_start: 0.9224 (mmm) cc_final: 0.8938 (mmp) REVERT: D 414 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7600 (ttt180) REVERT: D 444 LEU cc_start: 0.9274 (mt) cc_final: 0.9069 (mt) outliers start: 37 outliers final: 25 residues processed: 313 average time/residue: 0.3402 time to fit residues: 161.6109 Evaluate side-chains 307 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 282 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20292 Z= 0.223 Angle : 0.479 5.410 27572 Z= 0.251 Chirality : 0.039 0.255 3140 Planarity : 0.004 0.050 3436 Dihedral : 8.248 83.650 3324 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.72 % Allowed : 10.02 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2408 helix: 1.66 (0.13), residues: 1480 sheet: -1.56 (0.52), residues: 84 loop : -0.22 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 593 HIS 0.003 0.001 HIS A 201 PHE 0.016 0.001 PHE C 574 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG B 302 *********************** 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 346 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 310 time to evaluate : 2.285 Fit side-chains REVERT: A 31 GLN cc_start: 0.7700 (mt0) cc_final: 0.6862 (tt0) REVERT: A 233 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8225 (mt-10) REVERT: A 300 LYS cc_start: 0.8529 (mtpt) cc_final: 0.7981 (mttt) REVERT: A 318 SER cc_start: 0.9146 (t) cc_final: 0.8608 (m) REVERT: A 409 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7871 (ttt90) REVERT: A 414 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7643 (ttt90) REVERT: B 31 GLN cc_start: 0.7688 (mt0) cc_final: 0.6840 (tt0) REVERT: B 300 LYS cc_start: 0.8531 (mtpt) cc_final: 0.7981 (mttt) REVERT: B 318 SER cc_start: 0.9147 (t) cc_final: 0.8606 (m) REVERT: B 409 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7868 (ttt90) REVERT: B 414 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7644 (ttt90) REVERT: C 31 GLN cc_start: 0.7689 (mt0) cc_final: 0.6845 (tt0) REVERT: C 300 LYS cc_start: 0.8532 (mtpt) cc_final: 0.7981 (mttt) REVERT: C 318 SER cc_start: 0.9145 (t) cc_final: 0.8603 (m) REVERT: C 409 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7868 (ttt90) REVERT: C 414 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7644 (ttt90) REVERT: D 31 GLN cc_start: 0.7687 (mt0) cc_final: 0.6839 (tt0) REVERT: D 300 LYS cc_start: 0.8531 (mtpt) cc_final: 0.7982 (mttt) REVERT: D 318 SER cc_start: 0.9145 (t) cc_final: 0.8606 (m) REVERT: D 409 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7871 (ttt90) REVERT: D 414 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7644 (ttt90) outliers start: 36 outliers final: 32 residues processed: 334 average time/residue: 0.3382 time to fit residues: 172.7235 Evaluate side-chains 320 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 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 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 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 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 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 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 413 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20292 Z= 0.180 Angle : 0.453 5.152 27572 Z= 0.240 Chirality : 0.038 0.249 3140 Planarity : 0.004 0.050 3436 Dihedral : 7.895 67.947 3324 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.29 % Allowed : 10.78 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.17), residues: 2408 helix: 1.93 (0.13), residues: 1472 sheet: -1.46 (0.53), residues: 84 loop : -0.19 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE D 408 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG B 302 *********************** 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 348 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 300 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7636 (mt0) cc_final: 0.6828 (tt0) REVERT: A 233 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 300 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8007 (mttt) REVERT: A 318 SER cc_start: 0.9142 (t) cc_final: 0.8623 (m) REVERT: A 414 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7714 (ttt90) REVERT: B 31 GLN cc_start: 0.7597 (mt0) cc_final: 0.6778 (tt0) REVERT: B 300 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8006 (mttt) REVERT: B 318 SER cc_start: 0.9140 (t) cc_final: 0.8618 (m) REVERT: B 414 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7715 (ttt90) REVERT: C 31 GLN cc_start: 0.7599 (mt0) cc_final: 0.6783 (tt0) REVERT: C 300 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8006 (mttt) REVERT: C 318 SER cc_start: 0.9138 (t) cc_final: 0.8615 (m) REVERT: C 414 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7714 (ttt90) REVERT: D 31 GLN cc_start: 0.7598 (mt0) cc_final: 0.6776 (tt0) REVERT: D 300 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8008 (mttt) REVERT: D 318 SER cc_start: 0.9141 (t) cc_final: 0.8622 (m) REVERT: D 414 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7715 (ttt90) outliers start: 48 outliers final: 37 residues processed: 336 average time/residue: 0.3202 time to fit residues: 162.7871 Evaluate side-chains 319 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 282 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 354 LEU 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 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 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 123 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 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 223 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20292 Z= 0.134 Angle : 0.430 5.024 27572 Z= 0.228 Chirality : 0.037 0.193 3140 Planarity : 0.004 0.050 3436 Dihedral : 7.273 69.050 3324 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.77 % Allowed : 12.02 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.17), residues: 2408 helix: 2.10 (0.13), residues: 1496 sheet: -1.38 (0.54), residues: 84 loop : -0.08 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.002 0.000 HIS A 201 PHE 0.022 0.001 PHE C 574 TYR 0.011 0.001 TYR B 555 ARG 0.006 0.000 ARG B 302 *********************** 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 321 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7516 (mt0) cc_final: 0.6728 (tt0) REVERT: A 60 LEU cc_start: 0.8138 (tp) cc_final: 0.7654 (mm) REVERT: A 233 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 318 SER cc_start: 0.9131 (t) cc_final: 0.8661 (m) REVERT: B 31 GLN cc_start: 0.7505 (mt0) cc_final: 0.6725 (tt0) REVERT: B 60 LEU cc_start: 0.8139 (tp) cc_final: 0.7653 (mm) REVERT: B 318 SER cc_start: 0.9127 (t) cc_final: 0.8657 (m) REVERT: C 31 GLN cc_start: 0.7505 (mt0) cc_final: 0.6730 (tt0) REVERT: C 60 LEU cc_start: 0.8134 (tp) cc_final: 0.7650 (mm) REVERT: C 318 SER cc_start: 0.9127 (t) cc_final: 0.8642 (m) REVERT: D 31 GLN cc_start: 0.7508 (mt0) cc_final: 0.6728 (tt0) REVERT: D 60 LEU cc_start: 0.8134 (tp) cc_final: 0.7652 (mm) REVERT: D 318 SER cc_start: 0.9129 (t) cc_final: 0.8660 (m) outliers start: 37 outliers final: 32 residues processed: 309 average time/residue: 0.3077 time to fit residues: 146.0525 Evaluate side-chains 303 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 271 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 0.0970 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2646 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= 0.143 Angle : 0.442 7.615 27572 Z= 0.231 Chirality : 0.037 0.176 3140 Planarity : 0.004 0.051 3436 Dihedral : 7.145 69.521 3324 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.57 % Allowed : 13.26 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2408 helix: 2.19 (0.13), residues: 1492 sheet: -1.40 (0.53), residues: 84 loop : -0.04 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.002 0.000 HIS A 201 PHE 0.012 0.001 PHE B 408 TYR 0.010 0.001 TYR B 555 ARG 0.007 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 286 time to evaluate : 2.238 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7510 (mt0) cc_final: 0.6737 (tt0) REVERT: A 60 LEU cc_start: 0.8142 (tp) cc_final: 0.7657 (mm) REVERT: A 175 SER cc_start: 0.7589 (OUTLIER) cc_final: 0.7326 (t) REVERT: A 233 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8250 (mt-10) REVERT: A 318 SER cc_start: 0.9133 (t) cc_final: 0.8665 (m) REVERT: B 31 GLN cc_start: 0.7510 (mt0) cc_final: 0.6720 (tt0) REVERT: B 60 LEU cc_start: 0.8147 (tp) cc_final: 0.7658 (mm) REVERT: B 175 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.6922 (t) REVERT: B 318 SER cc_start: 0.9130 (t) cc_final: 0.8669 (m) REVERT: C 31 GLN cc_start: 0.7510 (mt0) cc_final: 0.6726 (tt0) REVERT: C 60 LEU cc_start: 0.8142 (tp) cc_final: 0.7656 (mm) REVERT: C 175 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.6987 (t) REVERT: C 318 SER cc_start: 0.9107 (t) cc_final: 0.8660 (m) REVERT: D 31 GLN cc_start: 0.7510 (mt0) cc_final: 0.6723 (tt0) REVERT: D 60 LEU cc_start: 0.8136 (tp) cc_final: 0.7645 (mm) REVERT: D 175 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.6933 (t) REVERT: D 318 SER cc_start: 0.9132 (t) cc_final: 0.8664 (m) outliers start: 33 outliers final: 25 residues processed: 310 average time/residue: 