Starting phenix.real_space_refine on Sat Jun 14 15:52:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vah_43092/06_2025/8vah_43092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vah_43092/06_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_43092/06_2025/8vah_43092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vah_43092/06_2025/8vah_43092.map" model { file = "/net/cci-nas-00/data/ceres_data/8vah_43092/06_2025/8vah_43092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vah_43092/06_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-5710/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: 10.53, per 1000 atoms: 0.65 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: 4.44 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: 2.35 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: 6.16 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4085 1.33 - 1.45: 2748 1.45 - 1.57: 9570 1.57 - 1.68: 31 1.68 - 1.80: 129 Bond restraints: 16563 Sorted by residual: bond pdb=" N ILE A 149 " pdb=" CA ILE A 149 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.82e+00 bond pdb=" N ILE B 149 " pdb=" CA ILE B 149 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.15e+00 bond pdb=" N VAL A 214 " pdb=" CA VAL A 214 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.61e+00 bond pdb=" N GLY B 150 " pdb=" CA GLY B 150 " ideal model delta sigma weight residual 1.444 1.473 -0.029 1.06e-02 8.90e+03 7.45e+00 bond pdb=" N HIS A 209 " pdb=" CA HIS A 209 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.85e+00 ... (remaining 16558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 22331 3.25 - 6.50: 137 6.50 - 9.76: 4 9.76 - 13.01: 2 13.01 - 16.26: 2 Bond angle restraints: 22476 Sorted by residual: angle pdb=" C3' A F 2 " pdb=" O3' A F 2 " pdb=" P C F 3 " ideal model delta sigma weight residual 120.20 103.94 16.26 1.50e+00 4.44e-01 1.18e+02 angle pdb=" C3' C D 3 " pdb=" O3' C D 3 " pdb=" P A D 4 " ideal model delta sigma weight residual 120.20 105.43 14.77 1.50e+00 4.44e-01 9.69e+01 angle pdb=" C3' A D 2 " pdb=" O3' A D 2 " pdb=" P C D 3 " ideal model delta sigma weight residual 120.20 108.78 11.42 1.50e+00 4.44e-01 5.80e+01 angle pdb=" C3' C F 3 " pdb=" O3' C F 3 " pdb=" P A F 4 " ideal model delta sigma weight residual 120.20 109.28 10.92 1.50e+00 4.44e-01 5.30e+01 angle pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 120.20 113.36 6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 22471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 8771 19.94 - 39.88: 1000 39.88 - 59.83: 289 59.83 - 79.77: 73 79.77 - 99.71: 25 Dihedral angle restraints: 10158 sinusoidal: 4239 harmonic: 5919 Sorted by residual: dihedral pdb=" C5' A F 4 " pdb=" C4' A F 4 " pdb=" C3' A F 4 " pdb=" O3' A F 4 " ideal model delta sinusoidal sigma weight residual 147.00 93.14 53.86 1 8.00e+00 1.56e-02 6.15e+01 dihedral pdb=" O4' A F 4 " pdb=" C4' A F 4 " pdb=" C3' A F 4 " pdb=" C2' A F 4 " ideal model delta sinusoidal sigma weight residual 24.00 -27.42 51.42 1 8.00e+00 1.56e-02 5.65e+01 dihedral pdb=" C4' A F 4 " pdb=" C3' A F 4 " pdb=" C2' A F 4 " pdb=" C1' A F 4 " ideal model delta sinusoidal sigma weight residual -35.00 10.35 -45.35 1 8.00e+00 1.56e-02 4.46e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2541 0.113 - 0.227: 80 0.227 - 0.340: 4 0.340 - 0.453: 5 0.453 - 0.567: 3 Chirality restraints: 2633 Sorted by residual: chirality pdb=" P A D 2 " pdb=" OP1 A D 2 " pdb=" OP2 A D 2 " pdb=" O5' A D 2 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" P A E 2 " pdb=" OP1 A E 2 " pdb=" OP2 A E 2 " pdb=" O5' A E 2 " both_signs ideal model delta sigma weight residual True 2.41 2.97 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" P A F 2 " pdb=" OP1 A F 2 " pdb=" OP2 A F 2 " pdb=" O5' A F 2 " both_signs ideal model delta sigma weight residual True 2.41 2.97 -0.56 2.00e-01 2.50e+01 7.85e+00 ... (remaining 2630 not shown) Planarity restraints: 2895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 144 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C PRO A 144 " -0.047 2.00e-02 2.50e+03 pdb=" O PRO A 144 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 145 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 125 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 