Starting phenix.real_space_refine on Sun Mar 24 12:22:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbn_14587/03_2024/7zbn_14587_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbn_14587/03_2024/7zbn_14587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbn_14587/03_2024/7zbn_14587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbn_14587/03_2024/7zbn_14587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbn_14587/03_2024/7zbn_14587_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbn_14587/03_2024/7zbn_14587_trim_updated.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 104 5.16 5 C 13520 2.51 5 N 3636 2.21 5 O 3860 1.98 5 H 20460 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41582 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9830 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9893 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 26, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 9830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9830 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 9893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9893 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 26, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Time building chain proxies: 16.77, per 1000 atoms: 0.40 Number of scatterers: 41582 At special positions: 0 Unit cell: (120.7, 108.63, 137.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 2 15.00 O 3860 8.00 N 3636 7.00 C 13520 6.00 H 20460 1.00 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 - 3.50 Amino acid : False - 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: 35.53 Conformation dependent library (CDL) restraints added in 4.0 seconds 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 14 sheets defined 49.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.442A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 120 through 137 removed outlier: 5.026A pdb=" N TRP A 124 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU A 127 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 133 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS A 137 " --> pdb=" O TRP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 167 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.714A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 removed outlier: 3.945A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.656A pdb=" N ARG A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 294 through 311 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 377 through 409 Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 579 through 596 removed outlier: 3.891A pdb=" N SER A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 5.237A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 4.444A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 120 through 137 removed outlier: 4.887A pdb=" N TRP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU B 127 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 130 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 131 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS B 137 " --> pdb=" O TRP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 167 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.702A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 removed outlier: 4.123A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.725A pdb=" N ARG B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 294 through 311 Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 377 through 409 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 560 through 576 Processing helix chain 'B' and resid 579 through 596 removed outlier: 3.935A pdb=" N SER B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASP B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 5.238A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 310 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 321 through 331 removed outlier: 4.397A pdb=" N TYR F 331 " --> pdb=" O LYS F 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.441A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 120 through 137 removed outlier: 5.030A pdb=" N TRP C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 127 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 130 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 133 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N CYS C 137 " --> pdb=" O TRP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 167 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.712A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.923A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 removed outlier: 3.657A pdb=" N ARG C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 294 through 311 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 377 through 409 Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 422 through 435 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'C' and resid 493 through 498 Processing helix chain 'C' and resid 514 through 521 Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 545 through 548 Processing helix