Starting phenix.real_space_refine on Fri Jul 3 21:13:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vah_43092/07_2026/8vah_43092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vah_43092/07_2026/8vah_43092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vah_43092/07_2026/8vah_43092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vah_43092/07_2026/8vah_43092.map" model { file = "/net/cci-nas-00/data/ceres_data/8vah_43092/07_2026/8vah_43092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vah_43092/07_2026/8vah_43092.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 3 5.21 5 S 66 5.16 5 C 10135 2.51 5 N 2880 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16307 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5306 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain: "B" Number of atoms: 5306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5306 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain: "C" Number of atoms: 5306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5306 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain: "G" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 122 Inner-chain residues flagged as termini: ['pdbres=" A G 13 "'] Classifications: {'DNA': 2, 'RNA': 7} Modifications used: {'5*END': 2, 'rna2p_pur': 3, 'rna3p_pur': 4} Link IDs: {'rna2p': 3, 'rna3p': 5} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A%rna3p_pur:plan': 3, ' A%rna3p_pur:plan2': 3, ' A%rna2p_pur:plan': 3, ' A%rna2p_pur:plan2': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1' A G 13 " occ=0.30 ... (9 atoms not shown) pdb=" C4 A G 13 " occ=0.30 residue: pdb=" C1' A G 14 " occ=0.30 ... (9 atoms not shown) pdb=" C4 A G 14 " occ=0.30 residue: pdb=" P A D 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A D 2 " occ=0.30 residue: pdb=" P A E 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A E 2 " occ=0.30 residue: pdb=" P A F 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A F 2 " occ=0.30 Time building chain proxies: 3.92, per 1000 atoms: 0.24 Number of scatterers: 16307 At special positions: 0 Unit cell: (110.816, 108.316, 149.143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 19 15.00 Mg 3 11.99 O 3204 8.00 N 2880 7.00 C 10135 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 753.0 milliseconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3798 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 25 sheets defined 37.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 85 through 103 Proline residue: A 98 - end of helix Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 125 through 142 removed outlier: 4.519A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.699A pdb=" N LYS A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 226 removed outlier: 4.166A pdb=" N VAL A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 removed outlier: 5.013A pdb=" N LEU A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 289 through 312 removed outlier: 3.621A pdb=" N LEU A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.616A pdb=" N ALA A 362 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 437 through 454 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.589A pdb=" N HIS A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 541 removed outlier: 3.658A pdb=" N MET A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 541 " --> pdb=" O MET A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 570 removed outlier: 4.084A pdb=" N VAL A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 601 through 615 removed outlier: 3.611A pdb=" N ILE A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 removed outlier: 3.510A pdb=" N TYR A 665 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.599A pdb=" N GLU A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 125 through 142 removed outlier: 4.339A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 197 through 227 removed outlier: 5.099A pdb=" N VAL B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 4.126A pdb=" N LEU B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 Processing helix chain 'B' and resid 289 through 312 Processing helix chain 'B' and resid 397 through 412 removed outlier: 3.784A pdb=" N ARG B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 454 Processing helix chain 'B' and resid 483 through 487 removed outlier: 3.636A pdb=" N HIS B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.922A pdb=" N GLN B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 541 " --> pdb=" O MET B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 601 through 616 Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.987A pdb=" N GLU B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 125 through 142 removed outlier: 4.271A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.793A pdb=" N GLU C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 227 removed outlier: 5.071A pdb=" N VAL C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.715A pdb=" N LEU C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.647A pdb=" N ARG C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 312 Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.511A pdb=" N ALA C 362 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 413 removed