126 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 97 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 98 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " 0.030 5.00e-02 4.00e+02 ... (remaining 2892 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 34 2.36 - 2.99: 9226 2.99 - 3.63: 24457 3.63 - 4.26: 35296 4.26 - 4.90: 59634 Nonbonded interactions: 128647 Sorted by model distance: nonbonded pdb=" NH1 ARG C 93 " pdb=" OP1 A F 4 " model vdw 1.722 3.120 nonbonded pdb=" OG1 THR A 344 " pdb=" NE2 GLN A 349 " model vdw 2.063 3.120 nonbonded pdb=" NH1 ARG C 398 " pdb=" O2' A F 2 " model vdw 2.095 3.120 nonbonded pdb=" OE2 GLU B 430 " pdb=" OH TYR C 68 " model vdw 2.108 3.040 nonbonded pdb=" O THR C 424 " pdb=" OG1 THR C 424 " model vdw 2.186 3.040 ... (remaining 128642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.910 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- 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 : 1.663 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: 0.2340 time to fit residues: 83.0978 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 : 1.883 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.057919 restraints weight = 42791.369| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.92 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 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 = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 0.58966 (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 : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.9084 (m-80) REVERT: A 323 MET cc_start: 0.8659 (mtp) cc_final: 0.8127 (ptp) REVERT: A 369 MET cc_start: 0.9157 (mmm) cc_final: 0.8328 (mmt) REVERT: A 493 PHE cc_start: 0.7003 (m-80) cc_final: 0.6650 (m-80) REVERT: A 668 MET cc_start: 0.2713 (mmt) cc_final: 0.2354 (mmt) REVERT: B 1 MET cc_start: 0.7618 (ppp) cc_final: 0.7400 (ppp) REVERT: B 167 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: B 188 MET cc_start: 0.9266 (ttp) cc_final: 0.9038 (tmm) REVERT: B 365 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8117 (pp) REVERT: B 369 MET cc_start: 0.8983 (mmm) cc_final: 0.8679 (mmm) REVERT: B 694 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5170 (pm20) REVERT: C 190 GLU cc_start: 0.8548 (tt0) cc_final: 0.8333 (tp30) REVERT: C 232 ASP cc_start: 0.8909 (p0) cc_final: 0.8664 (p0) REVERT: C 323 MET cc_start: 0.8589 (mtp) cc_final: 0.8343 (ptp) REVERT: C 418 MET cc_start: 0.8664 (ttm) cc_final: 0.8441 (tpp) REVERT: C 601 ASP cc_start: 0.8305 (p0) cc_final: 0.8003 (p0) REVERT: C 603 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8654 (tm-30) REVERT: C 611 ARG cc_start: 0.9521 (OUTLIER) cc_final: 0.9051 (tpt-90) outliers start: 101 outliers final: 61 residues processed: 186 average time/residue: 0.2539 time to fit residues: 74.3925 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 : 1.774 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.5990 ------------------------------------------------------------------------------- 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** B 264 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061685 restraints weight = 42777.469| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.65 r_work: 0.2619 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 16566 Z= 0.344 Angle : 0.637 9.462 22476 Z= 0.332 Chirality : 0.045 0.203 2633 Planarity : 0.004 0.056 2895 Dihedral : 13.884 101.108 2601 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 6.12 % Allowed : 19.96 % Favored : 73.91 % 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: 0.46 (0.19), residues: 2079 helix: 1.68 (0.19), residues: 683 sheet: -0.63 (0.24), residues: 462 loop : -0.12 (0.21), residues: 934 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 0.016 0.002 PHE B 41 TYR 0.021 0.002 TYR A 380 ARG 0.005 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 743) hydrogen bonds : angle 4.78015 ( 2142) covalent geometry : bond 0.00782 (16563) covalent geometry : angle 0.63689 (22476) Misc. bond : bond 0.00270 ( 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 193 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 89 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9591 (OUTLIER) cc_final: 0.9310 (ptm) REVERT: A 267 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.9086 (m-80) REVERT: A 323 MET cc_start: 0.8820 (mtp) cc_final: 0.8306 (ptp) REVERT: A 369 MET cc_start: 0.9254 (mmm) cc_final: 0.8633 (mmm) REVERT: A 603 GLU cc_start: 0.9509 (mm-30) cc_final: 0.8952 (tp30) REVERT: A 668 MET cc_start: 0.3110 (mmt) cc_final: 0.2652 (mmt) REVERT: B 1 MET cc_start: 0.8039 (ppp) cc_final: 0.7723 (ppp) REVERT: B 167 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: B 188 MET cc_start: 0.9345 (ttp) cc_final: 0.9030 (tmm) REVERT: B 365 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8110 (pp) REVERT: B 369 MET cc_start: 0.9088 (mmm) cc_final: 0.8744 (mmm) REVERT: B 392 MET cc_start: 0.9011 (tpp) cc_final: 0.8507 (tmm) REVERT: B 466 MET cc_start: 0.8888 (mmm) cc_final: 0.7993 (mmm) REVERT: B 477 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8342 (p) REVERT: C 232 ASP cc_start: 0.9251 (p0) cc_final: 0.9009 (p0) REVERT: C 455 VAL cc_start: 0.9559 (OUTLIER) cc_final: 0.9305 (m) REVERT: C 491 MET cc_start: 0.8937 (ptm) cc_final: 0.8641 (ppp) REVERT: C 603 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8898 (tm-30) outliers start: 104 outliers final: 62 residues processed: 183 average time/residue: 0.2346 time to fit residues: 69.1339 Evaluate side-chains 152 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 84 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 482 LEU 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 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 VAL 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 533 ILE 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 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: 0.9990 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.100707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060454 restraints weight = 43030.572| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.89 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16566 Z= 0.161 Angle : 0.535 12.134 22476 Z= 0.278 Chirality : 0.043 0.192 2633 Planarity : 0.004 0.056 2895 Dihedral : 13.349 102.319 2575 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.59 % Allowed : 21.73 % 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: 0.88 (0.19), residues: 2079 helix: 2.02 (0.20), residues: 685 sheet: -0.22 (0.25), residues: 460 loop : 0.02 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 233 HIS 0.013 0.001 HIS A 487 PHE 0.017 0.001 PHE B 493 TYR 0.013 0.001 TYR A 380 ARG 0.006 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 743) hydrogen bonds : angle 4.39305 ( 2142) covalent geometry : bond 0.00360 (16563) covalent geometry : angle 0.53470 (22476) Misc. bond : bond 0.00264 ( 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 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 87 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.9065 (m-80) REVERT: A 323 MET cc_start: 0.8561 (mtp) cc_final: 0.8032 (ptp) REVERT: A 369 MET cc_start: 0.9107 (mmm) cc_final: 0.8453 (mmm) REVERT: A 603 GLU cc_start: 0.9456 (mm-30) cc_final: 0.8803 (tp30) REVERT: A 668 MET cc_start: 0.2484 (mmt) cc_final: 0.2047 (mmt) REVERT: B 167 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: B 188 MET cc_start: 0.9142 (ttp) cc_final: 0.8910 (tmm) REVERT: B 365 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7747 (pp) REVERT: B 369 MET cc_start: 0.8955 (mmm) cc_final: 0.8619 (mmm) REVERT: B 392 MET cc_start: 0.8429 (tpp) cc_final: 0.8082 (tmm) REVERT: B 451 MET cc_start: 0.8874 (mtp) cc_final: 0.8602 (mmm) REVERT: B 694 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5304 (pm20) REVERT: C 323 MET cc_start: 0.8676 (mtp) cc_final: 0.8312 (ptp) REVERT: C 451 MET cc_start: 0.8791 (mtp) cc_final: 0.8370 (mmm) REVERT: C 491 MET cc_start: 0.8665 (ptm) cc_final: 0.8280 (ppp) REVERT: C 603 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8817 (tm-30) outliers start: 78 outliers final: 57 residues processed: 156 average time/residue: 0.2476 time to fit residues: 61.5813 Evaluate side-chains 147 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 86 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 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 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 