Starting phenix.real_space_refine on Thu Aug 6 17:20:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vak_43093/08_2026/8vak_43093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vak_43093/08_2026/8vak_43093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vak_43093/08_2026/8vak_43093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vak_43093/08_2026/8vak_43093.map" model { file = "/net/cci-nas-00/data/ceres_data/8vak_43093/08_2026/8vak_43093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vak_43093/08_2026/8vak_43093.cif" } resolution = 3.3 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 66 5.16 5 C 10135 2.51 5 N 2880 2.21 5 O 3210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 residue(s): 0.02s 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: 16310 Number of models: 1 Model: "" Number of chains: 10 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Classifications: {'RNA': 2} Modifications used: {'rna2p': 1, 'rna3p': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Classifications: {'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Classifications: {'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Residues with excluded nonbonded symmetry interactions: 2 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 Time building chain proxies: 2.69, per 1000 atoms: 0.16 Number of scatterers: 16310 At special positions: 0 Unit cell: (142.88, 111.86, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 19 15.00 O 3210 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 744.4 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: 53 helices and 26 sheets defined 37.9% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 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: 4.534A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.725A pdb=" N LYS A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 227 removed outlier: 4.344A pdb=" N VAL A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 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: 3.739A pdb=" N LEU A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.625A 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 removed outlier: 3.571A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 4.151A pdb=" N HIS A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 541 removed outlier: 3.676A pdb=" N MET A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.923A 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: 4.025A pdb=" N VAL A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) removed outlier: 4.044A 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: 3.666A pdb=" N ILE A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 removed outlier: 3.516A pdb=" N ASP A 664 " --> pdb=" O LYS A 661 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 665 " --> pdb=" O VAL A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 661 through 665' Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.727A 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: 4.501A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.765A 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: 5.041A pdb=" N VAL B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 260 removed outlier: 4.134A pdb=" N LEU B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 3.563A pdb=" N ARG B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 312 Processing helix chain 'B' and resid 397 through 412 removed outlier: 3.809A 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 482 through 489 removed outlier: 4.003A pdb=" N HIS B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.510A pdb=" N MET B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.710A 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 584 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: 4.077A 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: 4.381A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.837A pdb=" N GLU C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 227 removed outlier: 5.101A pdb=" N VAL C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.705A pdb=" N LEU C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.703A 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: 3.541A pdb=" N ALA C 362 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 413 removed outlier: 3.937A pdb=" N ARG C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 454 removed outlier: 3.534A pdb=" N ALA C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.512A pdb=" N LEU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.831A pdb=" N ALA C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 541 " --> pdb=" O MET C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 570 removed outlier: 3.956A 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: 3.960A pdb=" N ILE C 615 " --> pdb=" O ARG C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 695 removed outlier: 4.466A 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: 3.551A pdb=" N GLU A 19 " --> pdb=" O MET A 32 " (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: 3.533A pdb=" N ALA A 350 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 433 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 351 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE A 431 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 353 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER A 429 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR A 355 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 427 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.797A 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: 3.642A 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: 3.661A