outlier: 3.712A pdb=" N ARG C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 454 Processing helix chain 'C' and resid 482 through 489 removed outlier: 4.026A pdb=" N HIS C 487 " --> pdb=" O GLY C 483 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.783A pdb=" N ALA C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 570 removed outlier: 3.689A pdb=" N LYS C 566 " --> pdb=" O PRO C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 601 through 617 removed outlier: 3.898A pdb=" N ILE C 615 " --> pdb=" O ARG C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 689 through 695 removed outlier: 4.477A pdb=" N GLN C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.718A pdb=" N GLU A 19 " --> pdb=" O MET A 32 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 60 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA A 115 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN A 62 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 117 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN A 64 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N SER A 119 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 331 removed outlier: 3.585A pdb=" N GLU A 433 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 351 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE A 431 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 353 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER A 429 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 355 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 427 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU A 433 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 462 through 464 removed outlier: 3.780A pdb=" N ALA A 462 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 478 removed outlier: 3.522A pdb=" N LEU A 478 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 467 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 633 removed outlier: 3.704A pdb=" N THR A 630 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE A 638 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 632 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 10 removed outlier: 6.727A pdb=" N PHE B 41 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL B 117 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR B 43 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA B 115 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 45 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL B 113 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.731A pdb=" N GLY B 150 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.994A pdb=" N GLN B 506 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 492 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 462 " --> pdb=" O GLY B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.994A pdb=" N GLN B 506 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 492 " --> pdb=" O ASP B 508 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.532A pdb=" N ARG B 330 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 433 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 351 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE B 431 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 353 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N SER B 429 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR B 355 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL B 427 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU B 433 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 363 through 366 Processing sheet with id=AB7, first strand: chain 'B' and resid 554 through 559 removed outlier: 3.692A pdb=" N LYS B 596 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 588 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 629 through 632 removed outlier: 4.583A pdb=" N THR B 630 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N PHE B 638 " --> pdb=" O THR B 630 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.735A pdb=" N PHE C 41 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 117 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR C 43 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA C 115 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 45 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL C 113 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 60 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA C 115 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.735A pdb=" N PHE C 41 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 117 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR C 43 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA C 115 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 45 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL C 113 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN C 64 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER C 119 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 160 through 163 Processing sheet with id=AC3, first strand: chain 'C' and resid 327 through 331 removed outlier: 3.758A pdb=" N GLU C 433 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU C 351 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE C 431 