0.3136 time to fit residues: 149.4032 Evaluate side-chains 298 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 269 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20292 Z= 0.266 Angle : 0.499 8.972 27572 Z= 0.259 Chirality : 0.040 0.191 3140 Planarity : 0.004 0.050 3436 Dihedral : 7.395 67.497 3324 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.62 % Allowed : 13.55 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.17), residues: 2408 helix: 2.00 (0.13), residues: 1476 sheet: -1.48 (0.53), residues: 84 loop : -0.09 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 593 HIS 0.004 0.001 HIS A 201 PHE 0.013 0.001 PHE C 468 TYR 0.010 0.001 TYR C 526 ARG 0.008 0.000 ARG A 302 *********************** 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 320 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 286 time to evaluate : 2.338 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7631 (mt0) cc_final: 0.6815 (tt0) REVERT: A 233 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8249 (mt-10) REVERT: A 300 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8033 (mttt) REVERT: A 318 SER cc_start: 0.9133 (t) cc_final: 0.8586 (m) REVERT: B 31 GLN cc_start: 0.7599 (mt0) cc_final: 0.6803 (tt0) REVERT: B 300 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8031 (mttt) REVERT: B 318 SER cc_start: 0.9158 (t) cc_final: 0.8629 (m) REVERT: C 31 GLN cc_start: 0.7605 (mt0) cc_final: 0.6803 (tt0) REVERT: C 300 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8031 (mttt) REVERT: C 318 SER cc_start: 0.9142 (t) cc_final: 0.8620 (m) REVERT: D 31 GLN cc_start: 0.7603 (mt0) cc_final: 0.6798 (tt0) REVERT: D 300 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8029 (mttt) REVERT: D 318 SER cc_start: 0.9131 (t) cc_final: 0.8584 (m) REVERT: D 409 ARG cc_start: 0.8123 (ttt90) cc_final: 0.7796 (ttt90) outliers start: 34 outliers final: 30 residues processed: 311 average time/residue: 0.3082 time to fit residues: 147.3725 Evaluate side-chains 311 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 0.4980 chunk 220 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2719 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= 0.142 Angle : 0.449 7.158 27572 Z= 0.237 Chirality : 0.038 0.185 3140 Planarity : 0.004 0.051 3436 Dihedral : 7.197 70.131 3324 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.53 % Allowed : 13.31 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.17), residues: 2408 helix: 2.16 (0.13), residues: 1488 sheet: -1.41 (0.53), residues: 84 loop : -0.08 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.002 0.001 HIS B 185 PHE 0.012 0.001 PHE C 408 TYR 0.011 0.001 TYR A 555 ARG 0.009 0.000 ARG C 302 ********************** 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 310 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7528 (mt0) cc_final: 0.6738 (tt0) REVERT: A 233 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 318 SER cc_start: 0.9141 (t) cc_final: 0.8642 (m) REVERT: B 31 GLN cc_start: 0.7523 (mt0) cc_final: 0.6754 (tt0) REVERT: B 175 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.7554 (t) REVERT: B 318 SER cc_start: 0.9138 (t) cc_final: 0.8661 (m) REVERT: C 31 GLN cc_start: 0.7525 (mt0) cc_final: 0.6760 (tt0) REVERT: C 175 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7545 (t) REVERT: C 318 SER cc_start: 0.9119 (t) cc_final: 0.8669 (m) REVERT: D 31 GLN cc_start: 0.7522 (mt0) cc_final: 0.6754 (tt0) REVERT: D 175 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7543 (t) REVERT: D 318 SER cc_start: 0.9140 (t) cc_final: 0.8643 (m) outliers start: 32 outliers final: 26 residues processed: 301 average time/residue: 0.3133 time to fit residues: 144.6166 Evaluate side-chains 302 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 273 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.093478 restraints weight = 24414.612| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.46 r_work: 0.2786 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20292 Z= 0.160 Angle : 0.444 5.271 27572 Z= 0.237 Chirality : 0.038 0.176 3140 Planarity : 0.004 0.051 3436 Dihedral : 7.148 70.072 3324 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.57 % Allowed : 13.26 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2408 helix: 2.22 (0.13), residues: 1464 sheet: -1.41 (0.53), residues: 84 loop : -0.12 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 PHE 0.016 0.001 PHE D 574 TYR 0.010 0.001 TYR B 555 ARG 0.010 0.000 ARG A 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.60 seconds wall clock time: 77 minutes 8.87 seconds (4628.87 seconds total)