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 595 VAL Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 607 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.101074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062957 restraints weight = 42929.205| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.74 r_work: 0.2672 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16566 Z= 0.171 Angle : 0.517 10.204 22476 Z= 0.267 Chirality : 0.042 0.219 2633 Planarity : 0.004 0.055 2895 Dihedral : 13.126 103.163 2569 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.83 % Allowed : 21.85 % Favored : 73.32 % 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: 1.14 (0.19), residues: 2079 helix: 2.24 (0.20), residues: 686 sheet: 0.01 (0.25), residues: 460 loop : 0.13 (0.22), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 233 HIS 0.009 0.001 HIS B 487 PHE 0.018 0.001 PHE B 493 TYR 0.014 0.001 TYR A 380 ARG 0.007 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 743) hydrogen bonds : angle 4.20179 ( 2142) covalent geometry : bond 0.00385 (16563) covalent geometry : angle 0.51696 (22476) Misc. bond : bond 0.00220 ( 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 170 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 88 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.9029 (m-80) REVERT: A 323 MET cc_start: 0.8815 (mtp) cc_final: 0.8212 (ptp) REVERT: A 369 MET cc_start: 0.9163 (mmm) cc_final: 0.8538 (mmm) REVERT: A 415 MET cc_start: 0.9282 (ttm) cc_final: 0.8987 (tpp) REVERT: A 603 GLU cc_start: 0.9500 (mm-30) cc_final: 0.8865 (tp30) REVERT: A 668 MET cc_start: 0.3024 (mmt) cc_final: 0.2498 (mmt) REVERT: B 1 MET cc_start: 0.8047 (ppp) cc_final: 0.7731 (ppp) REVERT: B 167 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: B 365 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8061 (pp) REVERT: B 369 MET cc_start: 0.9051 (mmm) cc_final: 0.8728 (mmm) REVERT: B 392 MET cc_start: 0.9087 (tpp) cc_final: 0.8645 (tmm) REVERT: B 418 MET cc_start: 0.8969 (mmm) cc_final: 0.8394 (mmm) REVERT: B 466 MET cc_start: 0.8890 (mmm) cc_final: 0.8341 (mmm) REVERT: B 477 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (p) REVERT: B 481 ILE cc_start: 0.9461 (tp) cc_final: 0.9214 (tp) REVERT: B 694 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5370 (pm20) REVERT: C 323 MET cc_start: 0.8878 (mtp) cc_final: 0.8482 (ptp) REVERT: C 451 MET cc_start: 0.9023 (mtp) cc_final: 0.8675 (mmm) REVERT: C 491 MET cc_start: 0.8772 (ptm) cc_final: 0.8515 (ppp) REVERT: C 603 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8900 (tm-30) REVERT: C 614 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9352 (mp0) outliers start: 82 outliers final: 64 residues processed: 163 average time/residue: 0.2407 time to fit residues: 63.1156 Evaluate side-chains 155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 86 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 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 202 LEU 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 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 507 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 319 ARG 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 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 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: 0.9990 chunk 136 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.056899 restraints weight = 42076.915| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.52 r_work: 0.2542 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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: 0.8543 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16566 Z= 0.219 Angle : 0.537 9.806 22476 Z= 0.276 Chirality : 0.043 0.197 2633 Planarity : 0.004 0.056 2895 Dihedral : 13.013 103.455 2567 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.95 % Allowed : 22.32 % Favored : 72.73 % 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: 1.29 (0.19), residues: 2079 helix: 2.39 (0.20), residues: 679 sheet: 0.05 (0.25), residues: 462 loop : 0.24 (0.22), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.008 0.001 HIS B 487 PHE 0.018 0.001 PHE B 493 TYR 0.016 0.002 TYR A 380 ARG 0.005 0.000 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 