Starting phenix.real_space_refine on Thu Aug 6 16:50:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vah_43092/08_2026/8vah_43092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vah_43092/08_2026/8vah_43092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vah_43092/08_2026/8vah_43092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vah_43092/08_2026/8vah_43092.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vah_43092/08_2026/8vah_43092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vah_43092/08_2026/8vah_43092.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 3 5.21 5 S 66 5.16 5 C 10135 2.51 5 N 2880 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16307 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5306 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain: "B" Number of atoms: 5306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5306 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain: "C" Number of atoms: 5306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5306 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 28, 'TRANS': 666} Chain: "G" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 122 Inner-chain residues flagged as termini: ['pdbres=" A G 13 "'] Classifications: {'DNA': 2, 'RNA': 7} Modifications used: {'5*END': 2, 'rna2p_pur': 3, 'rna3p_pur': 4} Link IDs: {'rna2p': 3, 'rna3p': 5} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A%rna3p_pur:plan': 3, ' A%rna3p_pur:plan2': 3, ' A%rna2p_pur:plan': 3, ' A%rna2p_pur:plan2': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1' A G 13 " occ=0.30 ... (9 atoms not shown) pdb=" C4 A G 13 " occ=0.30 residue: pdb=" C1' A G 14 " occ=0.30 ... (9 atoms not shown) pdb=" C4 A G 14 " occ=0.30 residue: pdb=" P A D 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A D 2 " occ=0.30 residue: pdb=" P A E 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A E 2 " occ=0.30 residue: pdb=" P A F 2 " occ=0.30 ... (20 atoms not shown) pdb=" C4 A F 2 " occ=0.30 Time building chain proxies: 3.03, per 1000 atoms: 0.19 Number of scatterers: 16307 At special positions: 0 Unit cell: (110.816, 108.316, 149.143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 19 15.00 Mg 3 11.99 O 3204 8.00 N 2880 7.00 C 10135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 583.0 milliseconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3798 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 25 sheets defined 37.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 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: 2.45 Time building geometry restraints manager: 1.95 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 - 3.15: 22318 3.15 - 6.30: 149 6.30 - 9.46: 5 9.46 - 12.61: 2 12.61 - 15.76: 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 119.70 103.94 15.76 1.20e+00 6.94e-01 1.73e+02 angle pdb=" C3' C D 3 " pdb=" O3' C D 3 " pdb=" P A D 4 " ideal model delta sigma weight residual 119.70 105.43 14.27 1.20e+00 6.94e-01 1.41e+02 angle pdb=" C3' A D 2 " pdb=" O3' A D 2 " pdb=" P C D 3 " ideal model delta sigma weight residual 119.70 108.78 10.92 1.20e+00 6.94e-01 8.28e+01 angle pdb=" C3' C F 3 " pdb=" O3' C F 3 " pdb=" P A F 4 " ideal model delta sigma weight residual 119.70 109.28 10.42 1.20e+00 6.94e-01 7.54e+01 angle pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 119.70 113.36 6.34 1.20e+00 6.94e-01 2.80e+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: 2.010 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 16566 Z= 0.323 Angle : 0.737 15.762 22476 Z= 0.450 Chirality : 0.055 0.567 2633 Planarity : 0.004 0.056 2895 Dihedral : 19.419 99.711 6360 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 8.07 % Allowed : 15.72 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2079 helix: -0.18 (0.18), residues: 666 sheet: -1.64 (0.24), residues: 475 loop : -1.02 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 253 TYR 0.022 0.002 TYR A 385 PHE 0.027 0.002 PHE A 421 TRP 0.005 0.001 TRP A 233 HIS 0.014 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.32 (16563) covalent geometry : angle 0.73669 / 0.45 (22476) hydrogen bonds : bond 0.18110 / 12.10 ( 743) hydrogen bonds : angle 7.15568 / 5.01 ( 2142) Misc. bond : bond 0.04780 / 2.