Starting phenix.real_space_refine on Sun May 18 02:39:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vak_43093/05_2025/8vak_43093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vak_43093/05_2025/8vak_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_43093/05_2025/8vak_43093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vak_43093/05_2025/8vak_43093.map" model { file = "/net/cci-nas-00/data/ceres_data/8vak_43093/05_2025/8vak_43093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vak_43093/05_2025/8vak_43093.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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%rna2p_pur:plan': 3, ' A%rna2p_pur:plan2': 3, ' A%rna3p_pur:plan2': 3, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 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: 10.10, per 1000 atoms: 0.62 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: 4.42 Conformation dependent library (CDL) restraints added in 2.2 seconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3798 Finding SS restraints... Secondary structure from input PDB file: 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: 2.16 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: 5.83 Time building geometry restraints manager: 5.09 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 - 2.88: 22196 2.88 - 5.76: 266 5.76 - 8.64: 21 8.64 - 11.52: 3 11.52 - 14.41: 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 120.20 105.79 14.41 1.50e+00 4.44e-01 9.22e+01 angle pdb=" C3' C D 2 " pdb=" O3' C D 2 " pdb=" P A D 3 " ideal model delta sigma weight residual 120.20 106.88 13.32 1.50e+00 4.44e-01 7.88e+01 angle pdb=" C3' C F 2 " pdb=" O3' C F 2 " pdb=" P A F 3 " ideal model delta sigma weight residual 120.20 108.88 11.32 1.50e+00 4.44e-01 5.70e+01 angle pdb=" C3' 8GM D 4 " pdb=" O3' 8GM D 4 " pdb=" P 8GM D 5 " ideal model delta sigma weight residual 120.20 110.44 9.76 1.50e+00 4.44e-01 4.23e+01 angle pdb=" C3' C E 2 " pdb=" O3' C E 2 " pdb=" P A E 3 " ideal model delta sigma weight residual 120.20 110.50 9.70 1.50e+00 4.44e-01 4.18e+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: 2535 0.112 - 0.224: 85 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.540 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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= 0.970 Angle : 0.805 14.406 22488 Z= 0.480 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 : 16.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), 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 TRP 0.005 0.001 TRP C 231 HIS 0.008 0.001 HIS A 338 PHE 0.016 0.002 PHE A 145 TYR 0.019 0.002 TYR A 385 ARG 0.009 0.001 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.18384 ( 739) hydrogen bonds : angle 7.34516 ( 2187) covalent geometry : bond 0.00759 (16569) covalent geometry : angle 0.80509 (22488) Misc. bond : bond 0.43953 ( 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 : 1.983 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: 0.8829 (tptt) REVERT: C 629 VAL cc_start: 0.3771 (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: 0.2427 time to fit residues: 81.1894 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 : 1.833 ------------------------------------------------------------------------------- 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 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 200 GLN A 403 HIS A 506 GLN B 164 ASN B 200 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 653 GLN C 212 GLN ** C 379 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.088501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052762 restraints weight = 51566.870| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.85 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16576 Z= 0.143 Angle : 0.610 9.295 22488 Z= 0.320 Chirality : 0.045 0.168 2630 Planarity : 0.004 0.053 2895 Dihedral : 15.802 114.846 2728 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.48 % Allowed : 19.91 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 2079 helix: 1.22 (0.19), residues: 690 sheet: -1.10 (0.24), residues: 471 loop : -0.48 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 231 HIS 0.008 0.001 HIS B 487 PHE 0.011 0.001 PHE C 103 TYR 0.016 0.002 TYR C 385 ARG 0.009 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 739) hydrogen bonds : angle 5.10061 ( 2187) covalent geometry : bond 0.00303 (16569) covalent geometry : angle 0.61012 (22488) Misc. bond : bond 0.00295 ( 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 173 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 80 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8885 (m110) REVERT: A 188 MET cc_start: 0.8469 (tmm) cc_final: 0.7816 (tmm) REVERT: B 164 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9095 (t0) REVERT: B 176 