chain 'C' and resid 560 through 576 Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.897A pdb=" N SER C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 616 removed outlier: 5.235A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 4.446A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 120 through 137 removed outlier: 4.885A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU D 127 " --> pdb=" O TRP D 124 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 130 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS D 137 " --> pdb=" O TRP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 167 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.697A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 removed outlier: 4.120A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 236 removed outlier: 3.701A pdb=" N ARG D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'D' and resid 294 through 311 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 377 through 409 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 422 through 435 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 493 through 498 Processing helix chain 'D' and resid 514 through 521 Processing helix chain 'D' and resid 533 through 541 Processing helix chain 'D' and resid 545 through 548 Processing helix chain 'D' and resid 560 through 576 Processing helix chain 'D' and resid 579 through 596 removed outlier: 3.928A pdb=" N SER D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU D 595 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 616 removed outlier: 5.235A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 321 through 330 Processing helix chain 'H' and resid 302 through 310 Processing helix chain 'H' and resid 321 through 331 removed outlier: 4.400A pdb=" N TYR H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.203A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 254 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR A 204 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 256 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= C, first strand: chain 'A' and resid 323 through 328 removed outlier: 6.324A pdb=" N THR A 361 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE A 326 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 363 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 328 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE A 365 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= E, first strand: chain 'B' and resid 77 through 79 removed outlier: 4.018A pdb=" N LEU B 113 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 254 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR B 204 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 256 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.318A pdb=" N THR B 361 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE B 326 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 363 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE B 328 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE B 365 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 502 through 504 Processing sheet with id= H, first strand: chain 'C' and resid 62 through 65 removed outlier: 6.204A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 254 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR C 204 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 256 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 77 through 79 Processing sheet with id= J, first strand: chain 'C' and resid 323 through 328 removed outlier: 6.329A pdb=" N THR C 361 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE C 326 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 363 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 328 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE C 365 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 526 through 529 Processing sheet with id= L, first strand: chain 'D' and resid 77 through 79 removed outlier: 4.019A pdb=" N LEU D 113 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL D 65 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL D 254 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR D 204 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 256 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 323 through 328 removed outlier: 6.326A pdb=" N THR D 361 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE D 326 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL D 363 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE D 328 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE D 365 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 502 through 504 914 hydrogen bonds defined for protein. 2610 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: 17.28 Time building geometry restraints manager: 36.