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 105 time to evaluate : 0.639 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: 0.8104 (tmm) REVERT: A 323 MET cc_start: 0.8517 (mtp) cc_final: 0.8302 (ptp) REVERT: A 597 ILE cc_start: 0.9426 (mt) cc_final: 0.9075 (mp) REVERT: A 668 MET cc_start: 0.1141 (mmt) cc_final: 0.0780 (mmt) REVERT: B 167 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: B 365 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9169 (pp) REVERT: C 190 GLU cc_start: 0.7746 (tt0) cc_final: 0.7507 (tp30) REVERT: C 506 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: C 563 ASP cc_start: 0.9040 (t0) cc_final: 0.8834 (t0) REVERT: C 603 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 611 ARG cc_start: 0.9606 (OUTLIER) cc_final: 0.8909 (tmt170) outliers start: 137 outliers final: 84 residues processed: 223 average time/residue: 0.1002 time to fit residues: 36.2755 Evaluate side-chains 183 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 95 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 613 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 GLN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.057690 restraints weight = 42833.256| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 5.05 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 23 (29 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16566 Z= 0.227 Angle : 0.625 10.058 22476 Z= 0.331 Chirality : 0.045 0.230 2633 Planarity : 0.005 0.053 2895 Dihedral : 15.008 98.242 2665 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 6.36 % Allowed : 19.26 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2079 helix: 1.16 (0.19), residues: 681 sheet: -1.00 (0.25), residues: 457 loop : -0.38 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 308 TYR 0.013 0.002 TYR C 380 PHE 0.032 0.002 PHE B 493 TRP 0.006 0.001 TRP C 233 HIS 0.015 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (16563) covalent geometry : angle 0.62500 / 0.33 (22476) hydrogen bonds : bond 0.05298 / 3.65 ( 743) hydrogen bonds : angle 5.21560 / 3.70 ( 2142) Misc. bond : bond 0.00324 / 0.16 ( 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 206 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 98 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: A 267 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.9090 (m-80) REVERT: A 323 MET cc_start: 0.8701 (mtp) cc_final: 0.8180 (ptp) REVERT: A 369 MET cc_start: 0.9171 (mmm) cc_final: 0.8440 (mmm) REVERT: A 493 PHE cc_start: 0.7075 (m-80) cc_final: 0.6853 (m-80) REVERT: A 623 ARG cc_start: 0.3096 (OUTLIER) cc_final: 0.2436 (ptm160) REVERT: A 668 MET cc_start: 0.2950 (mmt) cc_final: 0.2623 (mmt) REVERT: B 1 MET cc_start: 0.7708 (ppp) cc_final: 0.7447 (ppp) REVERT: B 167 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: B 365 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8162 (pp) REVERT: B 369 MET cc_start: 0.9007 (mmm) cc_final: 0.8732 (mmm) REVERT: B 392 MET cc_start: 0.8280 (tpp) cc_final: 0.8070 (tmm) REVERT: C 190 GLU cc_start: 0.8543 (tt0) cc_final: 0.8305 (tp30) REVERT: C 232 ASP cc_start: 0.8876 (p0) cc_final: 0.8661 (p0) REVERT: C 323 MET cc_start: 0.8543 (mtp) cc_final: 0.8030 (ptp) REVERT: C 418 MET cc_start: 0.8665 (ttm) cc_final: 0.8434 (tpp) REVERT: C 455 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9301 (m) REVERT: C 601 ASP cc_start: 0.8205 (p0) cc_final: 0.7877 (p0) REVERT: C 603 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8637 (tm-30) REVERT: C 611 ARG cc_start: 0.9505 (OUTLIER) cc_final: 0.8923 (tmt170) outliers start: 108 outliers final: 73 residues processed: 190 average time/residue: 0.1052 time to fit residues: 31.8323 Evaluate side-chains 171 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 91 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 607 HIS Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 199 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 164 ASN A 298 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062219 restraints weight = 43363.832| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.70 r_work: 0.2626 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 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 = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 17 (27 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16566 Z= 0.290 Angle : 0.607 9.541 22476 Z= 0.317 Chirality : 0.044 0.208 2633 Planarity : 0.004 0.054 2895 Dihedral : 14.066 99.277 2620 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.36 % Allowed : 20.