Starting phenix.real_space_refine on Tue Aug 26 16:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8v_36965/08_2025/8k8v_36965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8v_36965/08_2025/8k8v_36965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k8v_36965/08_2025/8k8v_36965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8v_36965/08_2025/8k8v_36965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k8v_36965/08_2025/8k8v_36965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8v_36965/08_2025/8k8v_36965.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 7 5.49 5 S 49 5.16 5 C 24675 2.51 5 N 7000 2.21 5 O 7336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39067 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "G" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.13, per 1000 atoms: 0.18 Number of scatterers: 39067 At special positions: 0 Unit cell: (151.7, 153.34, 171.38, 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 49 16.00 P 7 15.00 O 7336 8.00 N 7000 7.00 C 24675 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=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 71 sheets defined 53.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 97 through 120 removed outlier: 4.222A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.592A pdb=" N LEU A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.138A pdb=" N ASN A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 241 removed outlier: 3.668A pdb=" N ARG A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.584A pdb=" N TRP A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.228A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.803A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 621 through 637 Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.158A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 654 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 32 through 46 Processing helix chain 'G' and resid 58 through 68 Processing helix chain 'G' and resid 97 through 120 removed outlier: 4.214A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASN G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 152 Processing helix chain 'G' and resid 173 through 221 removed outlier: 4.060A pdb=" N ASN G 212 " --> pdb=" O HIS G 208 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG G 213 " --> pdb=" O TYR G 209 " (cutoff:3.500A) Proline residue: G 216 - end of helix Processing helix chain 'G' and resid 224 through 242 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.653A pdb=" N TRP G 250 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 279 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 302 through 306 Processing helix chain 'G' and resid 314 through 320 Processing helix chain 'G' and resid 322 through 333 Processing helix chain 'G' and resid 363 through 372 removed outlier: 4.226A pdb=" N GLY G 369 " --> pdb=" O GLU G 365 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU G 370 " --> pdb=" O ALA G 366 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 379 Processing helix chain 'G' and resid 393 through 407 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 436 through 451 Processing helix chain 'G' and resid 456 through 471 removed outlier: 3.738A pdb=" N SER G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 485 Processing helix chain 'G' and resid 532 through 535 removed outlier: 3.884A pdb=" N ALA G 535 " --> pdb=" O ASP G 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 532 through 535' Processing helix chain 'G' and resid 543 through 557 removed outlier: 3.518A pdb=" N TYR G 557 " --> pdb=" O LEU G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 597 Processing helix chain 'G' and resid 621 through 636 Processing helix chain 'G' and resid 649 through 654 removed outlier: 3.977A pdb=" N ALA G 652 " --> pdb=" O ALA G 649 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU G 654 " --> pdb=" O LEU G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 666 Processing helix chain 'G' and resid 676 through 686 Processing helix chain 'G' and resid 694 through 717 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.804A pdb=" N THR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 removed outlier: 4.195A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 153 removed outlier: 3.695A pdb=" N ALA F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 221 removed outlier: 4.011A pdb=" N ASN F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 242 removed outlier: 3.505A pdb=" N ARG F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 251 removed outlier: 3.558A pdb=" N TRP F 250 " --> pdb=" O ASP F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 293 through 297 Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 320 Processing helix chain 'F' and resid 322 through 333 Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.564A pdb=" N GLU F 368 " --> pdb=" O PRO F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 380 Processing helix chain 'F' and resid 393 through 407 Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 436 through 452 Processing helix chain 'F' and resid 456 through 471 removed outlier: 3.755A pdb=" N SER F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 543 through 557 Processing helix chain 'F' and resid 584 through 597 Processing helix chain 'F' and resid 621 through 636 Processing helix chain 'F' and resid 649 through 654 removed outlier: 4.242A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 654 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 Processing helix chain 'F' and resid 694 through 719 removed outlier: 4.028A pdb=" N GLU F 716 " --> pdb=" O GLY F 712 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP F 717 " --> pdb=" O HIS F 713 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG F 718 " --> pdb=" O ASP F 714 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU F 719 " --> pdb=" O LYS F 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 45 Processing helix chain 'E' and resid 58 through 68 Processing helix chain 'E' and resid 97 through 120 removed outlier: 4.236A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 152 removed outlier: 3.507A pdb=" N GLU E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 221 removed outlier: 4.061A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG E 213 " --> pdb=" O TYR E 209 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 300 through 305 removed outlier: 3.513A pdb=" N ARG E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.669A pdb=" N GLU E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 380 Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 543 through 557 removed outlier: 3.585A pdb=" N TYR E 557 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.247A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 718 removed outlier: 3.724A pdb=" N ARG E 718 " --> pdb=" O ASP E 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 97 through 119 removed outlier: 4.167A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 152 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.080A pdb=" N ASN D 212 " --> pdb=" O HIS D 208 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.588A pdb=" N TRP D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 363 through 373 removed outlier: 4.377A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 436 through 452 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.804A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 543 through 557 removed outlier: 3.618A pdb=" N TYR D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.066A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 654 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 717 removed outlier: 3.692A