Starting phenix.real_space_refine on Sun May 18 00:07:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vah_43092/05_2025/8vah_43092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vah_43092/05_2025/8vah_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_43092/05_2025/8vah_43092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vah_43092/05_2025/8vah_43092.map" model { file = "/net/cci-nas-00/data/ceres_data/8vah_43092/05_2025/8vah_43092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vah_43092/05_2025/8vah_43092.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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%rna2p_pur:plan': 3, ' A%rna2p_pur:plan2': 3, ' A%rna3p_pur:plan2': 3, ' A%rna3p_pur:plan': 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: 10.17, per 1000 atoms: 0.62 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: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.24 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: 5.93 Time building geometry restraints manager: 5.08 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: 1.400 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 39.350 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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= 0.317 Angle : 0.739 16.262 22476 Z= 0.436 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 : 12.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (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 TRP 0.005 0.001 TRP A 233 HIS 0.014 0.001 HIS A 487 PHE 0.027 0.002 PHE A 421 TYR 0.022 0.002 TYR A 385 ARG 0.010 0.001 ARG C 253 Details of bonding type rmsd hydrogen bonds : bond 0.18110 ( 743) hydrogen bonds : angle 7.15568 ( 2142) covalent geometry : bond 0.00677 (16563) covalent geometry : angle 0.73897 (22476) Misc. bond : bond 0.04780 ( 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 : 1.687 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: 0.9427 (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: 0.9039 (t0) cc_final: 0.8834 (t0) REVERT: C 603 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8197 (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: 0.2368 time to fit residues: 83.7189 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 : 1.865 ------------------------------------------------------------------------------- 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 174 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 218 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 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 = 0.3688 r_free = 0.3688 target = 0.100565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.057881 restraints weight = 42791.369| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 5.00 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16566 Z= 0.186 Angle : 0.590 7.276 22476 Z= 0.310 Chirality : 0.044 0.207 2633 Planarity : 0.004 0.054 2895 Dihedral : 14.719 101.299 2665 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.95 % Allowed : 18.85 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 2079 helix: 1.37 (0.19), residues: 678 sheet: -0.99 (0.24), residues: 465 loop : -0.32 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 233 HIS 0.014 0.001 HIS A 487 PHE 0.025 0.002 PHE B 493 TYR 0.013 0.002 TYR B 68 ARG 0.007 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 743) hydrogen bonds : angle 5.00709 ( 2142) covalent geometry : bond 0.00416 (16563) covalent geometry : angle 0.58967 (22476) Misc. bond : bond 0.00352 ( 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 201 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 100 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.9086 (m-80) REVERT: A 323 MET cc_start: 0.8657 (mtp) cc_final: 0.8125 (ptp) REVERT: A 369 MET cc_start: 0.9160 (mmm) cc_final: 0.8335 (mmt) REVERT: A 493 PHE cc_start: 0.7000 (m-80) cc_final: 0.6650 (m-80) REVERT: A 668 MET cc_start: 0.2703 (mmt) cc_final: 0.2342 (mmt) REVERT: B 1 MET cc_start: 0.7620 (ppp) cc_final: 0.7400 (ppp) REVERT: B 167 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: B 188 MET cc_start: 0.9262 (ttp) cc_final: 0.9035 (tmm) REVERT: B 365 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8111 (pp) REVERT: B 369 MET cc_start: 0.8984 (mmm) cc_final: 0.8679 (mmm) REVERT: B 694 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5192 (pm20) REVERT: C 190 GLU cc_start: 0.8554 (tt0) cc_final: 0.8341 (tp30) REVERT: C 232 ASP cc_start: 0.8915 (p0) cc_final: 0.8669 (p0) REVERT: C 323 MET cc_start: 0.8591 (mtp) cc_final: 0.8342 (ptp) REVERT: C 418 MET cc_start: 0.8665 (ttm) cc_final: 0.8440 (tpp) REVERT: C 601 ASP cc_start: 0.8305 (p0) cc_final: 0.8003 (p0) REVERT: C 603 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8658 (tm-30) REVERT: C 