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8316 (p0) REVERT: B 191 SER cc_start: 0.9290 (m) cc_final: 0.9030 (p) REVERT: B 369 MET cc_start: 0.8487 (mmm) cc_final: 0.7776 (mmm) REVERT: B 399 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7679 (ptm160) REVERT: C 175 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8450 (tp) REVERT: C 323 MET cc_start: 0.8116 (mtp) cc_final: 0.7712 (mtp) REVERT: C 358 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8714 (t) REVERT: C 369 MET cc_start: 0.8706 (mmm) cc_final: 0.8011 (mmm) REVERT: C 430 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8717 (mt-10) REVERT: C 433 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 451 MET cc_start: 0.9138 (mmm) cc_final: 0.8836 (tpt) REVERT: C 507 MET cc_start: 0.8180 (mtp) cc_final: 0.7969 (mtm) REVERT: C 566 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9015 (tptt) REVERT: C 629 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.7078 (p) outliers start: 93 outliers final: 55 residues processed: 167 average time/residue: 0.2354 time to fit residues: 63.9503 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 : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 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 387 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 509 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain B residue 43 THR 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 164 ASN 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 486 ASP Chi-restraints excluded: chain B residue 515 THR 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 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 429 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 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 20 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 203 optimal weight: 0.0770 chunk 105 optimal weight: 8.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 164 ASN A 349 GLN ** B 338 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.087088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051312 restraints weight = 51466.747| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.84 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16576 Z= 0.168 Angle : 0.565 7.918 22488 Z= 0.293 Chirality : 0.044 0.208 2630 Planarity : 0.004 0.053 2895 Dihedral : 15.037 114.166 2651 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.36 % Allowed : 21.14 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 2079 helix: 1.69 (0.20), residues: 690 sheet: -0.66 (0.25), residues: 466 loop : -0.15 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 231 HIS 0.005 0.001 HIS C 607 PHE 0.011 0.001 PHE A 41 TYR 0.012 0.002 TYR A 380 ARG 0.004 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 739) hydrogen bonds : angle 4.69255 ( 2187) covalent geometry : bond 0.00375 (16569) covalent geometry : angle 0.56498 (22488) Misc. bond : bond 0.00214 ( 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 166 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 75 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8711 (ttp) cc_final: 0.8312 (ptm) REVERT: A 164 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8819 (m110) REVERT: A 360 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8510 (ttp80) REVERT: A 392 MET cc_start: 0.8016 (tmm) cc_final: 0.7774 (tmm) REVERT: A 451 MET cc_start: 0.9083 (ttm) cc_final: 0.8690 (mtp) REVERT: A 507 MET cc_start: 0.8818 (ptm) cc_final: 0.8565 (ptm) REVERT: B 1 MET cc_start: 0.7525 (ppp) cc_final: 0.7204 (ppp) REVERT: B 176 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8386 (p0) REVERT: B 191 SER cc_start: 0.9294 (m) cc_final: 0.9051 (p) REVERT: B 369 MET cc_start: 0.8585 (mmm) cc_final: 0.7997 (mmm) REVERT: B 417 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7724 (p0) REVERT: B 466 MET cc_start: 0.8517 (mmm) cc_final: 0.8312 (mmp) REVERT: B 491 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7636 (tmm) REVERT: B 507 MET cc_start: 0.7897 (ptp) cc_final: 0.7607 (ptp) REVERT: C 175 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 323 MET cc_start: 0.8149 (mtp) cc_final: 0.7788 (mtp) REVERT: C 348 THR cc_start: 0.9742 (OUTLIER) cc_final: 0.9411 (p) REVERT: C 358 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8669 (t) REVERT: C 369 MET cc_start: 0.8730 (mmm) cc_final: 0.8081 (mmm) REVERT: C 430 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: C 433 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 451 MET cc_start: 0.9241 (mmm) cc_final: 0.8914 (tpt) REVERT: C 466 MET cc_start: 0.8151 (mtp) cc_final: 0.7589 (mtt) REVERT: C 566 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9002 (tptt) outliers start: 91 outliers final: 63 residues processed: 162 average time/residue: 0.2196 time to fit residues: 58.5987 Evaluate side-chains 148 