pdb=" N ASP D 717 " --> pdb=" O HIS D 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 45 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 97 through 120 removed outlier: 4.146A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 152 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.044A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 241 removed outlier: 3.547A pdb=" N ARG B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 436 through 452 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.839A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.181A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 654 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 45 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 97 through 120 removed outlier: 4.189A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 151 removed outlier: 3.527A pdb=" N LEU C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.044A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.633A pdb=" N TRP C 250 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.890A pdb=" N ARG C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.584A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.810A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 543 through 557 removed outlier: 3.518A pdb=" N TYR C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 597 Processing helix chain 'C' and resid 621 through 636 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.053A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 removed outlier: 3.653A pdb=" N ASP C 717 " --> pdb=" O HIS C 713 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 719 " --> pdb=" O LYS C 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.783A pdb=" N HIS A 48 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA A 384 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 50 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 82 removed outlier: 3.554A pdb=" N VAL A 88 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 411 removed outlier: 7.007A pdb=" N GLN A 410 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA9, first strand: chain 'A' and resid 528 through 530 removed outlier: 6.770A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP A 511 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 584 removed outlier: 4.256A pdb=" N ALA A 583 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 2 through 3 removed outlier: 4.775A pdb=" N ILE G 671 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA G 605 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N GLU G 498 " --> pdb=" O LEU G 604 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL G 606 " --> pdb=" O GLU G 498 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN G 500 " --> pdb=" O VAL G 606 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE G 529 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE G 571 " --> pdb=" O ILE G 529 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 266 through 268 removed outlier: 6.749A pdb=" N HIS G 48 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA G 384 " --> pdb=" O HIS G 48 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR G 50 " --> pdb=" O ALA G 384 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 77 through 82 removed outlier: 3.734A pdb=" N VAL G 88 " --> pdb=" O GLU G 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 156 through 160 removed outlier: 3.591A pdb=" N ASN G 160 " --> pdb=" O ARG G 163 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG G 163 " --> pdb=" O ASN G 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AB7, first strand: chain 'G' and resid 334 through 335 Processing sheet with id=AB8, first strand: chain 'G' and resid 389 through 391 Processing sheet with id=AB9, first strand: chain 'G' and resid 410 through 411 removed outlier: 7.138A pdb=" N GLN G 410 " --> pdb=" O LEU G 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 496 Processing sheet with id=AC2, first strand: chain 'G' and resid 609 through 610 Processing sheet with id=AC3, first strand: chain 'F' and resid 266 through 268 removed outlier: 6.226A pdb=" N TYR F 50 " --> pdb=" O ALA F 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 77 through 82 Processing sheet with id=AC5, first strand: chain 'F' and resid 156 through 160 Processing sheet with id=AC6, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AC7, first strand: chain 'F' and resid 334 through 335 Processing sheet with id=AC8, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AC9, first strand: chain 'F' and resid 410 through 411 removed outlier: 7.290A pdb=" N GLN F 410 " --> pdb=" O LEU F 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AD2, first strand: chain 'F' and resid 528 through 530 removed outlier: 6.859A pdb=" N ILE F 529 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N PHE F 571 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AD4, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.306A pdb=" N TYR E 50 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 77 through 82 Processing sheet with id=AD6, first strand: chain 'E' and resid 156 through 160 Processing sheet with id=AD7, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AD8, first strand: chain 'E' and resid 334 through 335 Processing sheet with id=AD9, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AE1, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.327A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AE3, first strand: chain 'E' and resid 528 through 530 removed outlier: 6.828A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE E 571 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N GLU E 498 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL E 606 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN E 500 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.160A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 2 through 3 removed outlier: 4.697A pdb=" N ILE D 671 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.290A pdb=" N TYR D 50 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 77 through 82 removed outlier: 3.807A pdb=" N VAL D 88 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 156 through 160 Processing sheet with id=AE9, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AF1, first strand: chain 'D' and resid 334 through 335 Processing sheet with id=AF2, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AF3, first strand: chain 'D' and resid 410 through 411 removed outlier: 7.144A pdb=" N GLN D 410 " --> pdb=" O LEU D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AF5, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.165A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.324A pdb=" N TYR B 50 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AF8, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AF9, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AG1, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AG2, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AG3, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.281A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AG5, first strand: chain 'B' and resid 528 through 530 removed outlier: 6.802A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 609 through 610 Processing sheet with id=AG7, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.665A pdb=" N HIS C 48 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA C 384 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 50 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 77 through 82 Processing sheet with id=AG9, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AH1, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AH2, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AH3, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AH4, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AH5, first strand: chain 'C' and resid 410 through 411 removed outlier: 7.223A pdb=" N GLN C 410 " --> pdb=" O LEU C 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AH7, first strand: chain 'C' and resid 528 through 530 removed outlier: 6.875A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 644 " --> pdb=" O TYR C 672 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL C 674 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 609 through 610 2206 hydrogen bonds defined for protein. 