611 ARG cc_start: 0.9520 (OUTLIER) cc_final: 0.9053 (tpt-90) outliers start: 101 outliers final: 61 residues processed: 186 average time/residue: 0.2394 time to fit residues: 70.2048 Evaluate side-chains 158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 92 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 149 ILE 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 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 641 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 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 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 440 MET 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 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 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 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 515 THR Chi-restraints excluded: chain C residue 523 LEU 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 58 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** 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 212 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.100074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061743 restraints weight = 42664.142| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.71 r_work: 0.2628 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- 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: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16566 Z= 0.305 Angle : 0.614 9.232 22476 Z= 0.320 Chirality : 0.044 0.204 2633 Planarity : 0.004 0.056 2895 Dihedral : 13.778 101.281 2601 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.95 % Allowed : 20.20 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2079 helix: 1.75 (0.19), residues: 684 sheet: -0.58 (0.24), residues: 462 loop : -0.08 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 233 HIS 0.013 0.001 HIS B 487 PHE 0.015 0.002 PHE B 41 TYR 0.020 0.002 TYR A 380 ARG 0.009 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 743) hydrogen bonds : angle 4.68868 ( 2142) covalent geometry : bond 0.00697 (16563) covalent geometry : angle 0.61403 (22476) Misc. bond : bond 0.00263 ( 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 190 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 89 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.9295 (ptm) REVERT: A 212 GLN cc_start: 0.8022 (mt0) cc_final: 0.7779 (tt0) REVERT: A 267 TYR cc_start: 0.9299 (OUTLIER) cc_final: 0.9060 (m-80) REVERT: A 323 MET cc_start: 0.8820 (mtp) cc_final: 0.8306 (ptp) REVERT: A 369 MET cc_start: 0.9244 (mmm) cc_final: 0.8631 (mmm) REVERT: A 466 MET cc_start: 0.8212 (mtp) cc_final: 0.7613 (mtp) REVERT: A 603 GLU cc_start: 0.9501 (mm-30) cc_final: 0.8941 (tp30) REVERT: A 668 MET cc_start: 0.2995 (mmt) cc_final: 0.2518 (mmt) REVERT: B 1 MET cc_start: 0.8049 (ppp) cc_final: 0.7733 (ppp) REVERT: B 167 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: B 188 MET cc_start: 0.9327 (ttp) cc_final: 0.9079 (tmm) REVERT: B 365 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8111 (pp) REVERT: B 369 MET cc_start: 0.9087 (mmm) cc_final: 0.8739 (mmm) REVERT: B 392 MET cc_start: 0.9027 (tpp) cc_final: 0.8506 (tmm) REVERT: B 466 MET cc_start: 0.8870 (mmm) cc_final: 0.8026 (mmm) REVERT: B 477 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8333 (p) REVERT: C 455 VAL cc_start: 0.9559 (OUTLIER) cc_final: 0.9309 (m) REVERT: C 491 MET cc_start: 0.8901 (ptm) cc_final: 0.8687 (ppp) REVERT: C 603 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8904 (tm-30) REVERT: C 614 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9322 (mp0) outliers start: 101 outliers final: 60 residues processed: 180 average time/residue: 0.2326 time to fit residues: 67.5885 Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 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 164 ASN 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 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 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 615 ILE Chi-restraints excluded: chain A residue 663 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 390 THR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 600 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 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 319 ARG 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 536 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 122 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 298 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN C 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.101817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063421 restraints weight = 42349.277| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.82 r_work: 0.2681 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 