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR C 353 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 429 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR C 355 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL C 427 " --> pdb=" O THR C 355 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 363 through 366 Processing sheet with id=AC5, first strand: chain 'C' and resid 474 through 479 removed outlier: 3.554A pdb=" N ALA C 462 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 493 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 554 through 559 removed outlier: 3.502A pdb=" N ALA C 599 " --> pdb=" O ARG C 554 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 631 through 633 removed outlier: 4.969A pdb=" N ARG C 631 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE C 638 " --> pdb=" O ARG C 631 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4085 1.33 - 1.45: 2748 1.45 - 1.57: 9570 1.57 - 1.68: 31 1.68 - 1.80: 129 Bond restraints: 16563 Sorted by residual: bond pdb=" N ILE A 149 " pdb=" CA ILE A 149 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.82e+00 bond pdb=" N ILE B 149 " pdb=" CA ILE B 149 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.15e+00 bond pdb=" N VAL A 214 " pdb=" CA VAL A 214 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.61e+00 bond pdb=" N GLY B 150 " pdb=" CA GLY B 150 " ideal model delta sigma weight residual 1.444 1.473 -0.029 1.06e-02 8.90e+03 7.45e+00 bond pdb=" N HIS A 209 " pdb=" CA HIS A 209 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.85e+00 ... (remaining 16558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 22331 3.25 - 6.50: 137 6.50 - 9.76: 4 9.76 - 13.01: 2 13.01 - 16.26: 2 Bond angle restraints: 22476 Sorted by residual: angle pdb=" C3' A F 2 " pdb=" O3' A F 2 " pdb=" P C F 3 " ideal model delta sigma weight residual 120.20 103.94 16.26 1.50e+00 4.44e-01 1.18e+02 angle pdb=" C3' C D 3 " pdb=" O3' C D 3 " pdb=" P A D 4 " ideal model delta sigma weight residual 120.20 105.43 14.77 1.50e+00 4.44e-01 9.69e+01 angle pdb=" C3' A D 2 " pdb=" O3' A D 2 " pdb=" P C D 3 " ideal model delta sigma weight residual 120.20 108.78 11.42 1.50e+00 4.44e-01 5.80e+01 angle pdb=" C3' C F 3 " pdb=" O3' C F 3 " pdb=" P A F 4 " ideal model delta sigma weight residual 120.20 109.28 10.92 1.50e+00 4.44e-01 5.30e+01 angle pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 120.20 113.36 6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 22471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 8771 19.94 - 39.88: 1000 39.88 - 59.83: 289 59.83 - 79.77: 73 79.77 - 99.71: 25 Dihedral angle restraints: 10158 sinusoidal: 4239 harmonic: 5919 Sorted by residual: dihedral pdb=" C5' A F 4 " pdb=" C4' A F 4 " pdb=" C3' A F 4 " pdb=" O3' A F 4 " ideal model delta sinusoidal sigma weight residual 147.00 93.14 53.86 1 8.00e+00 1.56e-02 6.15e+01 dihedral pdb=" O4' A F 4 " pdb=" C4' A F 4 " pdb=" C3' A F 4 " pdb=" C2' A F 4 " ideal model delta sinusoidal sigma weight residual 24.00 -27.42 51.42 1 8.00e+00 1.56e-02 5.65e+01 dihedral pdb=" C4' A F 4 " pdb=" C3' A F 4 " pdb=" C2' A F 4 " pdb=" C1' A F 4 " ideal model delta sinusoidal sigma weight residual -35.00 10.35 -45.35 1 8.00e+00 1.56e-02 4.46e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2541 0.113 - 0.227: 80 0.227 - 0.340: 4 0.340 - 0.453: 5 0.453 - 0.567: 3 Chirality restraints: 2633 Sorted by residual: chirality pdb=" P A D 2 " pdb=" OP1 A D 2 " pdb=" OP2 A D 2 " pdb=" O5' A D 2 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" P A E 2 " pdb=" OP1 A E 2 " pdb=" OP2 A E 2 " pdb=" O5' A E 2 " both_signs ideal model delta sigma weight residual True 2.41 2.97 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" P A F 2 " pdb=" OP1 A F 2 " pdb=" OP2 A F 2 " pdb=" O5' A F 2 " both_signs ideal model delta sigma weight residual True 2.41 2.97 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 2630 not shown) Planarity restraints: 2895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 144 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C PRO A 144 " -0.047 2.00e-02 2.50e+03 pdb=" O PRO A 144 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 145 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 125 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 126 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 97 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 98 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " 0.030 5.00e-02 4.00e+02 ... (remaining 2892 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 34 2.36 - 2.99: 9226 2.99 - 3.63: 24457 3.63 - 4.26: 35296 4.26 - 4.90: 59634 Nonbonded interactions: 128647 Sorted by model distance: nonbonded pdb=" NH1 ARG C 93 " pdb=" OP1 A F 4 " model vdw 1.722 3.120 nonbonded pdb=" OG1 THR A 344 " pdb=" NE2 GLN A 349 " model vdw 2.063 3.120 nonbonded pdb=" NH1 ARG C 398 " pdb=" O2' A F 2 " model vdw 2.095 3.120 nonbonded pdb=" OE2 GLU B 430 " pdb=" OH TYR C 68 " model vdw 2.108 3.040 nonbonded pdb=" O THR C 424 " pdb=" OG1 THR C 424 " model vdw 2.186 3.040 ... (remaining 128642 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 16.840 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.007 0.064 16566 Z= 0.320 Angle : 0.739 16.262 22476 Z= 0.439 Chirality : 0.055 0.567 2633 Planarity : 0.004 0.056 2895 Dihedral : 19.419 99.711 6360 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 8.07 % Allowed : 15.72 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2079 helix: -0.18 (0.18), residues: 666 sheet: -1.64 (0.24), residues: 475 loop : -1.02 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 253 TYR 0.022 0.002 TYR A 385 PHE 0.027 0.002 PHE A 421 TRP 0.005 0.001 TRP A 233 HIS 0.014 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.31 (16563) covalent geometry : angle 0.73907 / 0.44 (22476) hydrogen bonds : bond 0.18110 / 12.10 ( 743) hydrogen bonds : angle 7.15568 / 5.01 ( 2142) Misc. bond : bond 0.04780 / 2.