pdb=" N LEU A 478 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.730A pdb=" N THR A 630 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE A 638 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 632 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 7.765A 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 'A' and resid 647 through 648 removed outlier: 3.987A pdb=" N LEU A 648 " --> pdb=" O ILE A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 5 through 10 removed outlier: 6.659A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 5 through 10 removed outlier: 6.659A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.789A pdb=" N GLY B 150 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB5, first strand: chain 'B' and resid 327 through 331 removed outlier: 3.536A pdb=" N ARG B 330 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 8.118A 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 365 Processing sheet with id=AB7, first strand: chain 'B' and resid 462 through 464 removed outlier: 3.520A pdb=" N ALA B 462 " --> pdb=" O GLY B 497 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 462 through 464 removed outlier: 3.520A pdb=" N ALA B 462 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 506 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 554 through 559 removed outlier: 3.636A pdb=" N ALA B 598 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.640A pdb=" N GLU C 19 " --> pdb=" O MET C 32 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 60 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.640A pdb=" N GLU C 19 " --> pdb=" O MET C 32 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE C 41 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL C 117 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR C 43 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA C 115 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN C 64 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER C 119 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.506A pdb=" N GLY C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 327 through 331 removed outlier: 3.735A pdb=" N GLU C 433 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 351 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE C 431 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR C 353 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER C 429 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR C 355 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 427 " --> pdb=" O THR C 355 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 363 through 366 Processing sheet with id=AC6, first strand: chain 'C' and resid 474 through 479 removed outlier: 3.624A pdb=" N ALA C 462 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 495 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 554 through 559 removed outlier: 3.559A pdb=" N ALA C 599 " --> pdb=" O ARG C 554 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 631 through 633 removed outlier: 4.910A pdb=" N ARG C 631 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 638 " --> pdb=" O ARG C 631 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2187 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: 2.83 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2848 1.31 - 1.43: 3854 1.43 - 1.56: 9707 1.56 - 1.68: 31 1.68 - 1.81: 129 Bond restraints: 16569 Sorted by residual: bond pdb=" C PRO A 148 " pdb=" O PRO A 148 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.14e-02 7.69e+03 2.21e+01 bond pdb=" C PRO B 148 " pdb=" O PRO B 148 " ideal model delta sigma weight residual 1.234 1.185 0.048 1.14e-02 7.69e+03 1.79e+01 bond pdb=" C PRO C 148 " pdb=" O PRO C 148 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.14e-02 7.69e+03 1.70e+01 bond pdb=" N PRO B 148 " pdb=" CA PRO B 148 " ideal model delta sigma weight residual 1.466 1.427 0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ILE A 149 " pdb=" CA ILE A 149 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.00e+01 ... (remaining 16564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 22183 2.78 - 5.56: 274 5.56 - 8.34: 25 8.34 - 11.12: 4 11.12 - 13.91: 2 Bond angle restraints: 22488 Sorted by residual: angle pdb=" C3' 8GM E 4 " pdb=" O3' 8GM E 4 " pdb=" P 8GM E 5 " ideal model delta sigma weight residual 119.70 105.79 13.91 1.20e+00 6.94e-01 1.34e+02 angle pdb=" C3' C D 2 " pdb=" O3' C D 2 " pdb=" P A D 3 " ideal model delta sigma weight residual 119.70 106.88 12.82 1.20e+00 6.94e-01 1.14e+02 angle pdb=" C3' C F 2 " pdb=" O3' C F 2 " pdb=" P A F 3 " ideal model delta sigma weight residual 119.70 108.88 10.82 1.20e+00 6.94e-01 8.14e+01 angle pdb=" C3' 8GM D 4 " pdb=" O3' 8GM D 4 " pdb=" P 8GM D 5 " ideal model delta sigma weight residual 119.70 110.44 9.26 1.20e+00 6.94e-01 5.95e+01 angle pdb=" C3' C E 2 " pdb=" O3' C E 2 " pdb=" P A E 3 " ideal model delta sigma weight residual 119.70 110.50 9.20 1.20e+00 6.94e-01 5.88e+01 ... (remaining 22483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 9063 24.05 - 48.09: 873 48.09 - 72.14: 218 72.14 - 96.18: 48 96.18 - 120.23: 4 Dihedral angle restraints: 10206 sinusoidal: 4287 harmonic: 5919 Sorted by residual: dihedral pdb=" C2' 8GM D 5 " pdb=" C3' 8GM D 5 " pdb=" C4' 8GM D 5 " pdb=" O4' 8GM D 5 " ideal model delta sinusoidal sigma weight residual 24.00 -34.87 58.87 1 8.00e+00 1.56e-02 7.24e+01 dihedral pdb=" O4' C F 2 " pdb=" C1' C F 2 " pdb=" N1 C F 2 " pdb=" C2 C F 2 " ideal model delta sinusoidal sigma weight residual 200.00 79.77 120.23 1 1.50e+01 4.44e-03 6.41e+01 dihedral pdb=" C1' 8GM D 5 " pdb=" C2' 8GM D 5 " pdb=" C3' 8GM D 5 " pdb=" C4' 8GM D 5 " ideal model delta sinusoidal sigma weight residual -35.00 20.07 -55.07 1 8.00e+00 1.56e-02 6.41e+01 ... (remaining 10203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2533 0.112 - 0.224: 87 0.224 - 0.336: 4 0.336 - 0.448: 3 0.448 - 0.559: 3 Chirality restraints: 2630 Sorted by residual: chirality pdb=" P C D 2 " pdb=" OP1 C D 2 " pdb=" OP2 C D 2 " pdb=" O5' C D 2 " both_signs ideal model delta sigma weight residual True 2.41 2.97 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" P C F 2 " pdb=" OP1 C F 2 " pdb=" OP2 C F 2 " pdb=" O5' C F 2 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" P C E 2 " pdb=" OP1 C E 2 " pdb=" OP2 C E 2 " pdb=" O5' C E 2 " both_signs ideal model delta sigma weight residual True 2.41 2.95 -0.54 2.00e-01 2.50e+01 7.28e+00 ... (remaining 2627 not shown) Planarity restraints: 2895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 208 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C GLY A 208 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY A 208 " -0.027 2.00e-02 2.50e+03 pdb=" N HIS A 209 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 144 " 0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO C 144 " -0.071 2.00e-02 2.50e+03 pdb=" O PRO C 144 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE C 145 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 144 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C PRO A 144 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO A 144 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 145 " -0.020 2.00e-02 2.50e+03 ... (remaining 2892 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 116 2.49 - 3.09: 12472 3.09 - 3.69: 24758 3.69 - 4.30: 33809 4.30 - 4.90: 56485 Nonbonded interactions: 127640 Sorted by model distance: nonbonded pdb=" NH2 ARG C 93 " pdb=" OP1 8GM F 4 " model vdw 1.887 2.496 nonbonded pdb=" OE2 GLU B 430 " pdb=" OH TYR C 68 " model vdw 2.095 3.040 nonbonded pdb=" OH TYR C 258 " pdb=" OE2 GLU C 301 " model vdw 2.177 3.040 nonbonded pdb=" O SER C 429 " pdb=" OG SER C 429 " model vdw 2.189 3.040 nonbonded pdb=" O THR C 424 " pdb=" OG1 THR C 424 " model vdw 2.204 3.040 ... (remaining 127635 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.010 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.012 0.775 16576 Z= 0.971 Angle : 0.804 13.906 22488 Z= 0.493 Chirality : 0.055 0.559 2630 Planarity : 0.005 0.056 2895 Dihedral : 19.958 120.231 6408 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 8.89 % Allowed : 16.37 % Favored : 74.73 % 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: -1.71 (0.17), residues: 2079 helix: -0.26 (0.18), residues: 670 sheet: -1.93 (0.23), residues: 486 loop : -1.18 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 306 TYR 0.019 0.002 TYR A 385 PHE 0.016 0.002 PHE A 145 TRP 0.005 0.001 TRP C 231 HIS 0.008 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.36 (16569) covalent geometry : angle 0.80442 / 0.49 (22488) hydrogen bonds : bond 0.18384 / 11.89 ( 739) hydrogen bonds : angle 7.34516 / 5.24 ( 2187) Misc. bond : bond 0.43953 / 22.04 ( 7) *********************** 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 224 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 73 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8638 (ptp) REVERT: A 274 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7984 (pptt) REVERT: A 414 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9320 (p) REVERT: A 493 PHE cc_start: 0.7573 (m-80) cc_final: 0.7177 (m-80) REVERT: A 623 ARG cc_start: 0.2345 (OUTLIER) cc_final: 0.2019 (ptt180) REVERT: B 176 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 191 SER cc_start: 0.9176 (m) cc_final: 0.8957 (p) REVERT: B 369 MET cc_start: 0.8869 (mmm) cc_final: 0.8299 (mmm) REVERT: B 466 MET cc_start: 0.8660 (mmm) cc_final: 0.8447 (mmp) REVERT: B 486 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8295 (p0) REVERT: B 668 MET cc_start: 0.5355 (mmp) cc_final: 0.5135 (mmp) REVERT: C 323 MET cc_start: 0.8382 (mtp) cc_final: 0.8157 (mtp) REVERT: C 369 MET cc_start: 0.8529 (mmm) cc_final: 0.7853 (mmm) REVERT: C 566 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8906 (tptp) REVERT: C 629 VAL cc_start: 0.3772 (OUTLIER) cc_final: 0.3530 (p) REVERT: C 668 MET cc_start: 0.7772 (mmp) cc_final: 0.7387 (mmp) outliers start: 151 outliers final: 93 residues processed: 213 average time/residue: 0.0967 time to fit residues: 32.9550 Evaluate side-chains 172 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 71 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS 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 33 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 274 LYS 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 414 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 ASP 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 507 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 434 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 629 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 403 HIS A 506 GLN B 200 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 653 GLN ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.087860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050523 restraints weight = 52424.438| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 5.03 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 16 (22 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16576 Z= 0.245 Angle : 0.656 10.507 22488 Z= 0.352 Chirality : 0.046 0.304 2630 Planarity : 0.005 0.051 2895 Dihedral : 16.152 125.408 2728 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 6.48 % Allowed : 19.61 % 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: -0.34 (0.18), residues: 2079 helix: 1.03 (0.19), residues: 688 sheet: -1.15 (0.24), residues: 480 loop : -0.55 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 360 TYR 0.014 0.002 TYR C 385 PHE 0.014 0.001 PHE A 41 TRP 0.004 0.001 TRP C 231 HIS 0.010 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (16569) covalent geometry : angle 0.65621 / 0.35 (22488) hydrogen bonds : bond 0.05708 / 3.77 ( 739) hydrogen bonds : angle 5.43057 / 3.89 ( 2187) Misc. bond : bond 0.00789 / 0.40 ( 7) *********************** 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 185 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 75 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8502 (ptm) REVERT: A 188 MET cc_start: 0.8502 (tmm) cc_final: 0.7864 (tmm) REVERT: A 414 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9154 (p) REVERT: A 506 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: B 176 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8214 (p0) REVERT: B 191 SER cc_start: 0.9350 (m) cc_final: 0.9060 (p) REVERT: B 369 MET cc_start: 0.8580 (mmm) cc_final: 0.7995 (mmm) REVERT: B 399 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7706 (ptm160) REVERT: B 435 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8040 (t0) REVERT: C 323 MET cc_start: 0.8083 (mtp) cc_final: 0.7761 (mtp) REVERT: C 358 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8676 (t) REVERT: C 369 MET cc_start: 0.8652 (mmm) cc_final: 0.7896 (mmm) REVERT: C 430 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: C 451 MET cc_start: 0.9162 (mmm) cc_final: 0.8836 (tpt) REVERT: C 455 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9120 (m) REVERT: C 566 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9032 (tptt) REVERT: C 629 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7297 (p) outliers start: 110 outliers final: 68 residues processed: 176 average time/residue: 0.1084 time to fit residues: 31.3515 Evaluate side-chains 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 77 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain A residue 108 VAL 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 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 249 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 414 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 187 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 393 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 164 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 131 optimal weight: 0.0970 chunk 23 optimal weight: 0.3980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 164 ASN A 349 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS C 212 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.087221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051205 restraints weight = 51934.580| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.83 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (17 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16576 Z= 0.151 Angle : 0.569 7.243 22488 Z= 0.301 Chirality : 0.045 0.201 2630 Planarity : 0.004 0.053 2895 Dihedral : 15.451 133.805 2668 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.54 % Allowed : 21.85 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.19), residues: 2079 helix: 1.56 (0.20), residues: 690 sheet: -0.67 (0.25), residues: 471 loop : -0.25 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.015 0.002 TYR B 68 PHE 0.024 0.001 PHE B 41 TRP 0.003 0.001 TRP C 231 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16569) covalent geometry : angle 0.56924 / 0.30 (22488) hydrogen bonds : bond 0.04864 / 3.24 ( 739) hydrogen bonds : angle 4.86882 / 3.48 ( 2187) Misc. bond : bond 0.00614 / 0.33 ( 7) *********************** 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 173 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 79 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8762 (ttp) cc_final: 0.8412 (ptm) REVERT: A 23 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8659 (ptm) REVERT: A 164 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8966 (m-40) REVERT: A 188 MET cc_start: 0.8461 (tmm) cc_final: 0.7906 (tmm) REVERT: A 360 ARG cc_start: 0.8865 (tmm-80) cc_final: 0.8552 (ttp80) REVERT: A 392 MET cc_start: 0.8028 (tmm) cc_final: 0.7807 (tmm) REVERT: A 418 MET cc_start: 0.9213 (tpt) cc_final: 0.9010 (tpt) REVERT: B 1 MET cc_start: 0.7507 (ppp) cc_final: 0.7149 (ppp) REVERT: B 176 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8346 (p0) REVERT: B 191 SER cc_start: 0.9321 (m) cc_final: 0.9113 (p) REVERT: B 369 MET cc_start: 0.8550 (mmm) cc_final: 0.7972 (mmm) REVERT: B 399 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7712 (ptm160) REVERT: B 507 MET cc_start: 0.7861 (ptp) cc_final: 0.7652 (ptp) REVERT: C 175 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8462 (tp) REVERT: C 323 MET cc_start: 0.8139 (mtp) cc_final: 0.7731 (mtp) REVERT: C 348 THR cc_start: 0.9748 (OUTLIER) cc_final: 0.9419 (p) REVERT: C 358 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8706 (t) REVERT: C 369 MET cc_start: 0.8685 (mmm) cc_final: 0.7924 (mmm) REVERT: C 430 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: C 451 MET cc_start: 0.9148 (mmm) cc_final: 0.8798 (tpt) REVERT: C 466 MET cc_start: 0.8110 (mtp) cc_final: 0.7836 (mtt) REVERT: C 566 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9049 (tptt) outliers start: 94 outliers final: 61 residues processed: 167 average time/residue: 0.0972 time to fit residues: 26.9230 Evaluate side-chains 145 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 75 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 VAL 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 374 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 187 