6369 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: 8.89 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 13765 1.37 - 1.51: 11093 1.51 - 1.66: 14888 1.66 - 1.80: 70 1.80 - 1.95: 21 Bond restraints: 39837 Sorted by residual: bond pdb=" O4 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.568 1.946 -0.378 2.00e-02 2.50e+03 3.58e+02 bond pdb=" O4 PO4 F 801 " pdb=" P PO4 F 801 " ideal model delta sigma weight residual 1.568 1.946 -0.378 2.00e-02 2.50e+03 3.56e+02 bond pdb=" O4 PO4 D 801 " pdb=" P PO4 D 801 " ideal model delta sigma weight residual 1.568 1.945 -0.377 2.00e-02 2.50e+03 3.56e+02 bond pdb=" O4 PO4 G 801 " pdb=" P PO4 G 801 " ideal model delta sigma weight residual 1.568 1.945 -0.377 2.00e-02 2.50e+03 3.56e+02 bond pdb=" O4 PO4 C 801 " pdb=" P PO4 C 801 " ideal model delta sigma weight residual 1.568 1.945 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 39832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 53570 2.56 - 5.12: 468 5.12 - 7.68: 43 7.68 - 10.23: 7 10.23 - 12.79: 1 Bond angle restraints: 54089 Sorted by residual: angle pdb=" CA ALA E 507 " pdb=" C ALA E 507 " pdb=" N ALA E 508 " ideal model delta sigma weight residual 118.27 111.40 6.87 1.59e+00 3.96e-01 1.87e+01 angle pdb=" CA LEU C 143 " pdb=" CB LEU C 143 " pdb=" CG LEU C 143 " ideal model delta sigma weight residual 116.30 129.09 -12.79 3.50e+00 8.16e-02 1.34e+01 angle pdb=" N GLU B 106 " pdb=" CA GLU B 106 " pdb=" CB GLU B 106 " ideal model delta sigma weight residual 110.22 115.38 -5.16 1.54e+00 4.22e-01 1.12e+01 angle pdb=" C TYR D 80 " pdb=" N VAL D 81 " pdb=" CA VAL D 81 " ideal model delta sigma weight residual 123.33 120.76 2.57 8.70e-01 1.32e+00 8.73e+00 angle pdb=" N GLY A 539 " pdb=" CA GLY A 539 " pdb=" C GLY A 539 " ideal model delta sigma weight residual 115.32 111.46 3.86 1.31e+00 5.83e-01 8.68e+00 ... (remaining 54084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 22013 18.01 - 36.01: 1735 36.01 - 54.02: 251 54.02 - 72.02: 123 72.02 - 90.03: 56 Dihedral angle restraints: 24178 sinusoidal: 9793 harmonic: 14385 Sorted by residual: dihedral pdb=" CA ASN E 574 " pdb=" C ASN E 574 " pdb=" N TYR E 575 " pdb=" CA TYR E 575 " ideal model delta harmonic sigma weight residual -180.00 -134.82 -45.18 0 5.00e+00 4.00e-02 8.16e+01 dihedral pdb=" CA ASN C 574 " pdb=" C ASN C 574 " pdb=" N TYR C 575 " pdb=" CA TYR C 575 " ideal model delta harmonic sigma weight residual -180.00 -137.52 -42.48 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA ASN G 574 " pdb=" C ASN G 574 " pdb=" N TYR G 575 " pdb=" CA TYR G 575 " ideal model delta harmonic sigma weight residual -180.00 -138.15 -41.85 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 24175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4827 0.045 - 0.091: 957 0.091 - 0.136: 239 0.136 - 0.182: 2 0.182 - 0.227: 2 Chirality restraints: 6027 Sorted by residual: chirality pdb=" CB THR G 262 " pdb=" CA THR G 262 " pdb=" OG1 THR G 262 " pdb=" CG2 THR G 262 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR E 262 " pdb=" CA THR E 262 " pdb=" OG1 THR E 262 " pdb=" CG2 THR E 262 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA ILE D 487 " pdb=" N ILE D 487 " pdb=" C ILE D 487 " pdb=" CB ILE D 487 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 6024 not shown) Planarity restraints: 7217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 243 " -0.058 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 244 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 244 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 244 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 574 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C ASN A 574 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN A 574 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR A 575 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 574 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.70e+00 pdb=" C ASN F 574 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN F 574 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR F 575 " 0.016 2.00e-02 2.50e+03 ... (remaining 7214 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 282 2.57 - 3.15: 31047 3.15 - 3.74: 65191 3.74 - 4.32: 88821 4.32 - 4.90: 150796 Nonbonded interactions: 336137 Sorted by model distance: nonbonded pdb=" N LEU D 57 " pdb=" O1 PO4 D 801 " model vdw 1.988 3.120 nonbonded pdb=" N LEU G 57 " pdb=" O1 PO4 G 801 " model vdw 2.038 3.120 nonbonded pdb=" OG SER F 593 " pdb=" O LEU F 598 " model vdw 2.089 3.040 nonbonded pdb=" N GLY C 58 " pdb=" O1 PO4 C 801 " model vdw 2.114 3.120 nonbonded pdb=" OG SER B 593 " pdb=" O LEU B 598 " model vdw 2.116 3.040 ... (remaining 336132 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.760 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.006 0.378 39837 Z= 0.292 Angle : 0.582 12.794 54089 Z= 0.308 Chirality : 0.038 0.227 6027 Planarity : 0.004 0.085 7217 Dihedral : 14.379 90.027 14938 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.03 % Allowed : 0.13 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.12), residues: 5019 helix: 1.66 (0.10), residues: 2576 sheet: -0.47 (0.19), residues: 651 loop : -0.01 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 718 TYR 0.017 0.001 TYR D 271 PHE 0.013 0.001 PHE B 571 TRP 0.022 0.001 TRP E 511 HIS 0.004 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00591 (39837) covalent geometry : angle 0.58249 (54089) hydrogen bonds : bond 0.12032 ( 2206) hydrogen bonds : angle 5.63214 ( 6369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 THR cc_start: 0.6921 (m) cc_final: 0.6635 (p) REVERT: G 141 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8118 (tm-30) REVERT: E 141 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 136 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7990 (mmpt) REVERT: B 141 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7933 (tm130) REVERT: C 278 PHE cc_start: 0.7317 (m-10) cc_final: 0.7113 (m-80) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.9064 time to fit residues: 468.6767 Evaluate side-chains 288 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS G 355 GLN ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 696 GLN ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 696 GLN D 100 HIS ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS C 151 GLN C 160 ASN ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.148094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111863 restraints weight = 56470.189| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.56 r_work: 0.3693 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39837 Z= 0.189 Angle : 0.577 8.184 54089 Z= 0.288 Chirality : 0.039 0.156 6027 Planarity : 0.005 0.057 7217 Dihedral : 4.247 44.773 5600 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.96 % Allowed : 8.43 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 5019 helix: 1.59 (0.10), residues: 2639 sheet: -0.49 (0.20), residues: 637 loop : -0.05 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 708 TYR 0.022 0.002 TYR B 575 PHE 0.024 0.001 PHE C 326 TRP 0.021 