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 105 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.8310 (tmm) cc_final: 0.8102 (tmm) REVERT: A 323 MET cc_start: 0.8517 (mtp) cc_final: 0.8302 (ptp) REVERT: A 597 ILE cc_start: 0.9426 (mt) cc_final: 0.9075 (mp) REVERT: A 668 MET cc_start: 0.1141 (mmt) cc_final: 0.0780 (mmt) REVERT: B 167 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: B 365 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9168 (pp) REVERT: C 190 GLU cc_start: 0.7746 (tt0) cc_final: 0.7507 (tp30) REVERT: C 506 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: C 563 ASP cc_start: 0.9040 (t0) cc_final: 0.8834 (t0) REVERT: C 603 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 611 ARG cc_start: 0.9606 (OUTLIER) cc_final: 0.8909 (tmt170) outliers start: 137 outliers final: 84 residues processed: 223 average time/residue: 0.1115 time to fit residues: 40.1062 Evaluate side-chains 183 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 95 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 613 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059203 restraints weight = 42895.403| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.82 r_work: 0.2657 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 25 (32 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16566 Z= 0.226 Angle : 0.621 7.345 22476 Z= 0.330 Chirality : 0.045 0.204 2633 Planarity : 0.005 0.054 2895 Dihedral : 14.969 100.776 2665 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 6.30 % Allowed : 19.20 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2079 helix: 1.19 (0.19), residues: 677 sheet: -0.99 (0.25), residues: 457 loop : -0.38 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 308 TYR 0.013 0.002 TYR C 380 PHE 0.030 0.002 PHE B 493 TRP 0.005 0.001 TRP C 231 HIS 0.013 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (16563) covalent geometry : angle 0.62067 / 0.33 (22476) hydrogen bonds : bond 0.05300 / 3.65 ( 743) hydrogen bonds : angle 5.19715 / 3.68 ( 2142) Misc. bond : bond 0.00649 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 98 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: A 267 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.9070 (m-80) REVERT: A 323 MET cc_start: 0.8867 (mtp) cc_final: 0.8364 (ptp) REVERT: A 369 MET cc_start: 0.9196 (mmm) cc_final: 0.8468 (mmm) REVERT: A 623 ARG cc_start: 0.4031 (OUTLIER) cc_final: 0.3124 (ptm160) REVERT: A 668 MET cc_start: 0.3191 (mmt) cc_final: 0.2816 (mmt) REVERT: B 1 MET cc_start: 0.7927 (ppp) cc_final: 0.7638 (ppp) REVERT: B 167 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: B 365 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 369 MET cc_start: 0.9017 (mmm) cc_final: 0.8742 (mmm) REVERT: B 392 MET cc_start: 0.9015 (tpp) cc_final: 0.8516 (tmm) REVERT: C 232 ASP cc_start: 0.9104 (p0) cc_final: 0.8903 (p0) REVERT: C 323 MET cc_start: 0.8670 (mtp) cc_final: 0.8169 (ptp) REVERT: C 601 ASP cc_start: 0.8346 (p0) cc_final: 0.8043 (p0) REVERT: C 603 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8761 (tm-30) REVERT: C 611 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.8899 (tmt170) outliers start: 107 outliers final: 72 residues processed: 190 average time/residue: 0.1157 time to fit residues: 35.0347 Evaluate side-chains 168 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 90 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 199 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 164 ASN A 298 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.100843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062899 restraints weight = 43159.969| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.77 r_work: 0.2615 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 16 (25 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16566 Z= 0.266 Angle : 0.586 8.779 22476 Z= 0.309 Chirality : 0.044 0.189 2633 Planarity : 0.004 0.053 2895 Dihedral : 14.031 101.356 2618 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.01 % Allowed : 20.44 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 2079 helix: 1.65 (0.20), residues: 679 sheet: -0.60 (0.25), residues: 462 loop : -0.11 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 611 TYR 0.017 0.002 TYR A 380 PHE 0.023 0.002 PHE B 493 TRP 0.005 0.001 TRP B 233 HIS 0.013 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 (16563) covalent geometry : angle 0.58642 / 0.31 (22476) hydrogen bonds : bond 0.04824 / 3.30 ( 743) hydrogen bonds : angle 4.78157 / 3.39 ( 2142) Misc. bond : bond 0.00309 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 87 