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 2079 helix: 1.61 (0.19), residues: 679 sheet: -0.61 (0.25), residues: 462 loop : -0.13 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 611 TYR 0.018 0.002 TYR A 380 PHE 0.023 0.002 PHE B 493 TRP 0.005 0.001 TRP B 233 HIS 0.014 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.29 (16563) covalent geometry : angle 0.60663 / 0.32 (22476) hydrogen bonds : bond 0.04894 / 3.35 ( 743) hydrogen bonds : angle 4.82483 / 3.43 ( 2142) Misc. bond : bond 0.00244 / 0.12 ( 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 195 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 87 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9583 (OUTLIER) cc_final: 0.9304 (ptm) REVERT: A 194 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: A 267 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.9090 (m-80) REVERT: A 323 MET cc_start: 0.8796 (mtp) cc_final: 0.8294 (ptp) REVERT: A 369 MET cc_start: 0.9236 (mmm) cc_final: 0.8576 (mmm) REVERT: A 466 MET cc_start: 0.8219 (mtp) cc_final: 0.8006 (mtp) REVERT: A 493 PHE cc_start: 0.7498 (m-80) cc_final: 0.7282 (m-80) REVERT: A 668 MET cc_start: 0.2953 (mmt) cc_final: 0.2494 (mmt) REVERT: B 167 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 365 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8054 (pp) REVERT: B 369 MET cc_start: 0.9019 (mmm) cc_final: 0.8664 (mmm) REVERT: B 392 MET cc_start: 0.9072 (tpp) cc_final: 0.8516 (tmm) REVERT: B 477 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 694 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5193 (pm20) REVERT: C 232 ASP cc_start: 0.9232 (p0) cc_final: 0.8989 (p0) REVERT: C 451 MET cc_start: 0.9057 (mtp) cc_final: 0.8645 (mmm) REVERT: C 455 VAL cc_start: 0.9525 (OUTLIER) cc_final: 0.9238 (m) REVERT: C 603 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8851 (tm-30) outliers start: 108 outliers final: 63 residues processed: 184 average time/residue: 0.1043 time to fit residues: 31.0963 Evaluate side-chains 157 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 86 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 TYR Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 GLU 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 597 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 134 optimal weight: 50.0000 chunk 75 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 298 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** 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 = 0.3812 r_free = 0.3812 target = 0.101915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063637 restraints weight = 42293.198| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 4.61 r_work: 0.2662 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16566 Z= 0.136 Angle : 0.533 10.385 22476 Z= 0.279 Chirality : 0.043 0.186 2633 Planarity : 0.004 0.056 2895 Dihedral : 13.449 99.188 2579 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.83 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 2079 helix: 1.90 (0.20), residues: 684 sheet: -0.25 (0.25), residues: 460 loop : 0.02 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.014 0.001 TYR B 68 PHE 0.024 0.001 PHE B 493 TRP 0.002 0.000 TRP B 231 HIS 0.010 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16563) covalent geometry : angle 0.53275 / 0.28 (22476) hydrogen bonds : bond 0.04308 / 2.97 ( 743) hydrogen bonds : angle 4.50749 / 3.21 ( 2142) Misc. bond : bond 0.00250 / 0.12 ( 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 174 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 92 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9322 (ptm) REVERT: A 194 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: A 267 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.9059 (m-80) REVERT: A 323 MET cc_start: 0.8741 (mtp) cc_final: 0.8228 (ptp) REVERT: A 369 MET cc_start: 0.9130 (mmm) cc_final: 0.8499 (mmm) REVERT: A 399 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7261 (ttp80) REVERT: A 668 MET cc_start: 0.2878 (mmt) cc_final: 0.2426 (mmt) REVERT: B 1 MET cc_start: 0.7930 (ppp) cc_final: 0.7663 (ppp) REVERT: B 167 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: B 188 MET cc_start: 0.9422 (ttp) cc_final: 0.9151 (tmm) REVERT: B 365 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8014 (pp) REVERT: B 369 MET cc_start: 0.8975 (mmm) cc_final: 0.8662 (mmm) REVERT: B 418 MET cc_start: 0.8927 (mmm) cc_final: 0.8192 (mmm) REVERT: B 466 MET cc_start: 0.8598 (mmm) cc_final: 0.8129 (mmm) REVERT: B 694 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5221 (pm20) REVERT: C 232 ASP cc_start: 0.9230 (p0) cc_final: 0.8972 (p0) REVERT: C 323 MET cc_start: 0.8634 (mtp) cc_final: 0.8252 (ptp) REVERT: C 455 VAL cc_start: 0.9552 (OUTLIER) cc_final: 0.9271 (m) REVERT: C 491 MET cc_start: 0.8848 (ptm) cc_final: 0.8600 (ppp) REVERT: C 603 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8864 (tm-30) REVERT: C 611 ARG cc_start: 0.9434 (OUTLIER) cc_final: 0.9233 (tpt90) outliers start: 82 outliers final: 53 residues processed: 169 average time/residue: 0.1101 time to fit residues: 29.9794 Evaluate side-chains 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 87 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 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 399 ARG 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 533 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 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 149 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3817 r_free = 0.3817 target = 0.102060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064083 restraints weight = 42257.281| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.71 r_work: 0.2693 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16566 Z= 0.136 Angle : 0.509 10.383 22476 Z= 0.265 Chirality : 0.043 0.189 2633 Planarity : 0.004 0.054 2895 Dihedral : 13.103 99.281 2572 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.53 % Allowed : 21.79 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 2079 helix: 2.14 (0.20), residues: 685 sheet: 0.03 (0.25), residues: 458 loop : 0.08 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 399 TYR 0.013 0.001 TYR A 380 PHE 0.016 0.001 PHE B 493 TRP 0.002 0.000 TRP B 231 HIS 0.009 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16563) covalent geometry : angle 0.50888 / 0.27 (22476) hydrogen bonds : bond 0.03994 / 2.76 ( 743) hydrogen bonds : angle 4.28323 / 3.05 ( 2142) Misc. bond : bond 0.00221 / 0.11 ( 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 167 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 90 time to evaluate : 0.370 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: 0.9298 (OUTLIER) cc_final: 0.9055 (m-80) REVERT: A 323 MET cc_start: 0.8679 (mtp) cc_final: 0.8167 (ptp) REVERT: A 369 MET cc_start: 0.9094 (mmm) cc_final: 0.8467 (mmm) REVERT: A 466 MET cc_start: 0.8142 (mtp) cc_final: 0.7586 (mmm) REVERT: A 603 GLU cc_start: 0.9477 (mm-30) cc_final: 0.8895 (tp30) REVERT: A 668 MET cc_start: 0.2948 (mmt) cc_final: 0.2474 (mmt) REVERT: B 1 MET cc_start: 0.7957 (ppp) cc_final: 0.7679 (ppp) REVERT: B 167 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: B 171 LYS cc_start: 0.9661 (mtmt) cc_final: 0.9385 (mtmm) REVERT: B 188 MET cc_start: 0.9370 (ttp) cc_final: 0.9126 (tmm) REVERT: B 365 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7944 (pp) REVERT: B 369 MET cc_start: 0.8937 (mmm) cc_final: 0.8648 (mmm) REVERT: B 392 MET cc_start: 0.9018 (tpp) cc_final: 0.8545 (tmm) REVERT: B 466 MET cc_start: 0.8530 (mmm) cc_final: 0.8039 (mmm) REVERT: B 477 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 694 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5282 (pm20) REVERT: C 323 MET cc_start: 0.8656 (mtp) cc_final: 0.8242 (ptp) REVERT: C 451 MET cc_start: 0.8977 (mtp) cc_final: 0.8705 (mmm) REVERT: C 491 MET cc_start: 0.8771 (ptm) cc_final: 0.8517 (ppp) REVERT: C 603 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8894 (tm-30) outliers start: 77 outliers final: 58 residues processed: 161 average time/residue: 0.0970 time to fit residues: 25.3971 Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 88 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 33 VAL 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 149 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 16 optimal weight: 0.0570 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN A 164 ASN B 607 HIS ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS C 349 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.102732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062012 restraints weight = 42493.283| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.94 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16566 Z= 0.107 Angle : 0.502 10.430 22476 Z= 0.259 Chirality : 0.043 0.236 2633 Planarity : 0.003 0.053 2895 Dihedral : 12.848 99.390 2566 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.18 % Allowed : 22.