0.002 TRP E 511 HIS 0.002 0.001 HIS C 670 Details of bonding type rmsd covalent geometry : bond 0.00437 (39837) covalent geometry : angle 0.57673 (54089) hydrogen bonds : bond 0.04111 ( 2206) hydrogen bonds : angle 4.65538 ( 6369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 310 time to evaluate : 1.373 Fit side-chains REVERT: A 1 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6643 (ppp) REVERT: A 273 THR cc_start: 0.7022 (m) cc_final: 0.6598 (p) REVERT: A 573 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6112 (mp10) REVERT: A 688 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7145 (mmp-170) REVERT: G 137 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: G 141 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8237 (tm-30) REVERT: G 476 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: F 73 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7782 (pm20) REVERT: F 117 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7672 (tt0) REVERT: F 356 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8375 (ptt) REVERT: F 542 PHE cc_start: 0.7964 (m-10) cc_final: 0.7734 (m-10) REVERT: F 573 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6154 (mp10) REVERT: E 141 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8228 (tm130) REVERT: E 273 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6636 (p) REVERT: D 1 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6841 (ppp) REVERT: D 298 ARG cc_start: 0.8503 (mmt-90) cc_final: 0.8150 (mmt-90) REVERT: D 331 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7764 (mmm160) REVERT: B 1 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6620 (ppp) REVERT: B 136 LYS cc_start: 0.8232 (ttpp) cc_final: 0.8025 (tttp) REVERT: B 137 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: B 141 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8059 (tm130) REVERT: B 298 ARG cc_start: 0.8557 (mmt-90) cc_final: 0.8284 (mmt-90) REVERT: B 356 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8443 (ptt) REVERT: B 573 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5602 (mp10) REVERT: B 708 ARG cc_start: 0.7515 (mtt90) cc_final: 0.7156 (mtt-85) REVERT: B 710 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5901 (mm-30) REVERT: C 1 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6588 (ppp) REVERT: C 137 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: C 278 PHE cc_start: 0.7509 (m-10) cc_final: 0.6944 (m-80) outliers start: 78 outliers final: 21 residues processed: 355 average time/residue: 0.9363 time to fit residues: 384.2209 Evaluate side-chains 316 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain G residue 137 GLU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 597 ASN Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 560 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 97 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 479 optimal weight: 7.9990 chunk 384 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 489 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 462 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 306 GLN A 527 HIS F 527 HIS ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 623 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.148677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112688 restraints weight = 56215.984| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.55 r_work: 0.3705 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39837 Z= 0.144 Angle : 0.536 8.672 54089 Z= 0.265 Chirality : 0.038 0.153 6027 Planarity : 0.004 0.063 7217 Dihedral : 4.173 45.008 5600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.86 % Allowed : 10.29 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.12), residues: 5019 helix: 1.70 (0.10), residues: 2639 sheet: -0.46 (0.20), residues: 637 loop : -0.01 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 126 TYR 0.019 0.002 TYR B 575 PHE 0.019 0.001 PHE D 326 TRP 0.022 0.002 TRP E 511 HIS 0.003 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00330 (39837) covalent geometry : angle 0.53561 (54089) hydrogen bonds : bond 0.03748 ( 2206) hydrogen bonds : angle 4.36792 ( 6369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 1.494 Fit side-chains REVERT: A 1 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6667 (ppp) REVERT: A 126 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7823 (tpp80) REVERT: A 273 THR cc_start: 0.6963 (m) cc_final: 0.6669 (p) REVERT: A 559 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5441 (mp0) REVERT: A 573 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.5949 (mp10) REVERT: A 688 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7060 (mmp80) REVERT: G 1 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: G 141 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8253 (tm-30) REVERT: G 298 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.8364 (mmt-90) REVERT: G 326 PHE cc_start: 0.8290 (t80) cc_final: 0.8073 (t80) REVERT: G 476 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: F 73 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7809 (pm20) REVERT: F 117 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7729 (tt0) REVERT: F 356 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8348 (ptt) REVERT: F 542 PHE cc_start: 0.7902 (m-10) cc_final: 0.7679 (m-10) REVERT: F 688 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7285 (mmp-170) REVERT: F 690 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: E 141 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8216 (tm130) REVERT: E 356 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8521 (ptt) REVERT: D 1 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6813 (ppp) REVERT: D 331 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7838 (mmm160) REVERT: D 573 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.5925 (mp-120) REVERT: B 1 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: B 136 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7990 (mmpt) REVERT: B 141 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8043 (tm130) REVERT: B 296 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7653 (mt) REVERT: B 356 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8462 (ptt) REVERT: B 573 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5560 (mp10) REVERT: B 708 ARG cc_start: 0.7452 (mtt90) cc_final: 0.7133 (mtt-85) REVERT: C 1 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6620 (ppp) REVERT: C 143 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7986 (pt) REVERT: C 278 PHE cc_start: 0.7631 (m-10) cc_final: 0.7003 (m-80) REVERT: C 581 ASP cc_start: 0.6631 (p0) cc_final: 0.5755 (t70) outliers start: 74 outliers final: 25 residues processed: 334 average time/residue: 0.9117 time to fit residues: 355.8559 Evaluate side-chains 310 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 327 LYS Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 573 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 305 optimal weight: 0.6980 chunk 316 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 317 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 446 optimal weight: 6.9990 chunk 490 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS A 653 ASN G 16 ASN ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.158567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120585 restraints weight = 58801.242| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.37 r_work: 0.3679 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 39837 Z= 0.209 Angle : 0.564 8.680 54089 Z= 0.280 Chirality : 0.039 0.153 6027 Planarity : 0.005 0.057 7217 Dihedral : 4.282 44.534 5600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 2.31 % Allowed : 11.54 