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20408 1.03 - 1.23: 79 1.23 - 1.42: 9509 1.42 - 1.61: 11980 1.61 - 1.81: 156 Bond restraints: 42132 Sorted by residual: bond pdb=" CB THR B 589 " pdb=" CG2 THR B 589 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CB THR D 589 " pdb=" CG2 THR D 589 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.86e+00 bond pdb=" CB THR A 589 " pdb=" CG2 THR A 589 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB THR C 589 " pdb=" CG2 THR C 589 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CG LEU B 188 " pdb=" CD1 LEU B 188 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.34e+00 ... (remaining 42127 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.19: 1085 107.19 - 113.91: 47923 113.91 - 120.63: 15666 120.63 - 127.35: 10758 127.35 - 134.07: 278 Bond angle restraints: 75710 Sorted by residual: angle pdb=" N GLU D 235 " pdb=" CA GLU D 235 " pdb=" CB GLU D 235 " ideal model delta sigma weight residual 110.32 114.99 -4.67 1.70e+00 3.46e-01 7.54e+00 angle pdb=" N GLU B 235 " pdb=" CA GLU B 235 " pdb=" CB GLU B 235 " ideal model delta sigma weight residual 110.32 114.92 -4.60 1.70e+00 3.46e-01 7.33e+00 angle pdb=" N ALA C 206 " pdb=" CA ALA C 206 " pdb=" C ALA C 206 " ideal model delta sigma weight residual 110.80 106.51 4.29 2.13e+00 2.20e-01 4.05e+00 angle pdb=" N ALA A 206 " pdb=" CA ALA A 206 " pdb=" C ALA A 206 " ideal model delta sigma weight residual 110.80 106.55 4.25 2.13e+00 2.20e-01 3.98e+00 angle pdb=" CA LEU C 282 " pdb=" CB LEU C 282 " pdb=" CG LEU C 282 " ideal model delta sigma weight residual 116.30 123.12 -6.82 3.50e+00 8.16e-02 3.80e+00 ... (remaining 75705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 17800 17.40 - 34.81: 1486 34.81 - 52.21: 437 52.21 - 69.61: 175 69.61 - 87.01: 36 Dihedral angle restraints: 19934 sinusoidal: 10518 harmonic: 9416 Sorted by residual: dihedral pdb=" CA ASP A 219 " pdb=" C ASP A 219 " pdb=" N PHE A 220 " pdb=" CA PHE A 220 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP C 219 " pdb=" C ASP C 219 " pdb=" N PHE C 220 " pdb=" CA PHE C 220 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 561 " pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " pdb=" OD1 ASP B 561 " ideal model delta sinusoidal sigma weight residual -30.00 -85.95 55.95 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 19931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2775 0.064 - 0.128: 320 0.128 - 0.192: 13 0.192 - 0.256: 0 0.256 - 0.320: 2 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CB ILE C 524 " pdb=" CA ILE C 524 " pdb=" CG1 ILE C 524 " pdb=" CG2 ILE C 524 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE A 524 " pdb=" CA ILE A 524 " pdb=" CG1 ILE A 524 " pdb=" CG2 ILE A 524 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA HIS D 180 " pdb=" N HIS D 180 " pdb=" C HIS D 180 " pdb=" CB HIS D 180 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 3107 not shown) Planarity restraints: 6276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 585 " 0.008 2.00e-02 2.50e+03 1.46e-02 3.20e+00 pdb=" CD GLN D 585 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN D 585 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN D 585 " 0.006 2.00e-02 2.50e+03 pdb="HE21 GLN D 585 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN D 585 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 585 " -0.008 2.00e-02 2.50e+03 1.28e-02 2.46e+00 pdb=" CD GLN B 585 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN B 585 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 585 " -0.005 2.00e-02 2.50e+03 pdb="HE21 GLN B 585 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 591 " 0.134 9.50e-02 1.11e+02 4.49e-02 2.29e+00 pdb=" NE ARG D 591 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 591 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 591 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 591 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG D 591 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG D 591 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 591 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 591 " -0.000 2.00e-02 2.50e+03 ... (remaining 6273 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2824 2.18 - 2.79: 88036 2.79 - 3.39: 130283 3.39 - 4.00: 176073 4.00 - 4.60: 270533 Nonbonded interactions: 667749 Sorted by model distance: nonbonded pdb=" O PRO D 506 " pdb="HH11 ARG D 555 " model vdw 1.578 1.850 nonbonded pdb=" O PRO B 506 " pdb="HH11 ARG B 555 " model vdw 1.583 1.850 nonbonded pdb=" O PRO A 506 " pdb="HH11 ARG A 555 " model vdw 1.591 1.850 nonbonded pdb=" O PRO C 506 " pdb="HH11 ARG C 555 " model vdw 1.592 1.850 nonbonded pdb=" OD2 ASP D 145 " pdb=" HE2 HIS D 240 " model vdw 1.610 1.850 ... (remaining 667744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 13 through 637 or (resid 638 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)))) selection = chain 'C' selection = (chain 'D' and (resid 13 through 637 or (resid 638 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=1.00 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: 1.050 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: 0.580 Extract box with map and model: 7.160 Check model and map are aligned: 0.570 Set scattering table: 0.390 Process input model: 130.680 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 0.065 21672 Z= 0.365 Angle : 