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 = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16566 Z= 0.130 Angle : 0.524 12.389 22476 Z= 0.271 Chirality : 0.043 0.190 2633 Planarity : 0.004 0.055 2895 Dihedral : 13.224 102.443 2573 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.42 % Allowed : 21.91 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2079 helix: 2.07 (0.20), residues: 685 sheet: -0.17 (0.25), residues: 459 loop : 0.04 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 233 HIS 0.016 0.001 HIS A 487 PHE 0.022 0.001 PHE B 493 TYR 0.013 0.001 TYR C 385 ARG 0.006 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 743) hydrogen bonds : angle 4.32213 ( 2142) covalent geometry : bond 0.00284 (16563) covalent geometry : angle 0.52397 (22476) Misc. bond : bond 0.00258 ( 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 164 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 89 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.9295 (ptm) REVERT: A 267 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.9046 (m-80) REVERT: A 323 MET cc_start: 0.8709 (mtp) cc_final: 0.8195 (ptp) REVERT: A 369 MET cc_start: 0.9140 (mmm) cc_final: 0.8497 (mmm) REVERT: A 603 GLU cc_start: 0.9481 (mm-30) cc_final: 0.8846 (tp30) REVERT: A 668 MET cc_start: 0.2896 (mmt) cc_final: 0.2393 (mmt) REVERT: B 167 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: B 171 LYS cc_start: 0.9670 (mtmt) cc_final: 0.9396 (mtmm) REVERT: B 365 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8047 (pp) REVERT: B 369 MET cc_start: 0.9017 (mmm) cc_final: 0.8711 (mmm) REVERT: B 392 MET cc_start: 0.9079 (tpp) cc_final: 0.8569 (tmm) REVERT: B 466 MET cc_start: 0.8740 (mmm) cc_final: 0.8342 (mmm) REVERT: B 694 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5337 (pm20) REVERT: C 323 MET cc_start: 0.8896 (mtp) cc_final: 0.8518 (ptp) REVERT: C 451 MET cc_start: 0.9025 (mtp) cc_final: 0.8683 (mmm) REVERT: C 491 MET cc_start: 0.8825 (ptm) cc_final: 0.8599 (ppp) REVERT: C 603 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8868 (tm-30) REVERT: C 614 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9311 (mp0) outliers start: 75 outliers final: 52 residues processed: 156 average time/residue: 0.2500 time to fit residues: 61.2150 Evaluate side-chains 145 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 88 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET 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 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 509 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 393 VAL 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 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 319 ARG 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 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 589 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 182 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 607 HIS B 653 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.100208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060056 restraints weight = 43536.383| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.92 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 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 = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16566 Z= 0.199 Angle : 0.533 10.479 22476 Z= 0.274 Chirality : 0.043 0.213 2633 Planarity : 0.004 0.056 2895 Dihedral : 13.116 102.932 2568 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.53 % Allowed : 21.79 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 2079 helix: 2.24 (0.20), residues: 685 sheet: -0.02 (0.25), residues: 462 loop : 0.17 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 233 HIS 0.009 0.001 HIS B 487 PHE 0.017 0.001 PHE B 493 TYR 0.015 0.002 TYR A 380 ARG 0.006 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 743) hydrogen bonds : angle 4.22675 ( 2142) covalent geometry : bond 0.00453 (16563) covalent geometry : angle 0.53307 (22476) Misc. bond : bond 0.00216 ( 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 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 88 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.9063 (m-80) REVERT: A 323 MET cc_start: 0.8558 (mtp) cc_final: 0.8058 (ptp) REVERT: A 369 MET cc_start: 0.9121 (mmm) cc_final: 0.8470 (mmm) REVERT: A 466 MET cc_start: 0.7838 (mtp) cc_final: 0.7353 (mmt) REVERT: A 603 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8796 (tp30) REVERT: A 668 MET cc_start: 0.2580 (mmt) cc_final: 0.2124 (mmt) REVERT: B 1 MET cc_start: 0.7839 (ppp) cc_final: 0.7521 (ppp) REVERT: B 167 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: B 349 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8904 (pt0) REVERT: B 365 