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 5019 helix: 1.62 (0.10), residues: 2639 sheet: -0.50 (0.19), residues: 637 loop : -0.01 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 708 TYR 0.021 0.002 TYR G 557 PHE 0.015 0.001 PHE E 326 TRP 0.022 0.002 TRP D 511 HIS 0.003 0.001 HIS G 670 Details of bonding type rmsd covalent geometry : bond 0.00488 (39837) covalent geometry : angle 0.56423 (54089) hydrogen bonds : bond 0.03879 ( 2206) hydrogen bonds : angle 4.39158 ( 6369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 283 time to evaluate : 1.266 Fit side-chains REVERT: A 1 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6763 (ppp) REVERT: A 126 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7885 (tpp80) REVERT: A 273 THR cc_start: 0.7056 (m) cc_final: 0.6612 (p) REVERT: A 542 PHE cc_start: 0.7450 (m-10) cc_final: 0.7198 (m-10) REVERT: A 559 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5567 (mp0) REVERT: A 573 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6039 (mp10) REVERT: A 688 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7134 (mmp80) REVERT: G 141 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8244 (tm-30) REVERT: F 117 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7787 (tt0) REVERT: F 318 LYS cc_start: 0.7444 (ptmm) cc_final: 0.7221 (pptt) REVERT: F 356 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8320 (ptt) REVERT: F 542 PHE cc_start: 0.7978 (m-10) cc_final: 0.7774 (m-10) REVERT: F 573 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: F 690 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: E 141 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8204 (tm130) REVERT: E 356 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8556 (ptt) REVERT: E 690 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: D 1 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6901 (ppp) REVERT: D 331 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7900 (mmm160) REVERT: B 1 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6691 (ppp) REVERT: B 141 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7987 (tm130) REVERT: B 331 ARG cc_start: 0.7615 (mmp80) cc_final: 0.7408 (mmp80) REVERT: B 356 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8437 (ptt) REVERT: B 506 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5517 (mp0) REVERT: B 573 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.5737 (mp10) REVERT: B 708 ARG cc_start: 0.7522 (mtt90) cc_final: 0.7192 (mtt-85) REVERT: B 710 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5970 (mm-30) REVERT: C 1 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6686 (ppp) REVERT: C 14 ILE cc_start: 0.8081 (pt) cc_final: 0.7867 (pp) REVERT: C 143 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8033 (pt) REVERT: C 237 ARG cc_start: 0.7884 (tmm-80) cc_final: 0.7557 (ttt180) REVERT: C 278 PHE cc_start: 0.7605 (m-10) cc_final: 0.7025 (m-80) REVERT: C 298 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.7974 (mmp80) REVERT: C 506 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: C 581 ASP cc_start: 0.6648 (p0) cc_final: 0.5810 (t70) outliers start: 92 outliers final: 39 residues processed: 337 average time/residue: 0.8562 time to fit residues: 339.7365 Evaluate side-chains 325 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 597 ASN Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 690 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 610 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 85 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 150 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 486 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.119244 restraints weight = 58569.111| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.41 r_work: 0.3655 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39837 Z= 0.131 Angle : 0.518 8.986 54089 Z= 0.255 Chirality : 0.037 0.153 6027 Planarity : 0.004 0.052 7217 Dihedral : 4.129 44.922 5600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.26 % Allowed : 12.45 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.12), residues: 5019 helix: 1.82 (0.10), residues: 2632 sheet: -0.42 (0.20), residues: 637 loop : 0.04 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 708 TYR 0.018 0.002 TYR B 575 PHE 0.018 0.001 PHE A 326 TRP 0.025 0.001 TRP E 511 HIS 0.002 0.000 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00294 (39837) covalent geometry : angle 0.51756 (54089) hydrogen bonds : bond 0.03599 ( 2206) hydrogen bonds : angle 4.18958 ( 6369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 288 time to evaluate : 1.622 Fit side-chains REVERT: A 1 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6620 (ppp) REVERT: A 126 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7910 (tpp80) REVERT: A 273 THR cc_start: 0.7000 (m) cc_final: 0.6582 (p) REVERT: A 542 PHE cc_start: 0.7362 (m-10) cc_final: 0.7128 (m-10) REVERT: A 559 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5455 (mp0) REVERT: A 573 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.5854 (mp10) REVERT: A 688 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7059 (mmp80) REVERT: G 141 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8263 (tm-30) REVERT: G 298 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8389 (mmt-90) REVERT: G 476 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: G 542 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: F 117 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7746 (mt-10) REVERT: F 126 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7854 (tpp80) REVERT: F 139 ARG cc_start: 0.8006 (tmm-80) cc_final: 0.7693 (ttm-80) REVERT: F 573 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: F 688 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7287 (mmp-170) REVERT: F 690 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: E 141 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8230 (tm130) REVERT: E 273 THR cc_start: 0.7028 (m) cc_final: 0.6697 (p) REVERT: E 326 PHE cc_start: 0.8192 (t80) cc_final: 0.7944 (t80) REVERT: E 356 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8525 (ptt) REVERT: D 1 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6854 (ppp) REVERT: D 125 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (mt) REVERT: B 1 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6658 (ppp) REVERT: B 137 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: B 141 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7967 (tm130) REVERT: B 506 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5606 (mp0) REVERT: B 573 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.5764 (mp10) REVERT: B 708 ARG cc_start: 0.7436 (mtt90) cc_final: 0.7072 (mtt-85) REVERT: C 1 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6711 (ppp) REVERT: C 143 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7910 (pt) REVERT: C 278 PHE cc_start: 0.7647 (m-10) cc_final: 0.7060 (m-80) REVERT: C 298 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.8047 (mmp80) REVERT: C 506 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: C 581 ASP cc_start: 0.6541 (p0) cc_final: 0.5656 (t70) outliers start: 90 outliers final: 30 residues processed: 341 average time/residue: 0.8765 time to fit residues: 354.1830 Evaluate side-chains 323 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 476 GLU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 542 PHE Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 610 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 336 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 325 optimal weight: 0.9990 chunk 475 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 315 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 