0.551 6.825 29356 Z= 0.299 Chirality : 0.041 0.320 3110 Planarity : 0.004 0.060 3790 Dihedral : 15.388 87.014 7866 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2572 helix: 0.71 (0.13), residues: 1352 sheet: -1.53 (0.25), residues: 376 loop : 0.56 (0.24), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 129 HIS 0.005 0.001 HIS B 180 PHE 0.019 0.002 PHE B 307 TYR 0.014 0.002 TYR D 332 ARG 0.005 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7825 (ttt) cc_final: 0.7526 (ttm) REVERT: B 88 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7793 (ttmm) REVERT: B 92 ASP cc_start: 0.7085 (m-30) cc_final: 0.6884 (m-30) REVERT: B 427 MET cc_start: 0.7814 (ttt) cc_final: 0.7534 (ttm) REVERT: C 427 MET cc_start: 0.7817 (ttt) cc_final: 0.7518 (ttm) REVERT: D 88 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7775 (ttmm) REVERT: D 92 ASP cc_start: 0.7031 (m-30) cc_final: 0.6825 (m-30) REVERT: D 246 ARG cc_start: 0.8286 (ttt180) cc_final: 0.8078 (ttt180) REVERT: D 427 MET cc_start: 0.7820 (ttt) cc_final: 0.7528 (ttm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 3.0407 time to fit residues: 1180.2028 Evaluate side-chains 295 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 131 optimal weight: 0.0000 chunk 104 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 overall best weight: 2.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 577 GLN D 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21672 Z= 0.338 Angle : 0.526 5.531 29356 Z= 0.281 Chirality : 0.040 0.152 3110 Planarity : 0.004 0.053 3790 Dihedral : 5.052 63.350 2886 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.94 % Allowed : 6.62 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2572 helix: 0.74 (0.13), residues: 1346 sheet: -1.60 (0.25), residues: 380 loop : 0.62 (0.24), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 308 HIS 0.005 0.001 HIS A 180 PHE 0.019 0.002 PHE D 307 TYR 0.013 0.002 TYR D 332 ARG 0.005 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 298 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7400 (t) REVERT: A 427 MET cc_start: 0.7824 (ttt) cc_final: 0.7510 (ttm) REVERT: B 92 ASP cc_start: 0.7037 (m-30) cc_final: 0.6835 (m-30) REVERT: B 147 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: B 181 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6320 (mt-10) REVERT: B 427 MET cc_start: 0.7837 (ttt) cc_final: 0.7535 (ttm) REVERT: C 377 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7423 (t) REVERT: C 419 MET cc_start: 0.8026 (mmt) cc_final: 0.7628 (mmt) REVERT: C 427 MET cc_start: 0.7835 (ttt) cc_final: 0.7548 (ttm) REVERT: D 88 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7791 (ttmm) REVERT: D 92 ASP cc_start: 0.6983 (m-30) cc_final: 0.6772 (m-30) REVERT: D 181 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6305 (mt-10) REVERT: D 427 MET cc_start: 0.7819 (ttt) cc_final: 0.7513 (ttm) outliers start: 21 outliers final: 2 residues processed: 314 average time/residue: 3.2487 time to fit residues: 1157.4478 Evaluate side-chains 295 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 288 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 436 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21672 Z= 0.231 Angle : 0.480 5.373 29356 Z= 0.254 Chirality : 0.038 0.143 3110 Planarity : 0.004 0.036 3790 Dihedral : 4.809 65.933 2886 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.07 % Allowed : 7.16 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2572 helix: 0.98 (0.14), residues: 1348 sheet: -1.63 (0.25), residues: 390 loop : 0.67 (0.25), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 308 HIS 0.004 0.001 HIS D 180 PHE 0.014 0.001 PHE D 307 TYR 0.008 0.001 TYR A 221 ARG 0.003 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7349 (t) REVERT: A 427 MET cc_start: 0.7869 (ttt) cc_final: 0.7534 (ttm) REVERT: B 181 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: B 427 MET cc_start: 0.7857 (ttt) cc_final: 0.7527 (ttm) REVERT: C 246 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7821 (ttt180) REVERT: C 377 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7352 (t) REVERT: C 427 MET cc_start: 0.7831 (ttt) cc_final: 0.7502 (ttm) REVERT: D 181 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6162 (mt-10) REVERT: D 427 MET cc_start: 0.7824 (ttt) cc_final: 0.7496 (ttm) outliers start: 24 outliers final: 6 residues processed: 323 average time/residue: 3.1323 time to fit residues: 1142.5814 Evaluate side-chains 305 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 295 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 181 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21672 Z= 0.231 Angle : 0.477 5.129 29356 Z= 0.251 Chirality : 0.038 0.137 3110 Planarity : 0.003 0.034 3790 Dihedral : 4.739 65.287 2886 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.12 % Allowed : 8.72 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2572 helix: 1.07 (0.14), residues: 1348 sheet: -1.65 (0.25), residues: 400 loop : 0.74 (0.25), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 308 HIS 0.004 0.001 HIS D 180 PHE 0.014 0.001 PHE D 307 TYR 0.008 0.001 