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 393 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 662 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 200 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.085813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.049804 restraints weight = 52299.342| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.89 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16576 Z= 0.240 Angle : 0.581 9.764 22488 Z= 0.304 Chirality : 0.044 0.169 2630 Planarity : 0.004 0.053 2895 Dihedral : 15.003 138.605 2648 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.83 % Allowed : 22.26 % Favored : 71.91 % 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: 0.63 (0.19), residues: 2079 helix: 1.78 (0.20), residues: 690 sheet: -0.49 (0.25), residues: 482 loop : -0.01 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.014 0.002 TYR A 380 PHE 0.018 0.001 PHE B 41 TRP 0.004 0.001 TRP A 231 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (16569) covalent geometry : angle 0.58077 / 0.30 (22488) hydrogen bonds : bond 0.04700 / 3.14 ( 739) hydrogen bonds : angle 4.73513 / 3.36 ( 2187) Misc. bond : bond 0.00207 / 0.10 ( 7) *********************** 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 173 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 74 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8848 (ttp) cc_final: 0.8355 (ptm) REVERT: A 23 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8746 (ptm) REVERT: A 164 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8932 (m110) REVERT: A 188 MET cc_start: 0.8549 (tmm) cc_final: 0.7959 (tmm) REVERT: A 392 MET cc_start: 0.8155 (tmm) cc_final: 0.7946 (tmm) REVERT: A 415 MET cc_start: 0.8966 (mtp) cc_final: 0.8734 (mtp) REVERT: A 451 MET cc_start: 0.9118 (ttm) cc_final: 0.8723 (mtp) REVERT: B 1 MET cc_start: 0.7583 (ppp) cc_final: 0.7140 (ppp) REVERT: B 94 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8873 (tm) REVERT: B 176 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8441 (p0) REVERT: B 369 MET cc_start: 0.8779 (mmm) cc_final: 0.8065 (mmm) REVERT: B 417 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7740 (p0) REVERT: B 451 MET cc_start: 0.9316 (tpt) cc_final: 0.9092 (mmm) REVERT: B 466 MET cc_start: 0.8636 (mmm) cc_final: 0.8270 (mmp) REVERT: B 491 MET cc_start: 0.7521 (tmm) cc_final: 0.6842 (tmm) REVERT: B 507 MET cc_start: 0.8092 (ptp) cc_final: 0.7845 (ptp) REVERT: C 175 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8528 (tp) REVERT: C 323 MET cc_start: 0.8205 (mtp) cc_final: 0.7848 (mtp) REVERT: C 348 THR cc_start: 0.9757 (OUTLIER) cc_final: 0.9468 (p) REVERT: C 358 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8672 (t) REVERT: C 369 MET cc_start: 0.8770 (mmm) cc_final: 0.7970 (mmm) REVERT: C 430 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: C 451 MET cc_start: 0.9248 (mmm) cc_final: 0.8793 (mmm) REVERT: C 466 MET cc_start: 0.8143 (mtp) cc_final: 0.7927 (mtt) REVERT: C 566 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9024 (tptt) outliers start: 99 outliers final: 75 residues processed: 167 average time/residue: 0.0871 time to fit residues: 24.3384 Evaluate side-chains 158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 73 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 VAL 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 374 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 187 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 393 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 152 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 487 HIS B 218 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.086068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.049599 restraints weight = 52530.443| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.89 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16576 Z= 0.178 Angle : 0.538 9.158 22488 Z= 0.282 Chirality : 0.043 0.179 2630 Planarity : 0.004 0.058 2895 Dihedral : 14.768 142.239 2642 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.54 % Allowed : 23.14 % Favored : 71.32 % 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: 0.84 (0.19), residues: 2079 helix: 1.96 (0.20), residues: 689 sheet: -0.28 (0.25), residues: 477 loop : 0.05 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 611 TYR 0.013 0.002 TYR C 385 PHE 0.017 0.001 PHE B 41 TRP 0.003 0.001 TRP A 231 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (16569) covalent geometry : angle 0.53819 / 0.28 (22488) hydrogen bonds : bond 0.04393 / 2.93 ( 739) hydrogen bonds : angle 4.52324 / 3.21 ( 2187) Misc. bond : bond 0.00172 / 0.11 ( 7) *********************** 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: 94 poor density : 73 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8831 (ttp) cc_final: 0.8386 (ptm) REVERT: A 23 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8782 (ptm) REVERT: A 164 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8955 (m-40) REVERT: A 188 MET cc_start: 0.8541 (tmm) cc_final: 0.7976 (tmm) REVERT: A 392 MET cc_start: 0.8211 (tmm) cc_final: 0.7982 (tmm) REVERT: A 451 MET cc_start: 0.9122 (ttm) cc_final: 0.8711 (mtp) REVERT: B 176 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8430 (p0) REVERT: B 369 MET cc_start: 0.8707 (mmm) cc_final: 0.8028 (mmm) REVERT: B 417 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7730 (p0) REVERT: B 466 MET cc_start: 0.8575 (mmm) cc_final: 0.8233 (mmp) REVERT: B 491 MET cc_start: 0.7598 (tmm) cc_final: 0.6876 (tmm) REVERT: B 507 MET cc_start: 0.8075 (ptp) cc_final: 0.7848 (ptp) REVERT: C 323 MET cc_start: 0.8196 (mtp) cc_final: 0.7783 (mtp) REVERT: C 348 THR cc_start: 0.9748 (OUTLIER) cc_final: 0.9438 (p) REVERT: C 358 