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 76 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 515 THR 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 348 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 374 ASP 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 491 MET 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 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 132 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** 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 = 0.3673 r_free = 0.3673 target = 0.085281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.049489 restraints weight = 52254.414| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.75 r_work: 0.2568 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16576 Z= 0.272 Angle : 0.606 9.929 22488 Z= 0.313 Chirality : 0.044 0.184 2630 Planarity : 0.004 0.059 2895 Dihedral : 14.679 112.450 2635 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.42 % Allowed : 21.97 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 2079 helix: 1.85 (0.20), residues: 689 sheet: -0.48 (0.25), residues: 481 loop : 0.01 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 231 HIS 0.006 0.001 HIS A 338 PHE 0.014 0.001 PHE B 41 TYR 0.016 0.002 TYR B 380 ARG 0.004 0.001 ARG C 611 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 739) hydrogen bonds : angle 4.64418 ( 2187) covalent geometry : bond 0.00615 (16569) covalent geometry : angle 0.60576 (22488) Misc. bond : bond 0.00143 ( 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 165 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 73 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.9093 (ttp) cc_final: 0.8685 (ptm) REVERT: A 360 ARG cc_start: 0.9163 (tmm-80) cc_final: 0.8844 (ttp80) REVERT: A 392 MET cc_start: 0.8785 (tmm) cc_final: 0.8479 (tmm) REVERT: A 451 MET cc_start: 0.9297 (ttm) cc_final: 0.8931 (mtp) REVERT: B 1 MET cc_start: 0.7943 (ppp) cc_final: 0.7506 (ppp) REVERT: B 176 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8525 (p0) REVERT: B 369 MET cc_start: 0.8829 (mmm) cc_final: 0.8176 (mmm) REVERT: B 415 MET cc_start: 0.9485 (ttm) cc_final: 0.9068 (tpp) REVERT: B 417 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.7868 (p0) REVERT: B 466 MET cc_start: 0.8911 (mmm) cc_final: 0.8404 (mmp) REVERT: B 491 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8098 (ptp) REVERT: C 175 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8635 (tp) REVERT: C 323 MET cc_start: 0.8363 (mtp) cc_final: 0.7966 (mtp) REVERT: C 348 THR cc_start: 0.9758 (OUTLIER) cc_final: 0.9495 (p) REVERT: C 358 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8830 (t) REVERT: C 369 MET cc_start: 0.8720 (mmm) cc_final: 0.8044 (mmm) REVERT: C 430 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8814 (mt-10) REVERT: C 451 MET cc_start: 0.9429 (mmm) cc_final: 0.9022 (mmm) REVERT: C 466 MET cc_start: 0.8630 (mtp) cc_final: 0.8223 (mtt) REVERT: C 566 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9015 (tptt) outliers start: 92 outliers final: 66 residues processed: 160 average time/residue: 0.2234 time to fit residues: 58.7790 Evaluate side-chains 146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 72 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 586 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 23 MET 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 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 417 ASP Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 515 THR 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 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 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 374 ASP 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 509 ILE Chi-restraints excluded: chain C residue 515 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.086878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.050209 restraints weight = 52671.953| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 5.01 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 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 = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16576 Z= 0.131 Angle : 0.521 9.303 22488 Z= 0.267 Chirality : 0.043 0.164 2630 Planarity : 0.004 0.057 2895 Dihedral : 14.264 109.578 2630 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.48 % Allowed : 23.44 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2079 helix: 2.09 (0.20), residues: 689 sheet: -0.20 (0.25), residues: 477 loop : 0.10 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 231 HIS 0.004 0.001 HIS A 338 PHE 0.017 0.001 PHE B 41 TYR 0.013 0.001 TYR C 385 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 739) hydrogen bonds : angle 4.30861 ( 2187) covalent geometry : bond 0.00287 (16569) covalent geometry : angle 0.52124 (22488) Misc. bond : bond 0.00115 ( 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 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 73 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8776 (ttp) cc_final: 0.8418 (ptm) REVERT: A 360 ARG cc_start: 0.8964 (tmm-80) cc_final: 0.8602 (ttp80) REVERT: A 392 MET cc_start: 0.8196 (tmm) cc_final: 0.7924 (tmm) REVERT: A 451 MET cc_start: 0.9074 (ttm) cc_final: 0.8751 (mtp) REVERT: B 1 MET cc_start: 0.7808 (ppp) cc_final: 0.7412 (ppp) REVERT: B 176 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8456 (p0) REVERT: B 369 MET cc_start: 0.8647 (mmm) cc_final: 0.8138 (mmm) REVERT: B 415 MET cc_start: 0.9334 (ttm) cc_final: 0.8966 (tpp) REVERT: B 451 MET cc_start: 0.9274 (tpt) cc_final: 0.9033 (mmm) REVERT: B 491 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7754 (ptp) REVERT: C 323 MET cc_start: 0.8145 (mtp) cc_final: 0.7640 (mtp) REVERT: C 358 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8583 (t) REVERT: C 369 MET cc_start: 0.8660 (mmm) cc_final: 0.7996 (mmm) REVERT: C 433 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 451 MET cc_start: 0.9297 (mmm) cc_final: 0.8760 (mmm) REVERT: C 466 MET cc_start: 0.7940 (mtp) cc_final: 0.7710 (mtt) REVERT: C 566 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9006 (tptt) outliers start: 76 outliers final: 59 residues processed: 145 average time/residue: 0.2334 time to fit residues: 55.2952 Evaluate side-chains 135 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 72 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 102 LEU 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 374 ASP 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 498 SER 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 23 MET 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 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 486 ASP Chi-restraints excluded: chain B residue 491 MET 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 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 358 THR Chi-restraints excluded: chain C residue 374 ASP 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 22 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3688 r_free = 0.3688 target = 0.086593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050099 restraints weight = 52040.275| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.86 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 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 = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16576 Z= 0.142 Angle : 0.516 9.111 22488 Z= 0.264 Chirality : 0.042 0.158 2630 Planarity : 0.003 0.057 2895 Dihedral : 13.954 107.637 2619 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.53 % Allowed : 23.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2079 helix: 2.21 (0.20), residues: 689 sheet: -0.03 (0.25), residues: 476 loop : 0.16 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 231 HIS 0.003 0.001 HIS A 338 PHE 0.016 0.001 PHE B 41 TYR 0.014 0.001 TYR A 68 ARG 0.002 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 739) hydrogen bonds : angle 4.18336 ( 2187) covalent geometry : bond 0.00315 (16569) covalent geometry : angle 0.51592 (22488) Misc. bond : bond 0.00107 ( 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 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 72 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7938 (tmm) cc_final: 0.7658 (tmm) REVERT: A 360 ARG cc_start: 0.8999 (tmm-80) cc_final: 0.8647 (ttp80) REVERT: A 392 MET cc_start: 0.8231 (tmm) cc_final: 0.7950 (tmm) REVERT: B 1 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7445 (ppp) REVERT: B 369 MET cc_start: 0.8631 (mmm) cc_final: 0.8123 (mmm) REVERT: B 415 MET cc_start: 0.9336 (ttm) cc_final: 0.8959 (tpp) REVERT: B 417 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7705 (p0) REVERT: B 491 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7843 (ptp) REVERT: C 323 MET cc_start: 0.8152 (mtp) cc_final: 0.7724 (mtp) REVERT: C 348 THR cc_start: 0.9740 (OUTLIER) cc_final: 0.9392 (p) REVERT: C 358 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8573 (t) REVERT: C 369 MET cc_start: 0.8667 (mmm) cc_final: 0.8083 (mmm) REVERT: C 415 MET cc_start: 0.9514 (mmm) cc_final: 0.9309 (mmm) REVERT: C 451 MET cc_start: 0.9297 (mmm) cc_final: 0.8847 (tpt) REVERT: C 566 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9032 (tptt) outliers start: 77 outliers final: 64 residues processed: 145 average time/residue: 0.2200 time to fit residues: 52.0337 Evaluate side-chains 141 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 71 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 102 LEU 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 374 ASP 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 1 MET Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 