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 369 MET cc_start: 0.8992 (mmm) cc_final: 0.8645 (mmm) REVERT: B 392 MET cc_start: 0.8483 (tpp) cc_final: 0.8282 (tpp) REVERT: B 418 MET cc_start: 0.8736 (mmm) cc_final: 0.8107 (mmm) REVERT: B 466 MET cc_start: 0.8530 (mmm) cc_final: 0.8031 (mmm) REVERT: B 477 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 694 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: C 323 MET cc_start: 0.8692 (mtp) cc_final: 0.8348 (ptp) REVERT: C 451 MET cc_start: 0.8802 (mtp) cc_final: 0.8354 (mmm) REVERT: C 491 MET cc_start: 0.8614 (ptm) cc_final: 0.8311 (ppp) REVERT: C 603 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8852 (tm-30) REVERT: C 614 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9352 (mp0) outliers start: 77 outliers final: 57 residues processed: 155 average time/residue: 0.2393 time to fit residues: 59.5445 Evaluate side-chains 148 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 85 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 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 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 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR 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 477 VAL Chi-restraints excluded: chain B residue 488 LEU 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 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 284 GLU Chi-restraints excluded: chain C residue 319 ARG 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 515 THR Chi-restraints excluded: chain C residue 531 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 95 optimal weight: 0.7980 chunk 136 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.101930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061634 restraints weight = 42599.023| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.81 r_work: 0.2683 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16566 Z= 0.109 Angle : 0.499 10.700 22476 Z= 0.257 Chirality : 0.042 0.186 2633 Planarity : 0.003 0.052 2895 Dihedral : 12.887 103.545 2567 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.12 % Allowed : 22.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 2079 helix: 2.47 (0.20), residues: 681 sheet: 0.21 (0.26), residues: 456 loop : 0.24 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 233 HIS 0.008 0.001 HIS B 487 PHE 0.013 0.001 PHE B 41 TYR 0.016 0.001 TYR A 68 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 743) hydrogen bonds : angle 4.02470 ( 2142) covalent geometry : bond 0.00236 (16563) covalent geometry : angle 0.49879 (22476) Misc. bond : bond 0.00176 ( 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 161 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 91 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.9041 (m-80) REVERT: A 323 MET cc_start: 0.8637 (mtp) cc_final: 0.8045 (ptp) REVERT: A 369 MET cc_start: 0.9083 (mmm) cc_final: 0.8457 (mmm) REVERT: A 451 MET cc_start: 0.8760 (mtp) cc_final: 0.8506 (mmm) REVERT: A 603 GLU cc_start: 0.9489 (mm-30) cc_final: 0.8849 (tp30) REVERT: A 668 MET cc_start: 0.3208 (mmt) cc_final: 0.2704 (mmt) REVERT: B 1 MET cc_start: 0.8039 (ppp) cc_final: 0.7835 (ppp) REVERT: B 167 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: B 171 LYS cc_start: 0.9650 (mtmt) cc_final: 0.9380 (mtmm) REVERT: B 369 MET cc_start: 0.8958 (mmm) cc_final: 0.8636 (mmm) REVERT: B 392 MET cc_start: 0.9078 (tpp) cc_final: 0.8632 (tmm) REVERT: B 418 MET cc_start: 0.8903 (mmm) cc_final: 0.8301 (mmm) REVERT: B 451 MET cc_start: 0.8880 (mmm) cc_final: 0.8549 (tpt) REVERT: B 466 MET cc_start: 0.8601 (mmm) cc_final: 0.8064 (mmm) REVERT: B 477 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 694 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5384 (pm20) REVERT: C 323 MET cc_start: 0.8942 (mtp) cc_final: 0.8603 (ptp) REVERT: C 392 MET cc_start: 0.8569 (tmm) cc_final: 0.8284 (tmm) REVERT: C 451 MET cc_start: 0.8997 (mtp) cc_final: 0.8662 (mmm) REVERT: C 491 MET cc_start: 0.8646 (ptm) cc_final: 0.8444 (ppp) REVERT: C 603 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8921 (tm-30) REVERT: C 614 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9398 (mp0) outliers start: 70 outliers final: 48 residues processed: 154 average time/residue: 0.2439 time to fit residues: 59.8579 Evaluate side-chains 139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 87 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 26 GLN 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 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 509 ILE Chi-restraints excluded: chain A residue 615 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 163 LEU 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 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 