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9304 (ptm) REVERT: A 194 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8290 (mp10) REVERT: A 267 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.9078 (m-80) REVERT: A 323 MET cc_start: 0.8741 (mtp) cc_final: 0.8236 (ptp) REVERT: A 369 MET cc_start: 0.9183 (mmm) cc_final: 0.8513 (mmm) REVERT: A 466 MET cc_start: 0.8230 (mtp) cc_final: 0.7843 (mtp) REVERT: A 668 MET cc_start: 0.3078 (mmt) cc_final: 0.2631 (mmt) REVERT: B 167 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: B 365 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7984 (pp) REVERT: B 369 MET cc_start: 0.8978 (mmm) cc_final: 0.8663 (mmm) REVERT: B 477 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 694 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5260 (pm20) REVERT: C 232 ASP cc_start: 0.9246 (p0) cc_final: 0.9005 (p0) REVERT: C 455 VAL cc_start: 0.9503 (OUTLIER) cc_final: 0.9233 (m) REVERT: C 603 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8885 (tm-30) outliers start: 102 outliers final: 61 residues processed: 179 average time/residue: 0.1083 time to fit residues: 31.3036 Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 85 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 134 optimal weight: 50.0000 chunk 75 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 298 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.101489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063200 restraints weight = 42430.166| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.76 r_work: 0.2653 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16566 Z= 0.166 Angle : 0.536 10.394 22476 Z= 0.282 Chirality : 0.043 0.190 2633 Planarity : 0.004 0.054 2895 Dihedral : 13.473 101.830 2579 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.18 % Allowed : 21.02 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 2079 helix: 1.91 (0.20), residues: 684 sheet: -0.27 (0.25), residues: 460 loop : 0.04 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.014 0.001 TYR A 380 PHE 0.022 0.001 PHE B 493 TRP 0.002 0.000 TRP B 231 HIS 0.010 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (16563) covalent geometry : angle 0.53646 / 0.28 (22476) hydrogen bonds : bond 0.04321 / 2.98 ( 743) hydrogen bonds : angle 4.51572 / 3.21 ( 2142) Misc. bond : bond 0.00282 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 90 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9319 (ptm) REVERT: A 194 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: A 267 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.9062 (m-80) REVERT: A 323 MET cc_start: 0.8793 (mtp) cc_final: 0.8289 (ptp) REVERT: A 369 MET cc_start: 0.9152 (mmm) cc_final: 0.8533 (mmm) REVERT: A 668 MET cc_start: 0.3062 (mmt) cc_final: 0.2617 (mmt) REVERT: B 1 MET cc_start: 0.7973 (ppp) cc_final: 0.7715 (ppp) REVERT: B 167 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: B 188 MET cc_start: 0.9415 (ttp) cc_final: 0.9158 (tmm) REVERT: B 365 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8010 (pp) REVERT: B 369 MET cc_start: 0.8992 (mmm) cc_final: 0.8698 (mmm) REVERT: B 392 MET cc_start: 0.9047 (tpp) cc_final: 0.8550 (tmm) REVERT: B 418 MET cc_start: 0.8954 (mmm) cc_final: 0.8228 (mmm) REVERT: B 466 MET cc_start: 0.8628 (mmm) cc_final: 0.8125 (mmm) REVERT: B 694 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5293 (pm20) REVERT: C 232 ASP cc_start: 0.9238 (p0) cc_final: 0.8984 (p0) REVERT: C 323 MET cc_start: 0.8645 (mtp) cc_final: 0.8264 (ptp) REVERT: C 451 MET cc_start: 0.9023 (mtp) cc_final: 0.8780 (mmm) REVERT: C 455 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9279 (m) REVERT: C 491 MET cc_start: 0.8846 (ptm) cc_final: 0.8582 (ppp) REVERT: C 603 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8882 (tm-30) outliers start: 88 outliers final: 60 residues processed: 171 average time/residue: 0.0983 time to fit residues: 26.9783 Evaluate side-chains 155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 88 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 202 optimal weight: 0.0020 chunk 122 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS C 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.101692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.061494 restraints weight = 42855.799| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 4.83 r_work: 0.2670 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16566 Z= 0.126 Angle : 0.506 10.615 22476 Z= 0.264 Chirality : 0.043 0.186 2633 Planarity : 0.004 0.052 2895 Dihedral : 13.176 102.269 2574 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.71 % Allowed : 21.73 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2079 helix: 2.16 (0.20), residues: 685 sheet: 0.05 (0.25), residues: 458 loop : 0.11 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 360 TYR 0.013 0.001 TYR B 68 PHE 0.015 0.001 PHE B 493 TRP 0.002 0.000 TRP C 233 HIS 0.009 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16563) covalent geometry : angle 0.50579 / 0.26 (22476) hydrogen bonds : bond 0.03915 / 2.70 ( 743) hydrogen bonds : angle 4.24451 / 3.02 ( 2142) Misc. bond : bond 0.00264 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 95 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8185 (mp10) REVERT: A 267 