23 MET 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 355 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET 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 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 374 ASP 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 491 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 5.9990 chunk 51 optimal weight: 0.0040 chunk 56 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3666 r_free = 0.3666 target = 0.085435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.048763 restraints weight = 52597.153| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 4.91 r_work (final): 0.2739 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2331 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= 0.226 Angle : 0.557 8.906 22488 Z= 0.287 Chirality : 0.043 0.199 2630 Planarity : 0.004 0.062 2895 Dihedral : 13.830 105.155 2616 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.01 % Allowed : 23.14 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 2079 helix: 2.15 (0.20), residues: 689 sheet: -0.05 (0.25), residues: 478 loop : 0.24 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 233 HIS 0.004 0.001 HIS A 338 PHE 0.015 0.001 PHE B 41 TYR 0.015 0.002 TYR B 380 ARG 0.004 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 739) hydrogen bonds : angle 4.25854 ( 2187) covalent geometry : bond 0.00511 (16569) covalent geometry : angle 0.55712 (22488) Misc. bond : bond 0.00105 ( 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 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 71 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8949 (m110) REVERT: A 188 MET cc_start: 0.8534 (tmm) cc_final: 0.8245 (tmm) REVERT: A 360 ARG cc_start: 0.9045 (tmm-80) cc_final: 0.8817 (tmm-80) REVERT: A 392 MET cc_start: 0.8246 (tmm) cc_final: 0.7951 (tmm) REVERT: A 418 MET cc_start: 0.9321 (tpp) cc_final: 0.9062 (tpt) REVERT: A 451 MET cc_start: 0.9133 (ttm) cc_final: 0.8790 (mtp) REVERT: A 506 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: B 1 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7638 (ppp) REVERT: B 188 MET cc_start: 0.8561 (tmm) cc_final: 0.8273 (tmm) REVERT: B 369 MET cc_start: 0.8807 (mmm) cc_final: 0.8219 (mmm) REVERT: B 415 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9119 (tpp) REVERT: B 417 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7660 (p0) REVERT: B 491 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7970 (ptt) REVERT: C 323 MET cc_start: 0.8265 (mtp) cc_final: 0.7818 (mtp) REVERT: C 348 THR cc_start: 0.9743 (OUTLIER) cc_final: 0.9435 (p) REVERT: C 358 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8560 (t) REVERT: C 369 MET cc_start: 0.8767 (mmm) cc_final: 0.8107 (mmm) REVERT: C 415 MET cc_start: 0.9519 (mmm) cc_final: 0.9246 (mmm) REVERT: C 451 MET cc_start: 0.9345 (mmm) cc_final: 0.8735 (mmm) REVERT: C 566 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9058 (tptt) outliers start: 85 outliers final: 69 residues processed: 149 average time/residue: 0.2253 time to fit residues: 54.9495 Evaluate side-chains 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 71 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 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 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 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 521 VAL 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 1 MET 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 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 447 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET 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 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 417 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 491 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3696 r_free = 0.3696 target = 0.086884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050236 restraints weight = 52006.140| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 4.91 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 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 = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16576 Z= 0.112 Angle : 0.508 9.028 22488 Z= 0.259 Chirality : 0.043 0.156 2630 Planarity : 0.003 0.061 2895 Dihedral : 13.663 102.098 2615 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.48 % Allowed : 24.09 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 2079 helix: 2.28 (0.20), residues: 691 sheet: 0.04 (0.25), residues: 475 loop : 0.24 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 231 HIS 0.003 0.001 HIS A 338 PHE 0.016 0.001 PHE B 41 TYR 0.014 0.001 TYR A 68 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 739) hydrogen bonds : angle 4.04027 ( 2187) covalent geometry : bond 0.00240 (16569) covalent geometry : angle 0.50759 (22488) Misc. bond : bond 0.00122 ( 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 150 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 74 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8947 (m-40) REVERT: A 188 MET cc_start: 0.8540 (tmm) cc_final: 0.8248 (tmm) REVERT: A 360 ARG cc_start: 0.9061 (tmm-80) cc_final: 0.8692 (ttp80) REVERT: A 392 MET cc_start: 0.8267 (tmm) cc_final: 0.7980 (tmm) REVERT: B 1 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7647 (ppp) REVERT: B 188 MET cc_start: 0.8511 (tmm) cc_final: 0.8227 (tmm) REVERT: B 369 MET cc_start: 0.8587 (mmm) cc_final: 0.7937 (mmm) REVERT: B 415 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9057 (tpp) REVERT: B 417 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7658 (p0) REVERT: C 323 MET cc_start: 0.8187 (mtp) cc_final: 0.7736 (mtp) REVERT: C 348 THR cc_start: 0.9729 (OUTLIER) cc_final: 0.9389 (p) REVERT: C 358 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8497 (t) REVERT: C 369 MET cc_start: 0.8666 (mmm) cc_final: 0.8123 (mmm) REVERT: C 390 THR cc_start: 0.9598 (OUTLIER) cc_final: 0.9378 (t) REVERT: C 433 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7830 (mt-10) REVERT: C 451 MET cc_start: 0.9294 (mmm) cc_final: 0.8690 (mmm) REVERT: C 566 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9072 (tptt) outliers start: 76 outliers final: 58 residues processed: 144 average time/residue: 0.2497 time to fit residues: 58.5380 Evaluate side-chains 139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 73 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 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 374 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 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 624 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 1 MET 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 364 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET 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 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 374 ASP 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 491 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 184 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 487 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 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 = 0.3674 r_free = 0.3674 target = 0.085724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049073 restraints weight = 52472.848| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.95 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16576 Z= 0.199 Angle : 0.543 9.206 22488 Z= 0.277 Chirality : 0.043 0.158 2630 Planarity : 0.004 0.060 2895 Dihedral : 13.598 100.590 2611 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.24 % Allowed : 24.15 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2079 helix: 2.36 (0.20), residues: 683 sheet: 0.06 (0.25), residues: 472 loop : 0.27 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 233 HIS 0.004 0.001 HIS A 338 PHE 0.015 0.001 PHE B 41 TYR 0.014 0.002 TYR B 380 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 739) hydrogen bonds : angle 4.11573 ( 2187) covalent geometry : bond 0.00448 (16569) covalent geometry : angle 0.54271 (22488) Misc. bond : bond 0.00104 ( 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 144 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 72 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.8882 (m110) REVERT: A 188 MET cc_start: 0.8571 (tmm) cc_final: 0.8255 (tmm) REVERT: A 360 ARG cc_start: 0.9091 (tmm-80) cc_final: 0.8724 (ttp80) REVERT: A 392 MET cc_start: 0.8274 (tmm) cc_final: 0.7975 (tmm) REVERT: B 1 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7649 (ppp) REVERT: B 188 MET cc_start: 0.8460 (tmm) cc_final: 0.8153 (tmm) REVERT: B 369 MET cc_start: 0.8778 (mmm) cc_final: 0.8185 (mmm) REVERT: B 417 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7642 (p0) REVERT: C 323 MET cc_start: 0.8256 (mtp) cc_final: 0.7795 (mtp) REVERT: C 348 THR cc_start: 0.9739 (OUTLIER) cc_final: 0.9433 (p) REVERT: C 358 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8514 (t) REVERT: C 369 MET cc_start: 0.8756 (mmm) cc_final: 0.8105 (mmm) REVERT: C 451 MET cc_start: 0.9304 (mmm) cc_final: 0.8840 (mmm) REVERT: C 466 MET cc_start: 0.8261 (mtp) cc_final: 0.7908 (mtt) REVERT: C 566 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9090 (tptt) outliers start: 72 outliers final: 61 residues processed: 138 average time/residue: 0.2346 time to fit residues: 52.8733 Evaluate side-chains 139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 72 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 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 374 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 1 MET 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 