334 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS G 16 ASN ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111192 restraints weight = 56351.634| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.56 r_work: 0.3720 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39837 Z= 0.168 Angle : 0.541 12.542 54089 Z= 0.267 Chirality : 0.038 0.153 6027 Planarity : 0.004 0.054 7217 Dihedral : 4.170 44.570 5600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 2.31 % Allowed : 13.03 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.12), residues: 5019 helix: 1.79 (0.10), residues: 2632 sheet: -0.41 (0.20), residues: 637 loop : 0.06 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 708 TYR 0.020 0.002 TYR B 575 PHE 0.020 0.001 PHE G 326 TRP 0.021 0.002 TRP G 511 HIS 0.003 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00387 (39837) covalent geometry : angle 0.54105 (54089) hydrogen bonds : bond 0.03684 ( 2206) hydrogen bonds : angle 4.20813 ( 6369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 282 time to evaluate : 1.572 Fit side-chains REVERT: A 1 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6713 (ppp) REVERT: A 126 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7919 (tpp80) REVERT: A 273 THR cc_start: 0.6998 (m) cc_final: 0.6592 (p) REVERT: A 542 PHE cc_start: 0.7373 (m-10) cc_final: 0.7165 (m-10) REVERT: A 559 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5516 (mp0) REVERT: A 573 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5882 (mp10) REVERT: A 688 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7093 (mmp80) REVERT: G 1 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6946 (ppp) REVERT: G 121 GLN cc_start: 0.7831 (mm110) cc_final: 0.7483 (mm-40) REVERT: G 141 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8285 (tm-30) REVERT: G 542 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: F 117 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7798 (mt-10) REVERT: F 126 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7893 (tpp80) REVERT: F 139 ARG cc_start: 0.8029 (tmm-80) cc_final: 0.7731 (ttm-80) REVERT: F 356 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8378 (ptt) REVERT: F 573 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6758 (mp10) REVERT: F 690 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: E 141 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8240 (tm130) REVERT: E 200 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7379 (tpp-160) REVERT: D 1 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6851 (ppp) REVERT: D 125 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7968 (mt) REVERT: D 491 THR cc_start: 0.8193 (p) cc_final: 0.7967 (m) REVERT: D 573 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.5999 (mp10) REVERT: B 1 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6680 (ppp) REVERT: B 137 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: B 141 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8007 (tm130) REVERT: B 356 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8488 (ptt) REVERT: B 506 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5619 (mp0) REVERT: B 573 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.5758 (mp10) REVERT: B 708 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7100 (mtt-85) REVERT: C 1 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6679 (ppp) REVERT: C 143 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7934 (pt) REVERT: C 237 ARG cc_start: 0.7831 (tmm-80) cc_final: 0.7445 (ttt180) REVERT: C 278 PHE cc_start: 0.7672 (m-10) cc_final: 0.7087 (m-80) REVERT: C 298 ARG cc_start: 0.8370 (mmt-90) cc_final: 0.8091 (mmp80) REVERT: C 581 ASP cc_start: 0.6506 (p0) cc_final: 0.5653 (t70) outliers start: 92 outliers final: 46 residues processed: 337 average time/residue: 0.8912 time to fit residues: 355.3574 Evaluate side-chains 338 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 542 PHE Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 476 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 573 GLN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 447 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 486 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS G 560 HIS ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.158454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120376 restraints weight = 58749.631| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.36 r_work: 0.3629 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 39837 Z= 0.217 Angle : 0.575 11.288 54089 Z= 0.285 Chirality : 0.039 0.154 6027 Planarity : 0.004 0.055 7217 Dihedral : 4.283 44.359 5600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 2.46 % Allowed : 13.28 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.12), residues: 5019 helix: 1.70 (0.10), residues: 2625 sheet: -0.46 (0.19), residues: 637 loop : 0.03 (0.16), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 708 TYR 0.022 0.002 TYR A 510 PHE 0.021 0.001 PHE D 326 TRP 0.020 0.002 TRP D 511 HIS 0.003 0.001 HIS G 670 Details of bonding type rmsd covalent geometry : bond 0.00507 (39837) covalent geometry : angle 0.57535 (54089) hydrogen bonds : bond 0.03863 ( 2206) hydrogen bonds : angle 4.31359 ( 6369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 289 time to evaluate : 1.343 Fit side-chains REVERT: A 1 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6734 (ppp) REVERT: A 273 THR cc_start: 0.7083 (m) cc_final: 0.6675 (p) REVERT: A 542 PHE cc_start: 0.7533 (m-10) cc_final: 0.7295 (m-10) REVERT: A 559 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5501 (mp0) REVERT: A 573 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6016 (mp10) REVERT: A 688 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7131 (mmp80) REVERT: G 121 GLN cc_start: 0.7881 (mm110) cc_final: 0.7575 (mm-40) REVERT: G 141 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8281 (tm-30) REVERT: F 139 ARG cc_start: 0.8073 (tmm-80) cc_final: 0.7782 (ttm-80) REVERT: F 356 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8382 (ptt) REVERT: F 573 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: F 690 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: E 141 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8259 (tm130) REVERT: E 200 ARG cc_start: 0.7604 (tpp-160) cc_final: 0.7400 (tpp-160) REVERT: E 378 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: D 1 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6867 (ppp) REVERT: D 125 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8050 (mt) REVERT: D 573 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6138 (mp10) REVERT: B 1 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6672 (ppp) REVERT: B 137 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: B 141 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8010 (tm130) REVERT: B 356 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8485 (ptt) REVERT: B 506 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: B 573 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.5952 (mp10) REVERT: B 708 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7169 (mtt-85) REVERT: C 1 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6708 (ppp) REVERT: C 143 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7969 (pt) REVERT: C 237 ARG cc_start: 0.7877 (tmm-80) cc_final: 0.7594 (ttt-90) REVERT: C 278 PHE cc_start: 0.7711 (m-10) cc_final: 0.7132 (m-80) REVERT: C 298 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.8071 (mmp80) REVERT: C 581 ASP cc_start: 0.6527 (p0) cc_final: 0.5682 (t70) outliers start: 98 outliers final: 45 residues processed: 346 average time/residue: 0.8996 time to fit residues: 366.5065 Evaluate