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.9058 (m-80) REVERT: A 323 MET cc_start: 0.8699 (mtp) cc_final: 0.8180 (ptp) REVERT: A 369 MET cc_start: 0.9088 (mmm) cc_final: 0.8459 (mmm) REVERT: A 451 MET cc_start: 0.8928 (mtp) cc_final: 0.8513 (mmm) REVERT: A 466 MET cc_start: 0.8111 (mtp) cc_final: 0.7843 (mmt) REVERT: A 491 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8574 (tmm) REVERT: A 603 GLU cc_start: 0.9479 (mm-30) cc_final: 0.8894 (tp30) REVERT: A 668 MET cc_start: 0.3290 (mmt) cc_final: 0.2833 (mmt) REVERT: B 1 MET cc_start: 0.7940 (ppp) cc_final: 0.7659 (ppp) REVERT: B 167 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: B 171 LYS cc_start: 0.9658 (mtmt) cc_final: 0.9383 (mtmm) REVERT: B 188 MET cc_start: 0.9371 (ttp) cc_final: 0.9158 (tmm) REVERT: B 365 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7944 (pp) REVERT: B 369 MET cc_start: 0.8951 (mmm) cc_final: 0.8660 (mmm) REVERT: B 392 MET cc_start: 0.9074 (tpp) cc_final: 0.8573 (tmm) REVERT: B 466 MET cc_start: 0.8547 (mmm) cc_final: 0.8055 (mmm) REVERT: B 477 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 694 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5340 (pm20) REVERT: C 323 MET cc_start: 0.8687 (mtp) cc_final: 0.8282 (ptp) REVERT: C 440 MET cc_start: 0.8741 (mmp) cc_final: 0.8103 (mmp) REVERT: C 451 MET cc_start: 0.9010 (mtp) cc_final: 0.8761 (mmm) REVERT: C 491 MET cc_start: 0.8754 (ptm) cc_final: 0.8516 (ppp) REVERT: C 603 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8914 (tm-30) outliers start: 80 outliers final: 57 residues processed: 167 average time/residue: 0.1111 time to fit residues: 30.2269 Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 90 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 16 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 185 optimal weight: 0.4980 chunk 191 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN B 607 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.103657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.066241 restraints weight = 41619.337| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.80 r_work: 0.2703 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (17 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16566 Z= 0.106 Angle : 0.496 10.365 22476 Z= 0.257 Chirality : 0.043 0.235 2633 Planarity : 0.003 0.051 2895 Dihedral : 12.939 102.428 2568 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.30 % Allowed : 22.50 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 2079 helix: 2.34 (0.20), residues: 687 sheet: 0.18 (0.26), residues: 456 loop : 0.19 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 399 TYR 0.012 0.001 TYR C 385 PHE 0.023 0.001 PHE B 493 TRP 0.002 0.000 TRP C 233 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (16563) covalent geometry : angle 0.49601 / 0.26 (22476) hydrogen bonds : bond 0.03580 / 2.47 ( 743) hydrogen bonds : angle 4.08198 / 2.90 ( 2142) Misc. bond : bond 0.00228 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 92 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9273 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: A 323 MET cc_start: 0.8632 (mtp) cc_final: 0.8031 (ptp) REVERT: A 369 MET cc_start: 0.8992 (mmm) cc_final: 0.8359 (mmm) REVERT: A 451 MET cc_start: 0.8861 (mtp) cc_final: 0.8420 (mmm) REVERT: A 603 GLU cc_start: 0.9455 (mm-30) cc_final: 0.8847 (tp30) REVERT: A 668 MET cc_start: 0.3005 (mmt) cc_final: 0.2516 (mmt) REVERT: B 1 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (ppp) REVERT: B 167 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: B 171 LYS cc_start: 0.9634 (mtmt) cc_final: 0.9376 (mtmm) REVERT: B 188 MET cc_start: 0.9283 (ttp) cc_final: 0.9071 (tmm) REVERT: B 365 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7773 (pp) REVERT: B 369 MET cc_start: 0.8838 (mmm) cc_final: 0.8523 (mmm) REVERT: B 392 MET cc_start: 0.9051 (tpp) cc_final: 0.8545 (tmm) REVERT: B 418 MET cc_start: 0.8820 (mmm) cc_final: 0.8107 (mmm) REVERT: B 477 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8333 (p) REVERT: B 694 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5298 (pm20) REVERT: C 323 MET cc_start: 0.8695 (mtp) cc_final: 0.8342 (ptp) REVERT: C 440 MET cc_start: 0.8707 (mmp) cc_final: 0.8085 (mmp) REVERT: C 451 MET cc_start: 0.8926 (mtp) cc_final: 0.8703 (mmm) REVERT: C 466 MET cc_start: 0.8825 (mmm) cc_final: 0.7813 (mmm) REVERT: C 603 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8903 (tm-30) REVERT: C 614 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9381 (mp0) outliers start: 73 outliers final: 52 residues processed: 156 average time/residue: 0.1124 time to fit residues: 28.3197 Evaluate side-chains 146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 88 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 47 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 202 optimal weight: 0.0870 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062162 restraints weight = 42576.789| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.52 r_work: 0.2620 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 16566 Z= 0.334 Angle : 0.621 8.852 22476 Z= 0.319 Chirality : 0.044 0.207 2633 Planarity : 0.004 0.054 2895 Dihedral : 12.996 101.682 2564 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.77 % Allowed : 22.56 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2079 helix: 2.29 (0.20), residues: 683 sheet: 0.07 (0.25), residues: 459 loop : 0.23 (0.22), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 319 TYR 0.020 0.002 TYR A 380 PHE 0.011 0.001 PHE A 41 TRP 0.007 0.001 TRP B 233 HIS 0.009 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.33 (16563) covalent geometry : angle 0.62091 / 0.32 (22476) hydrogen bonds : bond 0.04366 / 2.97 ( 743) hydrogen bonds : angle 4.31693 / 3.06 ( 2142) Misc. bond : bond 0.00191 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 84 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.9058 (m-80) REVERT: A 369 MET cc_start: 0.9205 (mmm) cc_final: 0.8584 (mmm) REVERT: A 603 GLU cc_start: 0.9526 (mm-30) cc_final: 0.8926 (tp30) REVERT: A 668 MET cc_start: 0.3124 (mmt) cc_final: 0.2622 (mmt) REVERT: B 1 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7813 (ppp) REVERT: B 167 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: B 392 MET cc_start: 0.9102 (tpp) cc_final: 0.8599 (tmm) REVERT: B 451 MET cc_start: 0.9177 (tpt) cc_final: 0.8958 (tpt) REVERT: B 694 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5338 (pm20) REVERT: C 323 MET cc_start: 0.8728 (mtp) cc_final: 0.8249 (ptp) REVERT: C 603 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8961 (tm-30) REVERT: C 614 GLU cc_start: 0.9674 (mm-30) cc_final: 0.9412 (mp0) outliers start: 81 outliers final: 62 residues processed: 155 average time/residue: 0.1100 time to fit residues: 27.8280 Evaluate side-chains 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 83 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 0.0170 chunk 159 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.056481 restraints weight = 42732.965| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.89 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (16 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16566 Z= 0.114 Angle : 0.525 12.744 22476 Z= 0.266 Chirality : 0.043 0.189 2633 Planarity : 0.003 0.056 2895 Dihedral : 12.831 102.787 2564 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.59 % Allowed : 24.20 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 2079 helix: 2.54 (0.20), residues: 678 sheet: 0.29 (0.26), residues: 455 loop : 0.23 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 308 TYR 0.016 0.001 TYR A 68 PHE 0.023 0.001 PHE B 493 TRP 0.002 0.000 TRP C 233 HIS 0.008 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (16563) covalent geometry : angle 0.52489 / 0.27 (22476) hydrogen bonds : bond 0.03787 / 2.60 ( 743) hydrogen bonds : angle 4.07975 / 2.89 ( 2142) Misc. bond : bond 0.00173 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 85 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9266 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: A 323 MET cc_start: 0.8594 (mtp) cc_final: 0.8261 (ptp) REVERT: A 369 MET cc_start: 0.9112 (mmm) cc_final: 0.8465 (mmm) REVERT: A 451 MET cc_start: 0.8594 (mtp) cc_final: 0.8330 (mmm) REVERT: A 603 GLU cc_start: 0.9444 (mm-30) cc_final: 0.8825 (tp30) REVERT: A 668 MET cc_start: 0.2827 (mmt) cc_final: 0.2394 (mmt) REVERT: B 167 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: B 360 ARG cc_start: 0.8947 (tmm-80) cc_final: 0.8702 (ttp-110) REVERT: B 392 MET cc_start: 0.8437 (tpp) cc_final: 0.8190 (tmm) REVERT: B 418 MET cc_start: 0.8616 (mmm) cc_final: 0.7920 (mmm) REVERT: B 694 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5411 (pm20) REVERT: C 323 MET cc_start: 0.8658 (mtp) cc_final: 0.8194 (ptp) REVERT: C 451 MET cc_start: 0.8702 (mtp) cc_final: 0.8445 (mmm) REVERT: C 603 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 614 GLU cc_start: 0.9616 (mm-30) cc_final: 0.9393 (mp0) outliers start: 61 outliers final: 52 residues processed: 138 average time/residue: 0.1109 time to fit residues: 24.9713 Evaluate side-chains 140 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 85 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 6 optimal weight: 0.0050 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 58 optimal weight: 9.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056885 restraints weight = 42824.775| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 5.07 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16566 Z= 0.104 Angle : 0.515 12.472 22476 Z= 0.259 Chirality : 0.042 0.188 2633 Planarity : 0.003 0.052 2895 Dihedral : 12.619 103.236 2561 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.42 % Allowed : 24.32 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.19), residues: 2079 helix: 2.61 (0.20), residues: 680 sheet: 0.44 (0.26), residues: 453 loop : 0.22 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 545 TYR 0.014 0.001 TYR A 68 PHE 0.033 0.001 PHE B 493 TRP 0.003 0.000 TRP C 233 HIS 0.007 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (16563) covalent geometry : angle 0.51544 / 0.26 (22476) hydrogen bonds : bond 0.03473 / 2.38 ( 743) hydrogen bonds : angle 3.99361 / 2.82 ( 2142) Misc. bond : bond 0.00141 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 87 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8561 (mtp) cc_final: 0.8222 (ptp) REVERT: A 369 MET cc_start: 0.9083 (mmm) cc_final: 0.8426 (mmm) REVERT: A 451 MET cc_start: 0.8542 (mtp) cc_final: 0.8304 (mmm) REVERT: A 512 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 603 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8800 (tp30) REVERT: A 668 MET cc_start: 0.3226 (mmt) cc_final: 0.2812 (mmt) REVERT: B 1 MET cc_start: 0.7680 (ppp) cc_final: 0.7450 (ppp) REVERT: B 167 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: B 171 LYS cc_start: 0.9632 (mtmt) cc_final: 0.9335 (mtmm) REVERT: B 360 ARG cc_start: 0.8955 (tmm-80) cc_final: 0.8705 (ttp-110) REVERT: B 392 MET cc_start: 0.8434 (tpp) cc_final: 0.8221 (tmm) REVERT: B 418 MET cc_start: 0.8640 (mmm) cc_final: 0.7910 (mmm) REVERT: B 694 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5526 (pm20) REVERT: C 323 MET cc_start: 0.8662 (mtp) cc_final: 0.8216 (ptp) REVERT: C 451 MET cc_start: 0.8723 (mtp) cc_final: 0.8445 (mmm) REVERT: C 466 MET cc_start: 0.8577 (mmm) cc_final: 0.7548 (mmm) REVERT: C 603 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8878 (tm-30) REVERT: C 614 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9418 (mp0) outliers start: 58 outliers final: 49 residues processed: 138 average time/residue: 0.1180 time to fit residues: 26.1842 Evaluate side-chains 138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 87 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 137 optimal weight: 50.0000 chunk 191 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 206 optimal weight: 0.0060 chunk 156 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.100039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.056650 restraints weight = 42742.743| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 5.01 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (20 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16566 Z= 0.121 Angle : 0.512 13.109 22476 Z= 0.257 Chirality : 0.042 0.184 2633 Planarity : 0.003 0.051 2895 Dihedral : 12.533 103.159 2560 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.06 % Allowed : 24.73 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.19), residues: 2079 helix: 2.69 (0.20), residues: 679 sheet: 0.53 (0.26), residues: 453 loop : 0.23 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.013 0.001 TYR A 68 PHE 0.013 0.001 PHE B 493 TRP 0.003 0.000 TRP C 233 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16563) covalent geometry : angle 0.51208 / 0.26 (22476) hydrogen bonds : bond 0.03430 / 2.35 ( 743) hydrogen bonds : angle 3.93166 / 2.78 ( 2142) Misc. bond : bond 0.00120 / 0.06 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 89 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.8919 (m) REVERT: A 267 TYR cc_start: 0.8928 (m-80) cc_final: 0.8395 (m-10) REVERT: A 323 MET cc_start: 0.8576 (mtp) cc_final: 0.8256 (ptp) REVERT: A 369 MET cc_start: 0.9081 (mmm) cc_final: 0.8415 (mmm) REVERT: A 451 MET cc_start: 0.8514 (mtp) cc_final: 0.8314 (mmm) REVERT: A 603 GLU cc_start: 0.9451 (mm-30) cc_final: 0.8819 (tp30) REVERT: A 668 MET cc_start: 0.3345 (mmt) cc_final: 0.2930 (mmt) REVERT: B 1 MET cc_start: 0.7765 (ppp) cc_final: 0.7528 (ppp) REVERT: B 167 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: B 360 ARG cc_start: 0.8960 (tmm-80) cc_final: 0.8727 (ttp-110) REVERT: B 392 MET cc_start: 0.8442 (tpp) cc_final: 0.8235 (tmm) REVERT: B 418 MET cc_start: 0.8680 (mmm) cc_final: 0.8003 (mmm) REVERT: B 491 MET cc_start: 0.8548 (ttp) cc_final: 0.8115 (ppp) REVERT: B 493 PHE cc_start: 0.8269 (m-80) cc_final: 0.7730 (m-80) REVERT: B 694 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5476 (pm20) REVERT: C 323 MET cc_start: 0.8672 (mtp) cc_final: 0.8220 (ptp) REVERT: C 451 MET cc_start: 0.8738 (mtp) cc_final: 0.8461 (mmm) REVERT: C 466 MET cc_start: 0.8570 (mmm) cc_final: 0.7748 (mtp) REVERT: C 603 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8882 (tm-30) outliers start: 52 outliers final: 46 residues processed: 137 average time/residue: 0.1167 time to fit residues: 26.0052 Evaluate side-chains 136 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 87 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 202 optimal weight: 6.9990 chunk 140 optimal weight: 0.0370 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 150 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.099981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.059339 restraints weight = 41780.342| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.76 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16566 Z= 0.102 Angle : 0.515 13.794 22476 Z= 0.259 Chirality : 0.043 0.182 2633 Planarity : 0.003 0.050 2895 Dihedral : 12.460 103.310 2559 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.94 % Allowed : 24.38 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 2079 helix: 2.71 (0.20), residues: 682 sheet: 0.61 (0.26), residues: 451 loop : 0.27 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 611 TYR 0.013 0.001 TYR A 68 PHE 0.019 0.001 PHE B 493 TRP 0.003 0.000 TRP C 233 HIS 0.007 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (16563) covalent geometry : angle 0.51514 / 0.26 (22476) hydrogen bonds : bond 0.03307 / 2.27 ( 743) hydrogen bonds : angle 3.89606 / 2.75 ( 2142) Misc. bond : bond 0.00106 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.16 seconds wall clock time: 77 minutes 10.83 seconds (4630.83 seconds total)