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 565 ILE Chi-restraints excluded: chain C residue 595 VAL 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 92 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 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 = 0.3622 r_free = 0.3622 target = 0.097599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.056808 restraints weight = 42203.019| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.45 r_work: 0.2541 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2436 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= 0.235 Angle : 0.555 9.357 22476 Z= 0.284 Chirality : 0.043 0.185 2633 Planarity : 0.004 0.054 2895 Dihedral : 12.828 103.429 2564 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.95 % Allowed : 23.44 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 2079 helix: 2.53 (0.20), residues: 678 sheet: 0.18 (0.25), residues: 457 loop : 0.33 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 233 HIS 0.009 0.001 HIS B 487 PHE 0.014 0.001 PHE A 41 TYR 0.017 0.002 TYR A 380 ARG 0.004 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 743) hydrogen bonds : angle 4.11817 ( 2142) covalent geometry : bond 0.00538 (16563) covalent geometry : angle 0.55481 (22476) Misc. bond : bond 0.00148 ( 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 152 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 85 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.9043 (m-80) REVERT: A 369 MET cc_start: 0.9193 (mmm) cc_final: 0.8576 (mmm) REVERT: A 451 MET cc_start: 0.8876 (mtp) cc_final: 0.8652 (mmm) REVERT: A 603 GLU cc_start: 0.9528 (mm-30) cc_final: 0.8900 (tp30) REVERT: A 668 MET cc_start: 0.3356 (mmt) cc_final: 0.2828 (mmt) REVERT: B 1 MET cc_start: 0.8139 (ppp) cc_final: 0.7930 (ppp) REVERT: B 167 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: B 369 MET cc_start: 0.9047 (mmm) cc_final: 0.8746 (mmm) REVERT: B 392 MET cc_start: 0.9089 (tpp) cc_final: 0.8837 (tpp) REVERT: B 451 MET cc_start: 0.9143 (mmm) cc_final: 0.8656 (tpt) REVERT: B 477 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 694 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5316 (pm20) REVERT: C 323 MET cc_start: 0.9002 (mtp) cc_final: 0.8555 (ptp) REVERT: C 491 MET cc_start: 0.8721 (ptm) cc_final: 0.8521 (ppp) REVERT: C 603 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8954 (tm-30) REVERT: C 614 GLU cc_start: 0.9668 (mm-30) cc_final: 0.9431 (mp0) outliers start: 67 outliers final: 54 residues processed: 147 average time/residue: 0.2363 time to fit residues: 56.3072 Evaluate side-chains 143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 85 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 26 GLN 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 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 444 CYS 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 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 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 447 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 493 PHE 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 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 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 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 156 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3651 r_free = 0.3651 target = 0.099121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.058070 restraints weight = 41739.946| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.70 r_work: 0.2553 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16566 Z= 0.117 Angle : 0.507 10.017 22476 Z= 0.258 Chirality : 0.042 0.188 2633 Planarity : 0.003 0.050 2895 Dihedral : 12.623 103.943 2561 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.83 % Allowed : 23.56 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.19), residues: 2079 helix: 2.63 (0.20), residues: 680 sheet: 0.34 (0.26), residues: 453 loop : 0.30 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 233 HIS 0.008 0.001 HIS B 487 PHE 0.015 0.001 PHE A 41 TYR 0.013 0.001 TYR A 68 ARG 0.004 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 743) hydrogen bonds : angle 3.97069 ( 2142) covalent geometry : bond 0.00258 (16563) covalent geometry : angle 0.50730 (22476) Misc. bond : bond 0.00128 ( 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 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 86 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8819 (t80) REVERT: A 323 MET cc_start: 0.8710 (mtp) cc_final: 0.8372 (ptp) REVERT: A 369 MET cc_start: 0.9068 (mmm) cc_final: 0.8446 (mmm) REVERT: A 451 MET cc_start: 0.8752 (mtp) cc_final: 0.8517 (mmm) REVERT: A 603 GLU cc_start: 0.9503 (mm-30) cc_final: 0.8858 (tp30) REVERT: A 