743) hydrogen bonds : angle 4.18612 ( 2142) covalent geometry : bond 0.00499 (16563) covalent geometry : angle 0.53660 (22476) Misc. bond : bond 0.00171 ( 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 171 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 87 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.9046 (m-80) REVERT: A 323 MET cc_start: 0.8879 (mtp) cc_final: 0.8412 (ptp) REVERT: A 369 MET cc_start: 0.9207 (mmm) cc_final: 0.8586 (mmm) REVERT: A 415 MET cc_start: 0.9331 (ttm) cc_final: 0.9044 (tpp) REVERT: A 451 MET cc_start: 0.8910 (mtp) cc_final: 0.8575 (mmm) REVERT: A 603 GLU cc_start: 0.9526 (mm-30) cc_final: 0.8909 (tp30) REVERT: A 668 MET cc_start: 0.3253 (mmt) cc_final: 0.2724 (mmt) REVERT: B 167 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: B 369 MET cc_start: 0.9075 (mmm) cc_final: 0.8746 (mmm) REVERT: B 392 MET cc_start: 0.9091 (tpp) cc_final: 0.8857 (tpp) REVERT: B 418 MET cc_start: 0.8981 (mmm) cc_final: 0.8422 (mmm) REVERT: B 466 MET cc_start: 0.8962 (mmm) cc_final: 0.8530 (mmm) REVERT: B 477 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 481 ILE cc_start: 0.9504 (tp) cc_final: 0.9298 (tp) REVERT: B 694 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5344 (pm20) REVERT: C 323 MET cc_start: 0.8976 (mtp) cc_final: 0.8561 (ptp) REVERT: C 466 MET cc_start: 0.8899 (mmm) cc_final: 0.8003 (mmm) REVERT: C 491 MET cc_start: 0.8782 (ptm) cc_final: 0.8548 (ppp) REVERT: C 603 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8950 (tm-30) REVERT: C 614 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9397 (mp0) outliers start: 84 outliers final: 69 residues processed: 163 average time/residue: 0.2306 time to fit residues: 60.4616 Evaluate side-chains 161 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 88 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 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 287 THR 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 393 VAL 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 507 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 60 THR 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 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 81 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 154 optimal weight: 0.0270 chunk 61 optimal weight: 9.9990 overall best weight: 2.2644 ------------------------------------------------------------------------------- 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** ** C 349 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 = 0.3626 r_free = 0.3626 target = 0.097882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.056726 restraints weight = 42060.690| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 4.82 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16566 Z= 0.185 Angle : 0.515 9.315 22476 Z= 0.265 Chirality : 0.043 0.178 2633 Planarity : 0.004 0.055 2895 Dihedral : 12.790 104.037 2565 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.01 % Allowed : 22.38 % 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: 1.44 (0.19), residues: 2079 helix: 2.49 (0.20), residues: 679 sheet: 0.23 (0.25), residues: 458 loop : 0.28 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 233 HIS 0.008 0.001 HIS B 487 PHE 0.017 0.001 PHE B 493 TYR 0.014 0.001 TYR A 380 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 743) hydrogen bonds : angle 4.10723 ( 2142) covalent geometry : bond 0.00420 (16563) covalent geometry : angle 0.51550 (22476) Misc. bond : bond 0.00144 ( 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 172 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 87 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9256 (OUTLIER) cc_final: 0.9022 (m-80) REVERT: A 323 MET cc_start: 0.8681 (mtp) cc_final: 0.8189 (ptp) REVERT: A 369 MET cc_start: 0.9166 (mmm) cc_final: 0.8535 (mmm) REVERT: A 415 MET cc_start: 0.9176 (ttm) cc_final: 0.8910 (tpp) REVERT: A 451 MET cc_start: 0.8747 (mtp) cc_final: 0.8430 (mmm) REVERT: A 603 GLU cc_start: 0.9463 (mm-30) cc_final: 0.8809 (tp30) REVERT: A 668 MET cc_start: 0.2905 (mmt) cc_final: 0.2433 (mmt) REVERT: B 1 MET cc_start: 0.7853 (ppp) cc_final: 0.7610 (ppp) REVERT: B 167 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: B 369 MET cc_start: 0.8965 (mmm) cc_final: 0.8640 (mmm) REVERT: B 418 MET cc_start: 0.8762 (mmm) cc_final: 0.8147 (mmm) REVERT: B 466 MET cc_start: 0.8642 (mmm) cc_final: 0.8152 (mmm) REVERT: B 477 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 481 ILE cc_start: 0.9390 (tp) cc_final: 0.9168 (tp) REVERT: B 694 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5353 (pm20) REVERT: C 323 MET cc_start: 0.8775 (mtp) cc_final: 0.8335 (ptp) REVERT: C 451 MET cc_start: 0.8851 (mtp) cc_final: 0.8457 (mmm) REVERT: C 491 MET cc_start: 0.8647 (ptm) cc_final: 0.8268 (ppp) REVERT: C 603 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8863 (tm-30) REVERT: C 614 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9413 (mp0) outliers start: 85 outliers final: 65 residues processed: 163 average time/residue: 0.2434 time to fit residues: 63.5602 Evaluate side-chains 153 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 84 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 493 PHE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 533 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 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL 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 393 VAL 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 507 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 60 THR 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 140 LEU 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 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 425 VAL Chi-restraints excluded: chain C residue 443 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** C 349 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 = 0.3642 r_free = 0.3642 target = 0.098772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.055445 restraints weight = 42786.254| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 5.03 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16566 Z= 0.146 Angle : 0.524 11.538 22476 Z= 0.267 Chirality : 0.042 0.176 2633 Planarity : 0.004 0.054 2895 Dihedral : 12.591 104.324 2559 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.42 % Allowed : 23.26 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2079 helix: 2.56 (0.20), residues: 678 sheet: 0.30 (0.25), residues: 462 loop : 0.28 (0.22), residues: 939 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 0.019 0.001 PHE B 493 TYR 0.014 0.001 TYR A 68 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 743) hydrogen bonds : angle 4.03713 ( 2142) covalent geometry : bond 0.00331 (16563) covalent geometry : angle 0.52409 (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 163 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 88 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8814 (t80) REVERT: A 323 MET cc_start: 0.8682 (mtp) cc_final: 0.8185 (ptp) REVERT: A 369 MET cc_start: 0.9161 (mmm) cc_final: 0.8500 (mmm) REVERT: A 451 MET cc_start: 0.8710 (mtp) cc_final: 0.8437 (mmm) REVERT: A 603 GLU cc_start: 0.9469 (mm-30) cc_final: 0.8808 (tp30) REVERT: A 668 MET cc_start: 0.3393 (mmt) cc_final: 0.2933 (mmt) REVERT: B 167 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: B 369 MET cc_start: 0.8923 (mmm) cc_final: 0.8577 (mmm) REVERT: B 418 MET cc_start: 0.8791 (mmm) cc_final: 0.8207 (mmm) REVERT: B 451 MET cc_start: 0.9012 (mmm) cc_final: 0.8569 (tpt) REVERT: B 466 MET cc_start: 0.8336 (mmm) cc_final: 0.8085 (mtp) REVERT: B 477 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8384 (p) REVERT: B 481 ILE cc_start: 0.9407 (tp) cc_final: 0.9187 (tp) REVERT: B 694 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5454 (pm20) REVERT: C 323 MET cc_start: 0.8790 (mtp) cc_final: 0.8363 (ptp) REVERT: C 451 MET cc_start: 0.8794 (mtp) cc_final: 0.8466 (mmm) REVERT: C 466 MET cc_start: 0.8643 (mmm) cc_final: 0.7578 (mmm) REVERT: C 491 MET cc_start: 0.8628 (ptm) cc_final: 0.8246 (ppp) REVERT: C 603 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8884 (tm-30) outliers start: 75 outliers final: 62 residues processed: 154 average time/residue: 0.2455 time to fit residues: 60.3247 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 : 1.696 ------------------------------------------------------------------------------- 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 60 