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8616 (t) REVERT: C 369 MET cc_start: 0.8692 (mmm) cc_final: 0.7928 (mmm) REVERT: C 430 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: C 451 MET cc_start: 0.9256 (mmm) cc_final: 0.8695 (mmm) REVERT: C 566 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9044 (tptt) outliers start: 94 outliers final: 72 residues processed: 162 average time/residue: 0.1072 time to fit residues: 28.8258 Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 71 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 303 ASN 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 374 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 187 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 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 662 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 487 HIS ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3658 r_free = 0.3658 target = 0.085108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048588 restraints weight = 52846.798| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.98 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16576 Z= 0.272 Angle : 0.584 8.402 22488 Z= 0.304 Chirality : 0.044 0.168 2630 Planarity : 0.004 0.061 2895 Dihedral : 14.619 143.831 2635 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.18 % Allowed : 22.14 % Favored : 71.67 % 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: 0.88 (0.19), residues: 2079 helix: 1.98 (0.20), residues: 689 sheet: -0.27 (0.25), residues: 478 loop : 0.09 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.014 0.002 TYR A 380 PHE 0.013 0.001 PHE B 41 TRP 0.005 0.001 TRP B 233 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (16569) covalent geometry : angle 0.58372 / 0.30 (22488) hydrogen bonds : bond 0.04538 / 3.03 ( 739) hydrogen bonds : angle 4.55221 / 3.24 ( 2187) Misc. bond : bond 0.00112 / 0.06 ( 7) *********************** 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 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 71 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8907 (ttp) cc_final: 0.8376 (ptm) REVERT: A 23 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8803 (ptm) REVERT: A 164 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8896 (m110) REVERT: A 188 MET cc_start: 0.8585 (tmm) cc_final: 0.8193 (tmm) REVERT: A 392 MET cc_start: 0.8236 (tmm) cc_final: 0.7972 (tmm) REVERT: A 414 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9227 (p) REVERT: A 451 MET cc_start: 0.9132 (ttm) cc_final: 0.8717 (mtp) REVERT: B 176 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8539 (p0) REVERT: B 188 MET cc_start: 0.8598 (tmm) cc_final: 0.8279 (tmm) REVERT: B 369 MET cc_start: 0.8861 (mmm) cc_final: 0.8188 (mmm) REVERT: B 417 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7741 (p0) REVERT: B 466 MET cc_start: 0.8682 (mmm) cc_final: 0.8206 (mmp) REVERT: B 491 MET cc_start: 0.7770 (tmm) cc_final: 0.6967 (tmm) REVERT: B 507 MET cc_start: 0.8030 (ptp) cc_final: 0.7693 (ptp) REVERT: C 323 MET cc_start: 0.8291 (mtp) cc_final: 0.7855 (mtp) REVERT: C 348 THR cc_start: 0.9739 (OUTLIER) cc_final: 0.9431 (p) REVERT: C 358 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8622 (t) REVERT: C 369 MET cc_start: 0.8779 (mmm) cc_final: 0.8072 (mmm) REVERT: C 415 MET cc_start: 0.9482 (mmm) cc_final: 0.9202 (mmm) REVERT: C 430 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: C 451 MET cc_start: 0.9295 (mmm) cc_final: 0.8693 (mmm) REVERT: C 519 MET cc_start: 0.9257 (mtm) cc_final: 0.8902 (mtm) REVERT: C 566 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9082 (tptt) outliers start: 105 outliers final: 87 residues processed: 170 average time/residue: 0.1072 time to fit residues: 30.0591 Evaluate side-chains 167 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 71 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 303 ASN 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 374 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 140 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 487 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3676 r_free = 0.3676 target = 0.086051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049532 restraints weight = 52060.250| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.72 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16576 Z= 0.160 Angle : 0.527 8.622 22488 Z= 0.273 Chirality : 0.043 0.170 2630 Planarity : 0.004 0.061 2895 Dihedral : 14.445 145.714 2634 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.65 % Allowed : 23.14 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 2079 helix: 2.08 (0.20), residues: 689 sheet: -0.16 (0.25), residues: 476 loop : 0.14 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 611 TYR 0.013 0.002 TYR C 385 PHE 0.015 0.001 PHE B 41 TRP 0.004 0.001 TRP B 233 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16569) covalent geometry : angle 0.52678 / 0.27 (22488) hydrogen bonds : bond 0.04204 / 2.80 ( 739) hydrogen bonds : angle 4.37380 / 3.12 ( 2187) Misc. bond : bond 0.00145 / 0.08 ( 7) *********************** 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 167 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 71 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8852 (ttp) cc_final: 0.8435 (ptm) REVERT: A 23 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8781 (ptm) REVERT: A 164 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8999 (m-40) REVERT: A 323 MET cc_start: 0.8908 (ptp) cc_final: 0.8522 (pmm) REVERT: A 392 MET cc_start: 0.8252 (tmm) cc_final: 0.7982 (tmm) REVERT: A 414 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9208 (p) REVERT: A 451 MET cc_start: 0.9127 (ttm) cc_final: 