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 2079 helix: 2.30 (0.20), residues: 687 sheet: 0.14 (0.26), residues: 456 loop : 0.15 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 308 TYR 0.012 0.001 TYR B 68 PHE 0.026 0.001 PHE B 493 TRP 0.002 0.000 TRP C 233 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16563) covalent geometry : angle 0.50160 / 0.26 (22476) hydrogen bonds : bond 0.03654 / 2.51 ( 743) hydrogen bonds : angle 4.11337 / 2.93 ( 2142) Misc. bond : bond 0.00168 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 90 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.9038 (m-80) REVERT: A 323 MET cc_start: 0.8514 (mtp) cc_final: 0.7878 (ptp) REVERT: A 369 MET cc_start: 0.9017 (mmm) cc_final: 0.8395 (mmm) REVERT: A 451 MET cc_start: 0.8552 (mtp) cc_final: 0.8262 (mmm) REVERT: A 466 MET cc_start: 0.7613 (mtp) cc_final: 0.7203 (mtp) REVERT: A 603 GLU cc_start: 0.9425 (mm-30) cc_final: 0.8843 (tp30) REVERT: A 668 MET cc_start: 0.2766 (mmt) cc_final: 0.2333 (mmt) REVERT: B 1 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7464 (ppp) REVERT: B 167 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: B 171 LYS cc_start: 0.9617 (mtmt) cc_final: 0.9318 (mtmm) REVERT: B 188 MET cc_start: 0.9181 (ttp) cc_final: 0.8925 (tmm) REVERT: B 365 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7607 (pp) REVERT: B 369 MET cc_start: 0.8836 (mmm) cc_final: 0.8488 (mmm) REVERT: B 392 MET cc_start: 0.8415 (tpp) cc_final: 0.8138 (tmm) REVERT: B 418 MET cc_start: 0.8632 (mmm) cc_final: 0.7874 (mmm) REVERT: B 477 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 694 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5331 (pm20) REVERT: C 323 MET cc_start: 0.8516 (mtp) cc_final: 0.8087 (ptp) REVERT: C 440 MET cc_start: 0.8557 (mmp) cc_final: 0.7850 (mmp) REVERT: C 451 MET cc_start: 0.8725 (mtp) cc_final: 0.8395 (mmm) REVERT: C 491 MET cc_start: 0.8507 (ptm) cc_final: 0.8231 (ppp) REVERT: C 603 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8820 (tm-30) REVERT: C 614 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9350 (mp0) outliers start: 71 outliers final: 51 residues processed: 155 average time/residue: 0.1085 time to fit residues: 26.9611 Evaluate side-chains 144 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 87 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 164 ASN 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 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 47 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.100407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062745 restraints weight = 42220.155| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.58 r_work: 0.2645 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16566 Z= 0.284 Angle : 0.572 9.119 22476 Z= 0.295 Chirality : 0.043 0.201 2633 Planarity : 0.004 0.052 2895 Dihedral : 12.784 98.865 2563 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.30 % Allowed : 22.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 2079 helix: 2.35 (0.20), residues: 685 sheet: 0.10 (0.25), residues: 459 loop : 0.23 (0.22), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 399 TYR 0.019 0.002 TYR A 380 PHE 0.013 0.001 PHE A 41 TRP 0.004 0.001 TRP B 233 HIS 0.009 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (16563) covalent geometry : angle 0.57188 / 0.29 (22476) hydrogen bonds : bond 0.04067 / 2.78 ( 743) hydrogen bonds : angle 4.23781 / 3.01 ( 2142) Misc. bond : bond 0.00155 / 0.08 ( 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 157 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 84 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.9049 (m-80) REVERT: A 323 MET cc_start: 0.8788 (mtp) cc_final: 0.8304 (ptp) REVERT: A 369 MET cc_start: 0.9153 (mmm) cc_final: 0.8528 (mmm) REVERT: A 451 MET cc_start: 0.8843 (mtp) cc_final: 0.8535 (mmm) REVERT: A 603 GLU cc_start: 0.9503 (mm-30) cc_final: 0.8901 (tp30) REVERT: A 668 MET cc_start: 0.3193 (mmt) cc_final: 0.2683 (mmt) REVERT: B 1 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7794 (ppp) REVERT: B 167 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: B 369 MET cc_start: 0.8985 (mmm) cc_final: 0.8663 (mmm) REVERT: B 392 MET cc_start: 0.9065 (tpp) cc_final: 0.8833 (tpp) REVERT: B 418 MET cc_start: 0.8968 (mmm) cc_final: 0.8318 (mmm) REVERT: B 451 MET cc_start: 0.9158 (tpt) cc_final: 0.8884 (tpt) REVERT: B 694 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5357 (pm20) REVERT: C 323 MET cc_start: 0.8718 (mtp) cc_final: 0.8242 (ptp) REVERT: C 451 MET cc_start: 0.9035 (mtp) cc_final: 0.8647 (mmm) REVERT: C 491 MET cc_start: 0.8725 (ptm) cc_final: 0.8482 (ppp) REVERT: C 603 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8922 (tm-30) REVERT: C 614 GLU cc_start: 0.9659 (mm-30) cc_final: 0.9392 (mp0) outliers start: 73 outliers final: 61 residues