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 447 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET 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 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 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 491 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 179 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 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 = 0.3671 r_free = 0.3671 target = 0.085519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048827 restraints weight = 52601.436| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.92 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16576 Z= 0.208 Angle : 0.547 9.345 22488 Z= 0.280 Chirality : 0.043 0.159 2630 Planarity : 0.004 0.060 2895 Dihedral : 13.572 100.050 2611 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.00 % Allowed : 24.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 2079 helix: 2.34 (0.20), residues: 683 sheet: 0.10 (0.25), residues: 474 loop : 0.30 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.004 0.001 HIS A 338 PHE 0.017 0.001 PHE B 41 TYR 0.014 0.002 TYR B 380 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 739) hydrogen bonds : angle 4.14211 ( 2187) covalent geometry : bond 0.00467 (16569) covalent geometry : angle 0.54735 (22488) Misc. bond : bond 0.00095 ( 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 139 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 71 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.8605 (tmm) cc_final: 0.8288 (tmm) REVERT: A 360 ARG cc_start: 0.9114 (tmm-80) cc_final: 0.8739 (ttp80) REVERT: A 392 MET cc_start: 0.8276 (tmm) cc_final: 0.7979 (tmm) REVERT: A 506 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: B 1 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7780 (ppp) REVERT: B 188 MET cc_start: 0.8479 (tmm) cc_final: 0.8175 (tmm) REVERT: B 369 MET cc_start: 0.8778 (mmm) cc_final: 0.8187 (mmm) REVERT: B 417 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7568 (p0) REVERT: B 451 MET cc_start: 0.9253 (tpt) cc_final: 0.8954 (tpt) REVERT: C 323 MET cc_start: 0.8339 (mtp) cc_final: 0.7877 (mtp) REVERT: C 348 THR cc_start: 0.9739 (OUTLIER) cc_final: 0.9440 (p) REVERT: C 358 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8576 (m) REVERT: C 369 MET cc_start: 0.8778 (mmm) cc_final: 0.8125 (mmm) REVERT: C 451 MET cc_start: 0.9308 (mmm) cc_final: 0.8848 (mmm) REVERT: C 466 MET cc_start: 0.8234 (mtp) cc_final: 0.7627 (mtt) REVERT: C 566 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9130 (tptt) outliers start: 68 outliers final: 61 residues processed: 133 average time/residue: 0.2431 time to fit residues: 52.8113 Evaluate side-chains 138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 71 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 102 LEU 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 374 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 506 GLN 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 679 VAL Chi-restraints excluded: chain B residue 1 MET 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 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 447 SER Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 491 MET 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 633 VAL 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 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 491 MET 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 515 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 203 optimal weight: 40.0000 chunk 135 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 487 HIS ** 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 = 0.3664 r_free = 0.3664 target = 0.084591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.048324 restraints weight = 52569.276| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.84 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2709 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= 0.275 Angle : 0.595 9.546 22488 Z= 0.305 Chirality : 0.044 0.168 2630 Planarity : 0.004 0.062 2895 Dihedral : 13.649 100.139 2610 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.48 % Allowed : 23.91 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 2079 helix: 2.25 (0.20), residues: 683 sheet: 0.06 (0.25), residues: 476 loop : 0.31 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 233 HIS 0.010 0.001 HIS B 487 PHE 0.015 0.001 PHE B 41 TYR 0.018 0.002 TYR B 380 ARG 0.003 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 739) hydrogen bonds : angle 4.30029 ( 2187) covalent geometry : bond 0.00616 (16569) covalent geometry : angle 0.59547 (22488) Misc. bond : bond 0.00088 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7670.25 seconds wall clock time: 133 minutes 40.86 seconds (8020.86 seconds total)