0.8780 (mtp) REVERT: B 369 MET cc_start: 0.8712 (mmm) cc_final: 0.8055 (mmm) REVERT: B 417 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7743 (p0) REVERT: B 491 MET cc_start: 0.7794 (tmm) cc_final: 0.6990 (tmm) REVERT: B 507 MET cc_start: 0.7962 (ptp) cc_final: 0.7572 (ptp) REVERT: C 323 MET cc_start: 0.8244 (mtp) cc_final: 0.7741 (mtp) REVERT: C 348 THR cc_start: 0.9726 (OUTLIER) cc_final: 0.9411 (p) REVERT: C 358 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8575 (t) REVERT: C 369 MET cc_start: 0.8707 (mmm) cc_final: 0.8006 (mmm) REVERT: C 430 GLU cc_start: 0.8934 (pt0) cc_final: 0.8460 (mt-10) REVERT: C 451 MET cc_start: 0.9270 (mmm) cc_final: 0.8673 (mmm) REVERT: C 466 MET cc_start: 0.8110 (mtp) cc_final: 0.7401 (mtt) REVERT: C 519 MET cc_start: 0.9219 (mtm) cc_final: 0.8846 (mtm) REVERT: C 566 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9075 (tptt) outliers start: 96 outliers final: 77 residues processed: 162 average time/residue: 0.1043 time to fit residues: 28.1029 Evaluate side-chains 155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 71 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 VAL 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 374 ASP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 177 optimal weight: 7.9990 chunk 64 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.085468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.049073 restraints weight = 52977.533| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 4.95 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16576 Z= 0.217 Angle : 0.555 8.119 22488 Z= 0.287 Chirality : 0.043 0.201 2630 Planarity : 0.004 0.062 2895 Dihedral : 14.284 146.291 2626 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.71 % Allowed : 23.32 % Favored : 70.97 % 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: 1.02 (0.19), residues: 2079 helix: 2.08 (0.20), residues: 689 sheet: -0.17 (0.25), residues: 476 loop : 0.17 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.013 0.002 TYR B 380 PHE 0.013 0.001 PHE B 41 TRP 0.004 0.001 TRP B 233 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (16569) covalent geometry : angle 0.55451 / 0.29 (22488) hydrogen bonds : bond 0.04229 / 2.82 ( 739) hydrogen bonds : angle 4.39519 / 3.13 ( 2187) Misc. bond : bond 0.00099 / 0.06 ( 7) *********************** 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 168 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 71 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8839 (ttp) cc_final: 0.8387 (ptm) REVERT: A 23 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8814 (ptm) REVERT: A 392 MET cc_start: 0.8283 (tmm) cc_final: 0.8001 (tmm) REVERT: A 414 VAL cc_start: 0.9469 (OUTLIER) cc_final: 0.9204 (p) REVERT: A 451 MET cc_start: 0.9141 (ttm) cc_final: 0.8800 (mtp) REVERT: B 188 MET cc_start: 0.8533 (tmm) cc_final: 0.8186 (tmm) REVERT: B 369 MET cc_start: 0.8797 (mmm) cc_final: 0.8126 (mmm) REVERT: B 417 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7733 (p0) REVERT: B 491 MET cc_start: 0.7916 (tmm) cc_final: 0.7107 (tmm) REVERT: B 507 MET cc_start: 0.8046 (ptp) cc_final: 0.7672 (ptp) REVERT: C 323 MET cc_start: 0.8295 (mtp) cc_final: 0.7782 (mtp) REVERT: C 348 THR cc_start: 0.9730 (OUTLIER) cc_final: 0.9426 (p) REVERT: C 358 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8601 (t) REVERT: C 369 MET cc_start: 0.8748 (mmm) cc_final: 0.8056 (mmm) REVERT: C 415 MET cc_start: 0.9508 (mmm) cc_final: 0.9306 (mmm) REVERT: C 430 GLU cc_start: 0.8930 (pt0) cc_final: 0.8471 (mt-10) REVERT: C 451 MET cc_start: 0.9332 (mmm) cc_final: 0.8700 (mmm) REVERT: C 519 MET cc_start: 0.9234 (mtm) cc_final: 0.8857 (mtm) REVERT: C 566 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9087 (tptt) outliers start: 97 outliers final: 84 residues processed: 163 average time/residue: 0.1047 time to fit residues: 28.5665 Evaluate side-chains 161 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 71 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 238 VAL 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 374 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 145 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 189 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN A 487 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3702 r_free = 0.3702 target = 0.087164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050829 restraints weight = 51822.406| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.91 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16576 Z= 0.107 Angle : 0.522 8.664 22488 Z= 0.269 Chirality : 0.043 0.207 2630 Planarity : 0.003 0.058 2895 Dihedral : 14.079 148.451 2626 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.77 % Allowed : 24.50 % Favored : 70.73 % 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: 1.13 (0.19), residues: 2079 helix: 2.18 (0.20), residues: 689 sheet: 0.01 (0.25), residues: 475 loop : 0.16 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 611 TYR 0.013 0.001 TYR C 385 PHE 0.017 0.001 PHE B 41 TRP 0.002 0.000 TRP A 233 HIS 0.003 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (16569) covalent geometry : angle 0.52157 / 0.27 (22488) hydrogen bonds : bond 0.03777 / 2.50 ( 739) hydrogen bonds : angle 4.20138 / 3.02 ( 2187) Misc. bond : bond 0.00093 / 0.06 ( 7) *********************** 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 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 75 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8663 (ttp) cc_final: 0.8337 (ptm) REVERT: A 188 MET cc_start: 0.8540 (tmm) cc_final: 0.8284 (tmm) REVERT: A 360 ARG cc_start: 0.8801 (tmm-80) cc_final: 0.8547 (ttp80) REVERT: A 392 MET cc_start: 