side-chains 340 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 573 GLN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 84 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 340 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 479 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 443 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS C 219 GLN ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.158597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120601 restraints weight = 58548.924| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.35 r_work: 0.3673 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39837 Z= 0.201 Angle : 0.572 11.228 54089 Z= 0.283 Chirality : 0.039 0.153 6027 Planarity : 0.004 0.053 7217 Dihedral : 4.291 44.543 5600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.11 % Allowed : 14.16 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.12), residues: 5019 helix: 1.69 (0.10), residues: 2625 sheet: -0.48 (0.19), residues: 637 loop : 0.04 (0.16), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 280 TYR 0.022 0.002 TYR A 510 PHE 0.022 0.001 PHE G 326 TRP 0.024 0.002 TRP D 511 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00466 (39837) covalent geometry : angle 0.57212 (54089) hydrogen bonds : bond 0.03839 ( 2206) hydrogen bonds : angle 4.29132 ( 6369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 284 time to evaluate : 1.314 Fit side-chains REVERT: A 1 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6662 (ppp) REVERT: A 273 THR cc_start: 0.6978 (m) cc_final: 0.6595 (p) REVERT: A 559 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5574 (mp0) REVERT: A 573 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6112 (mp10) REVERT: A 688 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7126 (mmp80) REVERT: G 121 GLN cc_start: 0.7850 (mm110) cc_final: 0.7546 (mm-40) REVERT: G 141 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8303 (tm-30) REVERT: G 378 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: G 542 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: G 559 GLU cc_start: 0.5928 (pt0) cc_final: 0.4863 (pm20) REVERT: F 137 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: F 139 ARG cc_start: 0.8077 (tmm-80) cc_final: 0.7804 (ttm-80) REVERT: F 356 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8368 (ptt) REVERT: F 559 GLU cc_start: 0.7209 (pt0) cc_final: 0.6235 (pm20) REVERT: F 573 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6010 (mp10) REVERT: F 690 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: E 141 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8298 (tm130) REVERT: E 378 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: D 1 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6816 (ppp) REVERT: D 573 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: B 1 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6611 (ppp) REVERT: B 137 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: B 141 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7999 (tm130) REVERT: B 356 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8474 (ptt) REVERT: B 506 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5606 (mp0) REVERT: B 559 GLU cc_start: 0.7458 (pt0) cc_final: 0.6367 (pm20) REVERT: B 573 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6051 (mp10) REVERT: B 708 ARG cc_start: 0.7484 (mtt90) cc_final: 0.7158 (mtt-85) REVERT: C 1 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6674 (ppp) REVERT: C 143 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8021 (pt) REVERT: C 237 ARG cc_start: 0.7875 (tmm-80) cc_final: 0.7586 (ttt-90) REVERT: C 278 PHE cc_start: 0.7675 (m-10) cc_final: 0.7118 (m-80) REVERT: C 298 ARG cc_start: 0.8322 (mmt-90) cc_final: 0.8055 (mmp80) REVERT: C 506 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5477 (mp0) REVERT: C 581 ASP cc_start: 0.6498 (p0) cc_final: 0.5643 (t70) outliers start: 84 outliers final: 46 residues processed: 337 average time/residue: 0.8559 time to fit residues: 340.0001 Evaluate side-chains 349 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 378 GLU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 542 PHE Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 573 GLN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 469 optimal weight: 7.9990 chunk 489 optimal weight: 1.9990 chunk 406 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 470 optimal weight: 0.9980 chunk 443 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 380 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.158741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.120837 restraints weight = 58889.258| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.36 r_work: 0.3635 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 39837 Z= 0.188 Angle : 0.569 10.963 54089 Z= 0.281 Chirality : 0.039 0.153 6027 Planarity : 0.004 0.052 7217 Dihedral : 4.276 44.752 5600 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.04 % Allowed : 14.26 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.12), residues: 5019 helix: 1.69 (0.10), residues: 2639 sheet: -0.49 (0.19), residues: 637 loop : 0.07 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 126 TYR 0.020 0.002 TYR A 510 PHE 0.023 0.001 PHE D 326 TRP 0.024 0.002 TRP G 511 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00437 (39837) covalent geometry : angle 0.56877 (54089) hydrogen bonds : bond 0.03796 ( 2206) hydrogen bonds : angle 4.26539 ( 6369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 283 time to evaluate : 1.969 Fit side-chains REVERT: A 1 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6676 (ppp) REVERT: A 141 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7914 (tm130) REVERT: A 273 THR cc_start: 0.7000 (m) cc_final: 0.6639 (p) REVERT: A 559 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5494 (mp0) REVERT: A 573 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6027 (mp10) REVERT: A 688 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7146 (mmp80) REVERT: G 1 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7046 (ppp) REVERT: G 121 GLN cc_start: 0.7883 (mm110) cc_final: 0.7480 (mm-40) REVERT: G 141 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8026 (tm130) REVERT: G 378 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: G 542 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: F 126 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7457 (mtm110) REVERT: F 137 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: F 139 ARG cc_start: 0.8081 (tmm-80) cc_final: 0.7802 (ttm-80) REVERT: F 356 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8379 (ptt) REVERT: F 559 GLU cc_start: 0.7195 (pt0) cc_final: 0.6313 (pm20) REVERT: F 573 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: F 690 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: E 141 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 273 THR cc_start: 0.7112 (m) cc_final: 0.6882 (p) REVERT: E 378 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: E 690 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: D 1 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6859 (ppp) REVERT: D 573 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6151 (mp10) REVERT: B 1 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6635 (ppp) REVERT: B 136 LYS cc_start: 0.8296 (tttm) cc_final: 0.8046 (tttp) REVERT: B 137 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: B 141 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7993 (tm130) REVERT: B 219 GLN cc_start: 0.8627 (mp10) cc_final: 0.8344 (mp10) REVERT: B 356 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8465 (ptt) REVERT: B 506 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: B 559 GLU cc_start: 0.7398 (pt0) cc_final: 0.6310 (pm20) REVERT: B 573 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6019 (mp10) REVERT: B 708 ARG cc_start: 0.7507 (mtt90) cc_final: 0.7181 (mtt-85) REVERT: C 1 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6698 (ppp) REVERT: C 219 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7978 (mm-40) REVERT: C 237 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7599 (ttt-90) REVERT: C 278 PHE cc_start: 0.7662 (m-10) cc_final: 0.7118 (m-80) REVERT: C 298 ARG cc_start: 0.8342 (mmt-90) cc_final: 0.8080 (mmp80) REVERT: C 506 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5510 (mp0) REVERT: C 581 ASP cc_start: 0.6541 (p0) cc_final: 0.5685 (t70) outliers start: 81 outliers final: 50 residues processed: 335 average time/residue: 0.8946 time to fit residues: 354.0239 Evaluate side-chains 349 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 277 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 378 GLU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 542 PHE Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 690 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 573 GLN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 329 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 469 optimal weight: 7.9990 chunk 456 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 350 optimal weight: 0.8980 chunk 412 optimal weight: 1.9990 chunk 407 optimal weight: 5.9990 chunk 445 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.158687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120786 restraints weight = 58394.424| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.35 r_work: 0.3639 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 39837 Z= 0.165 Angle : 0.654 59.200 54089 Z= 0.345 Chirality : 0.038 0.152 6027 Planarity : 0.004 0.052 7217 Dihedral : 4.275 44.724 5600 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 1.84 % Allowed : 14.44 % Favored : 83.73 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.12), residues: 5019 helix: 1.72 (0.10), residues: 2639 sheet: -0.50 (0.19), residues: 637 loop : 0.07 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 331 TYR 0.020 0.002 TYR A 510 PHE 0.015 0.001 PHE E 326 TRP 0.025 0.002 TRP G 511 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00375 (39837) covalent geometry : angle 0.65398 (54089) hydrogen bonds : bond 0.03809 ( 2206) hydrogen bonds : angle 4.26404 ( 6369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10038 Ramachandran restraints generated. 5019 Oldfield, 0 Emsley, 5019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 275 time to evaluate : 1.651 Fit side-chains REVERT: A 1 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6675 (ppp) REVERT: A 273 THR cc_start: 0.6986 (m) cc_final: 0.6624 (p) REVERT: A 559 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5481 (mp0) REVERT: A 573 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6017 (mp10) REVERT: A 688 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7129 (mmp80) REVERT: G 1 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7038 (ppp) REVERT: G 121 GLN cc_start: 0.7885 (mm110) cc_final: 0.7529 (mm-40) REVERT: G 141 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8023 (tm130) REVERT: G 378 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: G 542 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: F 126 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7534 (mtm180) REVERT: F 137 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: F 139 ARG cc_start: 0.8076 (tmm-80) cc_final: 0.7800 (ttm-80) REVERT: F 356 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8368 (ptt) REVERT: F 559 GLU cc_start: 0.7191 (pt0) cc_final: 0.6305 (pm20) REVERT: F 573 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.5966 (mp10) REVERT: F 690 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: E 141 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 273 THR cc_start: 0.7113 (m) cc_final: 0.6883 (p) REVERT: E 378 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: E 690 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6517 (pm20) REVERT: D 1 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6844 (ppp) REVERT: D 573 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6148 (mp10) REVERT: B 1 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6638 (ppp) REVERT: B 136 LYS cc_start: 0.8306 (tttm) cc_final: 0.8056 (tttp) REVERT: B 137 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: B 141 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7989 (tm130) REVERT: B 219 GLN cc_start: 0.8629 (mp10) cc_final: 0.8345 (mp10) REVERT: B 356 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8451 (ptt) REVERT: B 506 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: B 559 GLU cc_start: 0.7393 (pt0) cc_final: 0.6264 (pm20) REVERT: B 573 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6005 (mp10) REVERT: B 708 ARG cc_start: 0.7506 (mtt90) cc_final: 0.7179 (mtt-85) REVERT: C 1 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6702 (ppp) REVERT: C 237 ARG cc_start: 0.7899 (tmm-80) cc_final: 0.7599 (ttt-90) REVERT: C 278 PHE cc_start: 0.7656 (m-10) cc_final: 0.7127 (m-80) REVERT: C 298 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.8076 (mmp80) REVERT: C 506 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5506 (mp0) REVERT: C 581 ASP cc_start: 0.6552 (p0) cc_final: 0.5677 (t70) outliers start: 73 outliers final: 47 residues processed: 323 average time/residue: 0.8899 time to fit residues: 340.5425 Evaluate side-chains 340 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 272 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 378 GLU Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 542 PHE Chi-restraints excluded: chain G residue 566 THR Chi-restraints excluded: chain G residue 690 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 273 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 573 GLN Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 690 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 378 GLU Chi-restraints excluded: chain E residue 566 THR Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 690 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 573 GLN Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 444 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 441 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 447 optimal weight: 20.0000 chunk 321 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 chunk 360 optimal weight: 0.7980 chunk 495 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN ** E 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.158711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120785 restraints weight = 58814.815| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.36 r_work: 0.3678 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 39837 Z= 0.165 Angle : 0.654 59.200 54089 Z= 0.345 Chirality : 0.038 0.152 6027 Planarity : 0.004 0.052 7217 Dihedral : 4.275 44.724 5600 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 1.71 % Allowed : 14.66 % Favored : 83.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.12), residues: 5019 helix: 1.72 (0.10), residues: 2639 sheet: -0.50 (0.19), residues: 637 loop : 0.07 (0.16), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 331 TYR 0.020 0.002 TYR A 510 PHE 0.015 0.001 PHE E 326 TRP 0.025 0.002 TRP G 511 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00375 (39837) covalent geometry : angle 0.65398 (54089) hydrogen bonds : bond 0.03809 ( 2206) hydrogen bonds : angle 4.26404 ( 6369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13952.59 seconds wall clock time: 237 minutes 59.47 seconds (14279.47 seconds total)