668 MET cc_start: 0.3418 (mmt) cc_final: 0.2904 (mmt) REVERT: B 1 MET cc_start: 0.8096 (ppp) cc_final: 0.7882 (ppp) REVERT: B 167 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: B 369 MET cc_start: 0.8875 (mmm) cc_final: 0.8539 (mmm) REVERT: B 392 MET cc_start: 0.9081 (tpp) cc_final: 0.8669 (tmm) REVERT: B 418 MET cc_start: 0.8796 (mmm) cc_final: 0.8155 (mmm) REVERT: B 477 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 491 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8768 (ttp) REVERT: B 694 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5420 (pm20) REVERT: C 323 MET cc_start: 0.8948 (mtp) cc_final: 0.8468 (ptp) REVERT: C 451 MET cc_start: 0.8976 (mtp) cc_final: 0.8709 (mmm) REVERT: C 466 MET cc_start: 0.8815 (mmm) cc_final: 0.7800 (mmm) REVERT: C 491 MET cc_start: 0.8643 (ptm) cc_final: 0.8432 (ppp) REVERT: C 603 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8964 (tm-30) REVERT: C 614 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9440 (mp0) outliers start: 65 outliers final: 52 residues processed: 144 average time/residue: 0.2548 time to fit residues: 57.5723 Evaluate side-chains 142 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 85 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS 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 267 TYR 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 444 CYS Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 509 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 163 LEU 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 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 447 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 531 LEU 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 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 25 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN C 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.099062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058190 restraints weight = 41749.192| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.65 r_work: 0.2557 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16566 Z= 0.125 Angle : 0.498 9.502 22476 Z= 0.253 Chirality : 0.042 0.171 2633 Planarity : 0.003 0.050 2895 Dihedral : 12.507 104.012 2561 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.30 % Allowed : 24.09 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2079 helix: 2.70 (0.20), residues: 680 sheet: 0.42 (0.25), residues: 453 loop : 0.35 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 233 HIS 0.007 0.001 HIS B 487 PHE 0.014 0.001 PHE A 41 TYR 0.012 0.001 TYR A 68 ARG 0.004 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 743) hydrogen bonds : angle 3.90399 ( 2142) covalent geometry : bond 0.00282 (16563) covalent geometry : angle 0.49775 (22476) Misc. bond : bond 0.00104 ( 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 144 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 88 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8813 (t80) REVERT: A 323 MET cc_start: 0.8750 (mtp) cc_final: 0.8428 (ptp) REVERT: A 369 MET cc_start: 0.9065 (mmm) cc_final: 0.8421 (mmm) REVERT: A 451 MET cc_start: 0.8742 (mtp) cc_final: 0.8535 (mmm) REVERT: A 512 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 603 GLU cc_start: 0.9504 (mm-30) cc_final: 0.8860 (tp30) REVERT: A 668 MET cc_start: 0.3459 (mmt) cc_final: 0.2927 (mmt) REVERT: B 167 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: B 369 MET cc_start: 0.8793 (mmm) cc_final: 0.8465 (mmm) REVERT: B 392 MET cc_start: 0.9080 (tpp) cc_final: 0.8672 (tmm) REVERT: B 418 MET cc_start: 0.8860 (mmm) cc_final: 0.8254 (mmm) REVERT: B 451 MET cc_start: 0.8985 (mmm) cc_final: 0.8641 (tpt) REVERT: B 491 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8623 (ttp) REVERT: B 694 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5366 (pm20) REVERT: C 323 MET cc_start: 0.8969 (mtp) cc_final: 0.8480 (ptp) REVERT: C 451 MET cc_start: 0.8961 (mtp) cc_final: 0.8713 (mmm) REVERT: C 466 MET cc_start: 0.8693 (mmm) cc_final: 0.8139 (mtp) REVERT: C 603 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8990 (tm-30) outliers start: 56 outliers final: 48 residues processed: 136 average time/residue: 0.2449 time to fit residues: 53.5310 Evaluate side-chains 138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 86 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS 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 267 TYR 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 444 CYS Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 595 VAL 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 163 LEU 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 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 461 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 