0.8284 (tmm) cc_final: 0.7992 (tmm) REVERT: A 418 MET cc_start: 0.9334 (tpp) cc_final: 0.9068 (tpt) REVERT: A 429 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9026 (p) REVERT: B 1 MET cc_start: 0.7741 (ppp) cc_final: 0.7408 (ppp) REVERT: B 188 MET cc_start: 0.8573 (tmm) cc_final: 0.8254 (tmm) REVERT: B 417 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7726 (p0) REVERT: B 491 MET cc_start: 0.8013 (tmm) cc_final: 0.7285 (tmm) REVERT: B 507 MET cc_start: 0.8011 (ptp) cc_final: 0.7681 (ptp) REVERT: C 319 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8205 (mtm-85) REVERT: C 323 MET cc_start: 0.8224 (mtp) cc_final: 0.7923 (mtp) REVERT: C 348 THR cc_start: 0.9721 (OUTLIER) cc_final: 0.9389 (p) REVERT: C 358 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 369 MET cc_start: 0.8646 (mmm) cc_final: 0.8089 (mmm) REVERT: C 390 THR cc_start: 0.9613 (OUTLIER) cc_final: 0.9394 (t) REVERT: C 430 GLU cc_start: 0.8874 (pt0) cc_final: 0.8431 (mt-10) REVERT: C 451 MET cc_start: 0.9303 (mmm) cc_final: 0.8807 (tpt) REVERT: C 566 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9079 (tptt) outliers start: 81 outliers final: 63 residues processed: 154 average time/residue: 0.1043 time to fit residues: 26.6417 Evaluate side-chains 142 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 72 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 VAL 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 374 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 131 optimal weight: 30.0000 chunk 146 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 205 optimal weight: 0.0670 chunk 118 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3703 r_free = 0.3703 target = 0.087315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050832 restraints weight = 51644.786| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.88 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.002 0.068 16576 Z= 0.109 Angle : 0.520 8.665 22488 Z= 0.266 Chirality : 0.043 0.181 2630 Planarity : 0.003 0.055 2895 Dihedral : 13.916 149.092 2615 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.77 % Allowed : 25.38 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.19), residues: 2079 helix: 2.19 (0.20), residues: 691 sheet: 0.13 (0.25), residues: 475 loop : 0.17 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 97 TYR 0.015 0.001 TYR A 68 PHE 0.014 0.001 PHE B 41 TRP 0.003 0.000 TRP A 233 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16569) covalent geometry : angle 0.52023 / 0.27 (22488) hydrogen bonds : bond 0.03573 / 2.39 ( 739) hydrogen bonds : angle 4.09071 / 2.93 ( 2187) Misc. bond : bond 0.00078 / 0.05 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 77 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.8575 (tmm) cc_final: 0.8343 (tmm) REVERT: A 360 ARG cc_start: 0.8834 (tmm-80) cc_final: 0.8560 (ttp80) REVERT: A 392 MET cc_start: 0.8284 (tmm) cc_final: 0.7999 (tmm) REVERT: A 418 MET cc_start: 0.9325 (tpp) cc_final: 0.9038 (tpt) REVERT: A 451 MET cc_start: 0.9015 (ttm) cc_final: 0.8796 (tpp) REVERT: B 1 MET cc_start: 0.7761 (ppp) cc_final: 0.7442 (ppp) REVERT: B 188 MET cc_start: 0.8551 (tmm) cc_final: 0.8254 (tmm) REVERT: B 369 MET cc_start: 0.9015 (mmm) cc_final: 0.8698 (mmm) REVERT: B 417 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7726 (p0) REVERT: B 491 MET cc_start: 0.8046 (tmm) cc_final: 0.7324 (tmm) REVERT: B 507 MET cc_start: 0.8040 (ptp) cc_final: 0.7712 (ptp) REVERT: C 319 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8262 (mtm-85) REVERT: C 323 MET cc_start: 0.8180 (mtp) cc_final: 0.7788 (mtp) REVERT: C 348 THR cc_start: 0.9705 (OUTLIER) cc_final: 0.9370 (p) REVERT: C 358 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8478 (t) REVERT: C 369 MET cc_start: 0.8676 (mmm) cc_final: 0.8192 (mmm) REVERT: C 390 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9359 (t) REVERT: C 430 GLU cc_start: 0.8842 (pt0) cc_final: 0.8431 (mt-10) REVERT: C 451 MET cc_start: 0.9294 (mmm) cc_final: 0.8681 (mmm) REVERT: C 566 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9122 (tptt) outliers start: 64 outliers final: 55 residues processed: 139 average time/residue: 0.1055 time to fit residues: 24.1236 Evaluate side-chains 134 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 73 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 566 LYS Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 LYS Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 0.0000 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** 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 = 0.3702 r_free = 0.3702 target = 0.087242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050733 restraints weight = 51468.645| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.95 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16576 Z= 0.120 Angle : 0.512 8.311 22488 Z= 0.263 Chirality : 0.043 0.179 2630 Planarity : 0.003 0.054 2895 Dihedral : 13.768 149.357 2611 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.89 % Allowed : 25.09 % Favored : 71.02 % 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: 1.27 (0.19), residues: 2079 helix: 2.22 (0.20), residues: 691 sheet: 0.27 (0.25), residues: 471 loop : 0.18 (0.22), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 372 TYR 0.012 0.001 TYR A 68 PHE 0.014 0.001 PHE B 41 TRP 0.002 0.000 TRP A 233 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16569) covalent geometry : angle 0.51234 / 0.26 (22488) hydrogen bonds : bond 0.03551 / 2.37 ( 739) hydrogen bonds : angle 4.05820 / 2.91 ( 2187) Misc. bond : bond 0.00073 / 0.05 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.46 seconds wall clock time: 59 minutes 10.02 seconds (3550.02 seconds total)