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 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 531 LEU Chi-restraints excluded: chain A residue 533 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 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 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 393 VAL 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 531 LEU 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 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 LEU 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 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 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 615 ILE 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: 0.9980 chunk 141 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.098234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.054479 restraints weight = 43090.664| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 5.09 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 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 = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2676 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= 0.200 Angle : 0.538 11.149 22476 Z= 0.276 Chirality : 0.043 0.176 2633 Planarity : 0.004 0.054 2895 Dihedral : 12.579 104.294 2559 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.36 % Allowed : 23.14 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.19), residues: 2079 helix: 2.56 (0.20), residues: 681 sheet: 0.36 (0.25), residues: 459 loop : 0.30 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 233 HIS 0.008 0.001 HIS B 487 PHE 0.018 0.001 PHE A 41 TYR 0.015 0.001 TYR A 380 ARG 0.007 0.000 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 743) hydrogen bonds : angle 4.06645 ( 2142) covalent geometry : bond 0.00455 (16563) covalent geometry : angle 0.53798 (22476) Misc. bond : bond 0.00120 ( 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 159 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 85 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8804 (t80) REVERT: A 323 MET cc_start: 0.8742 (mtp) cc_final: 0.8263 (ptp) REVERT: A 369 MET cc_start: 0.9199 (mmm) cc_final: 0.8563 (mmm) REVERT: A 451 MET cc_start: 0.8716 (mtp) cc_final: 0.8409 (mmm) REVERT: A 512 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 603 GLU cc_start: 0.9475 (mm-30) cc_final: 0.8832 (tp30) REVERT: B 167 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: B 369 MET cc_start: 0.8969 (mmm) cc_final: 0.8641 (mmm) REVERT: B 418 MET cc_start: 0.8843 (mmm) cc_final: 0.8275 (mmm) REVERT: B 451 MET cc_start: 0.9010 (mmm) cc_final: 0.8670 (tpt) REVERT: B 466 MET cc_start: 0.8396 (mmm) cc_final: 0.8128 (mtp) REVERT: B 477 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 694 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5365 (pm20) REVERT: C 323 MET cc_start: 0.8844 (mtp) cc_final: 0.8420 (ptp) REVERT: C 451 MET cc_start: 0.8829 (mtp) cc_final: 0.8478 (mmm) REVERT: C 491 MET cc_start: 0.8692 (ptm) cc_final: 0.8064 (ppp) REVERT: C 603 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8892 (tm-30) outliers start: 74 outliers final: 67 residues processed: 152 average time/residue: 0.2487 time to fit residues: 60.0840 Evaluate side-chains 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 85 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 337 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 469 VAL Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 533 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 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL 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 393 VAL 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 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 531 LEU 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 60 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 140 LEU 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 319 ARG Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 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 615 ILE 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: 3.9990 chunk 63 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 50.0000 chunk 181 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN C 298 HIS ** C 349 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 = 0.3662 r_free = 0.3662 target = 0.099617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.056410 restraints weight = 42697.960| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 5.08 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16566 Z= 0.109 Angle : 0.516 11.732 22476 Z= 0.263 Chirality : 0.043 0.452 2633 Planarity : 0.003 0.051 2895 Dihedral : 12.312 104.670 2555 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.24 % Allowed : 24.32 % Favored : 72.44 % 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: 1.67 (0.19), residues: 2079 helix: 2.63 (0.20), residues: 683 sheet: 0.57 (0.25), residues: 455 loop : 0.32 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 743) hydrogen bonds : angle 3.92400 ( 2142) covalent geometry : bond 0.00241 (16563) covalent geometry : angle 0.51588 (22476) Misc. bond : bond 0.00097 ( 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 143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8796 (t80) REVERT: A 323 MET cc_start: 0.8668 (mtp) cc_final: 0.8121 (ptp) REVERT: A 369 MET cc_start: 0.9101 (mmm) cc_final: 0.8494 (mmm) REVERT: A 451 MET cc_start: 0.8616 (mtp) cc_final: 0.8327 (mmm) REVERT: A 512 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 603 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8787 (tp30) REVERT: A 668 MET cc_start: 0.3651 (mmt) cc_final: 0.3420 (mmt) REVERT: B 167 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: B 360 ARG cc_start: 0.8979 (tmm-80) cc_final: 0.8768 (ttp-110) REVERT: B 369 MET cc_start: 0.8782 (mmm) cc_final: 0.8448 (mmm) REVERT: B 418 MET cc_start: 0.8817 (mmm) cc_final: 0.8247 (mmm) REVERT: B 451 MET cc_start: 0.8924 (mmm) cc_final: 0.8441 (tpt) REVERT: B 466 MET cc_start: 0.8327 (mmm) cc_final: 0.8033 (mtp) REVERT: B 477 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 481 ILE cc_start: 0.9298 (tt) cc_final: 0.9061 (tp) REVERT: B 694 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5416 (pm20) REVERT: C 323 MET cc_start: 0.8897 (mtp) cc_final: 0.8526 (ptp) REVERT: C 451 MET cc_start: 0.8733 (mtp) cc_final: 0.8459 (mmm) REVERT: C 466 MET cc_start: 0.8552 (mmm) cc_final: 0.7641 (mmm) REVERT: C 491 MET cc_start: 0.8589 (ptm) cc_final: 0.8191 (tmm) REVERT: C 603 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8925 (tm-30) outliers start: 55 outliers final: 44 residues processed: 137 average time/residue: 0.2433 time to fit residues: 53.1791 Evaluate side-chains 133 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 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 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 287 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 447 SER 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 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 149 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 319 ARG 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 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: 4.9990 chunk 149 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 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 = 0.3644 r_free = 0.3644 target = 0.098531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.055098 restraints weight = 43158.937| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 5.06 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16566 Z= 0.169 Angle : 0.525 11.179 22476 Z= 0.269 Chirality : 0.043 0.237 2633 Planarity : 0.004 0.051 2895 Dihedral : 12.287 104.417 2551 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.06 % Allowed : 24.26 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.19), residues: 2079 helix: 2.70 (0.20), residues: 683 sheet: 0.55 (0.25), residues: 459 loop : 0.37 (0.22), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 231 HIS 0.007 0.001 HIS B 487 PHE 0.016 0.001 PHE A 41 TYR 0.013 0.001 TYR A 380 ARG 0.005 0.000 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 743) hydrogen bonds : angle 3.94013 ( 2142) covalent geometry : bond 0.00386 (16563) covalent geometry : angle 0.52531 (22476) Misc. bond : bond 0.00093 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8204.59 seconds wall clock time: 141 minutes 3.82 seconds (8463.82 seconds total)