493 PHE 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 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 565 ILE Chi-restraints excluded: chain C residue 583 THR 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 145 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 137 optimal weight: 50.0000 chunk 181 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 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 = 0.3646 r_free = 0.3646 target = 0.098686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.055238 restraints weight = 43242.959| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 5.01 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16566 Z= 0.180 Angle : 0.525 9.448 22476 Z= 0.268 Chirality : 0.042 0.171 2633 Planarity : 0.003 0.048 2895 Dihedral : 12.399 103.818 2556 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.36 % Allowed : 24.09 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.19), residues: 2079 helix: 2.72 (0.20), residues: 680 sheet: 0.46 (0.25), residues: 453 loop : 0.38 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 233 HIS 0.007 0.001 HIS B 487 PHE 0.021 0.001 PHE A 41 TYR 0.014 0.001 TYR A 380 ARG 0.007 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 743) hydrogen bonds : angle 3.94066 ( 2142) covalent geometry : bond 0.00408 (16563) covalent geometry : angle 0.52477 (22476) Misc. bond : bond 0.00101 ( 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 142 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 85 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8789 (t80) REVERT: A 323 MET cc_start: 0.8710 (mtp) cc_final: 0.8391 (ptp) REVERT: A 369 MET cc_start: 0.9159 (mmm) cc_final: 0.8550 (mmm) REVERT: A 512 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 603 GLU cc_start: 0.9451 (mm-30) cc_final: 0.8785 (tp30) REVERT: A 668 MET cc_start: 0.3678 (mmt) cc_final: 0.3241 (mmt) REVERT: B 167 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: B 369 MET cc_start: 0.8876 (mmm) cc_final: 0.8565 (mmm) REVERT: B 418 MET cc_start: 0.8794 (mmm) cc_final: 0.8234 (mmm) REVERT: B 451 MET cc_start: 0.9035 (mmm) cc_final: 0.8589 (tpt) REVERT: B 491 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8405 (ttp) REVERT: B 694 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5468 (pm20) REVERT: C 323 MET cc_start: 0.8840 (mtp) cc_final: 0.8332 (ptp) REVERT: C 451 MET cc_start: 0.8794 (mtp) cc_final: 0.8501 (mmm) REVERT: C 466 MET cc_start: 0.8383 (mmm) cc_final: 0.7725 (mtp) REVERT: C 603 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8899 (tm-30) outliers start: 57 outliers final: 50 residues processed: 135 average time/residue: 0.2418 time to fit residues: 52.5851 Evaluate side-chains 139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 85 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 26 GLN 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 267 TYR 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 493 PHE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 595 VAL 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 163 LEU 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 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 461 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 592 ASP 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 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 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 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 187 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 203 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 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 = 0.3638 r_free = 0.3638 target = 0.098370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.054698 restraints weight = 43277.114| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 5.13 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16566 Z= 0.186 Angle : 0.534 9.339 22476 Z= 0.272 Chirality : 0.042 0.173 2633 Planarity : 0.004 0.046 2895 Dihedral : 12.384 103.818 2555 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.24 % Allowed : 24.20 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.19), residues: 2079 helix: 2.67 (0.20), residues: 681 sheet: 0.49 (0.25), residues: 455 loop : 0.41 (0.22), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 233 HIS 0.008 0.001 HIS B 487 PHE 0.019 0.001 PHE A 41 TYR 0.014 0.001 TYR A 380 ARG 0.005 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 743) hydrogen bonds : angle 3.99534 ( 2142) covalent geometry : bond 0.00422 (16563) covalent geometry : angle 0.53379 (22476) Misc. bond : bond 0.00098 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8838.46 seconds wall clock time: 153 minutes 14.65 seconds (9194.65 seconds total)