processed: 148 average time/residue: 0.0996 time to fit residues: 24.1417 Evaluate side-chains 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 84 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 THR Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 477 VAL 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 537 MET Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 200 optimal weight: 0.0570 chunk 159 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.060157 restraints weight = 42452.321| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.53 r_work: 0.2700 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16566 Z= 0.109 Angle : 0.501 10.015 22476 Z= 0.258 Chirality : 0.043 0.196 2633 Planarity : 0.003 0.052 2895 Dihedral : 12.577 99.489 2563 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.42 % Allowed : 24.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.19), residues: 2079 helix: 2.57 (0.20), residues: 680 sheet: 0.30 (0.26), residues: 455 loop : 0.23 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 308 TYR 0.015 0.001 TYR A 68 PHE 0.021 0.001 PHE B 493 TRP 0.002 0.000 TRP C 233 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16563) covalent geometry : angle 0.50060 / 0.26 (22476) hydrogen bonds : bond 0.03650 / 2.51 ( 743) hydrogen bonds : angle 4.04451 / 2.87 ( 2142) Misc. bond : bond 0.00139 / 0.07 ( 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 144 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 86 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.9043 (m-80) REVERT: A 323 MET cc_start: 0.8848 (mtp) cc_final: 0.8249 (ptp) REVERT: A 369 MET cc_start: 0.9110 (mmm) cc_final: 0.8520 (mmm) REVERT: A 603 GLU cc_start: 0.9481 (mm-30) cc_final: 0.8873 (tp30) REVERT: A 668 MET cc_start: 0.3298 (mmt) cc_final: 0.2796 (mmt) REVERT: B 1 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7815 (ppp) REVERT: B 167 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: B 171 LYS cc_start: 0.9690 (mtmt) cc_final: 0.9424 (mtmm) REVERT: B 369 MET cc_start: 0.8942 (mmm) cc_final: 0.8646 (mmm) REVERT: B 392 MET cc_start: 0.9042 (tpp) cc_final: 0.8596 (tmm) REVERT: B 694 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5386 (pm20) REVERT: C 323 MET cc_start: 0.8881 (mtp) cc_final: 0.8461 (ptp) REVERT: C 451 MET cc_start: 0.8988 (mtp) cc_final: 0.8764 (mmm) REVERT: C 603 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8884 (tm-30) REVERT: C 614 GLU cc_start: 0.9645 (mm-30) cc_final: 0.9398 (mp0) outliers start: 58 outliers final: 47 residues processed: 138 average time/residue: 0.0956 time to fit residues: 21.4561 Evaluate side-chains 134 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 83 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 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 477 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.100508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.056909 restraints weight = 42769.782| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 5.08 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2479 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= 0.104 Angle : 0.505 11.675 22476 Z= 0.255 Chirality : 0.042 0.189 2633 Planarity : 0.003 0.048 2895 Dihedral : 12.420 99.416 2562 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.36 % Allowed : 23.97 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2079 helix: 2.65 (0.20), residues: 680 sheet: 0.42 (0.26), residues: 451 loop : 0.23 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 545 TYR 0.014 0.001 TYR A 68 PHE 0.021 0.001 PHE B 493 TRP 0.003 0.000 TRP C 233 HIS 0.007 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (16563) covalent geometry : angle 0.50539 / 0.25 (22476) hydrogen bonds : bond 0.03466 / 2.38 ( 743) hydrogen bonds : angle 3.97190 / 2.81 ( 2142) Misc. bond : bond 0.00119 / 0.06 ( 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 143 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 86 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8619 (mtp) cc_final: 0.8038 (ptp) REVERT: A 369 MET cc_start: 0.9079 (mmm) cc_final: 0.8424 (mmm) REVERT: A 603 GLU cc_start: 0.9431 (mm-30) cc_final: 0.8784 (tp30) REVERT: A 668 MET cc_start: 0.3204 (mmt) cc_final: 0.2792 (mmt) REVERT: B 167 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: B 171 LYS cc_start: 0.9645 (mtmt) cc_final: 0.9354 (mtmm) REVERT: B 369 MET cc_start: 0.8766 (mmm) cc_final: 0.8442 (mmm) REVERT: B 694 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5475 (pm20) REVERT: C 323 MET cc_start: 0.8686 (mtp) cc_final: 0.8245 (ptp) REVERT: C 451 MET cc_start: 0.8736 (mtp) cc_final: 0.8442 (mmm) REVERT: C 466 MET cc_start: 0.8487 (mmm) cc_final: 0.7389 (mmm) REVERT: C 603 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8861 (tm-30) REVERT: C 614 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9409 (mp0) outliers start: 57 outliers final: 50 residues processed: 137 average time/residue: 0.0879 time to fit residues: 19.3253 Evaluate side-chains 137 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 85 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 477 VAL 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 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 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 488 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 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 137 optimal weight: 50.0000 chunk 191 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 206 optimal weight: 0.3980 chunk 156 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.056933 restraints weight = 42552.095| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.88 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16566 Z= 0.127 Angle : 0.512 12.920 22476 Z= 0.257 Chirality : 0.042 0.186 2633 Planarity : 0.003 0.047 2895 Dihedral : 12.338 99.118 2560 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.06 % Allowed : 24.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 2079 helix: 2.73 (0.20), residues: 679 sheet: 0.53 (0.26), residues: 453 loop : 0.26 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.013 0.001 TYR A 68 PHE 0.034 0.001 PHE B 493 TRP 0.002 0.000 TRP C 233 HIS 0.007 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16563) covalent geometry : angle 0.51156 / 0.26 (22476) hydrogen bonds : bond 0.03437 / 2.36 ( 743) hydrogen bonds : angle 3.93235 / 2.78 ( 2142) Misc. bond : bond 0.00104 / 0.05 ( 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 139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 87 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9002 (m) REVERT: A 267 TYR cc_start: 0.8924 (m-80) cc_final: 0.8393 (m-10) REVERT: A 323 MET cc_start: 0.8685 (mtp) cc_final: 0.8110 (ptp) REVERT: A 369 MET cc_start: 0.9065 (mmm) cc_final: 0.8411 (mmm) REVERT: A 451 MET cc_start: 0.8742 (tpt) cc_final: 0.8427 (mmm) REVERT: A 512 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 603 GLU cc_start: 0.9443 (mm-30) cc_final: 0.8813 (tp30) REVERT: A 668 MET cc_start: 0.3030 (mmt) cc_final: 0.2611 (mmt) REVERT: B 167 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: B 369 MET cc_start: 0.8751 (mmm) cc_final: 0.8453 (mmm) REVERT: B 694 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5382 (pm20) REVERT: C 323 MET cc_start: 0.8694 (mtp) cc_final: 0.8299 (ptp) REVERT: C 451 MET cc_start: 0.8741 (mtp) cc_final: 0.8419 (mmm) REVERT: C 466 MET cc_start: 0.8323 (mmm) cc_final: 0.7729 (mtp) REVERT: C 603 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8883 (tm-30) REVERT: C 614 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9428 (mp0) outliers start: 52 outliers final: 47 residues processed: 135 average time/residue: 0.0923 time to fit residues: 20.2168 Evaluate side-chains 136 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 477 VAL 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 615 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 202 optimal weight: 0.0770 chunk 140 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059513 restraints weight = 41760.131| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.55 r_work: 0.2588 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16566 Z= 0.103 Angle : 0.500 11.843 22476 Z= 0.251 Chirality : 0.042 0.183 2633 Planarity : 0.003 0.046 2895 Dihedral : 12.261 99.095 2559 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.12 % Allowed : 24.32 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 2079 helix: 2.78 (0.20), residues: 679 sheet: 0.64 (0.25), residues: 451 loop : 0.27 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.012 0.001 TYR A 68 PHE 0.017 0.001 PHE A 41 TRP 0.002 0.000 TRP C 233 HIS 0.006 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (16563) covalent geometry : angle 0.49956 / 0.25 (22476) hydrogen bonds : bond 0.03287 / 2.25 ( 743) hydrogen bonds : angle 3.86943 / 2.73 ( 2142) Misc. bond : bond 0.00092 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.20 seconds wall clock time: 66 minutes 30.18 seconds (3990.18 seconds total)