TYR C 221 ARG 0.006 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 300 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5968 (mp0) REVERT: A 296 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 427 MET cc_start: 0.7850 (ttt) cc_final: 0.7537 (ttm) REVERT: B 181 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.5901 (mp0) REVERT: B 296 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 427 MET cc_start: 0.7844 (ttt) cc_final: 0.7540 (ttm) REVERT: C 296 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7824 (mp) REVERT: C 427 MET cc_start: 0.7850 (ttt) cc_final: 0.7548 (ttm) REVERT: D 147 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6500 (mm-30) REVERT: D 181 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: D 296 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7846 (mp) REVERT: D 427 MET cc_start: 0.7850 (ttt) cc_final: 0.7534 (ttm) outliers start: 25 outliers final: 6 residues processed: 309 average time/residue: 3.2949 time to fit residues: 1158.3899 Evaluate side-chains 306 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 292 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain G residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 223 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 21672 Z= 0.392 Angle : 0.553 6.617 29356 Z= 0.294 Chirality : 0.041 0.157 3110 Planarity : 0.005 0.052 3790 Dihedral : 5.045 62.360 2886 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.79 % Allowed : 9.57 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2572 helix: 0.75 (0.13), residues: 1350 sheet: -1.60 (0.25), residues: 380 loop : 0.68 (0.24), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 308 HIS 0.006 0.001 HIS C 180 PHE 0.021 0.002 PHE A 307 TYR 0.012 0.002 TYR B 332 ARG 0.007 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 285 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 377 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7391 (t) REVERT: A 427 MET cc_start: 0.7828 (ttt) cc_final: 0.7537 (ttm) REVERT: B 181 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6263 (mt-10) REVERT: B 296 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7946 (mp) REVERT: B 427 MET cc_start: 0.7863 (ttt) cc_final: 0.7563 (ttm) REVERT: C 296 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7947 (mp) REVERT: C 377 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7440 (t) REVERT: C 427 MET cc_start: 0.7827 (ttt) cc_final: 0.7527 (ttm) REVERT: D 88 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7460 (mtmp) REVERT: D 181 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6271 (mt-10) REVERT: D 296 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7928 (mp) REVERT: D 427 MET cc_start: 0.7833 (ttt) cc_final: 0.7529 (ttm) REVERT: D 428 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8199 (mtm) outliers start: 40 outliers final: 10 residues processed: 312 average time/residue: 3.2020 time to fit residues: 1125.5366 Evaluate side-chains 306 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 287 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21672 Z= 0.423 Angle : 0.572 6.450 29356 Z= 0.303 Chirality : 0.042 0.172 3110 Planarity : 0.005 0.052 3790 Dihedral : 5.133 61.382 2886 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.39 % Allowed : 11.23 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2572 helix: 0.60 (0.13), residues: 1346 sheet: -1.59 (0.25), residues: 380 loop : 0.61 (0.24), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 308 HIS 0.006 0.001 HIS A 180 PHE 0.021 0.002 PHE A 307 TYR 0.010 0.002 TYR B 325 ARG 0.008 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 288 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 377 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7437 (t) REVERT: A 427 MET cc_start: 0.7834 (ttt) cc_final: 0.7552 (ttm) REVERT: B 181 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: B 296 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 427 MET cc_start: 0.7839 (ttt) cc_final: 0.7563 (ttm) REVERT: C 296 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7995 (mp) REVERT: C 377 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7479 (t) REVERT: C 427 MET cc_start: 0.7853 (ttt) cc_final: 0.7555 (ttm) REVERT: D 181 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6328 (mt-10) REVERT: D 296 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7995 (mp) REVERT: D 427 MET cc_start: 0.7857 (ttt) cc_final: 0.7568 (ttm) outliers start: 31 outliers final: 12 residues processed: 306 average time/residue: 3.3537 time to fit residues: 1163.1105 Evaluate side-chains 302 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 282 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain G residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21672 Z= 0.306 Angle : 0.524 5.780 29356 Z= 0.277 Chirality : 0.039 0.134 3110 Planarity : 0.004 0.058 3790 Dihedral : 4.965 62.530 2886 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.34 % Allowed : 11.72 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2572 helix: 0.76 (0.13), residues: 1336 sheet: -1.61 (0.25), residues: 384 loop : 0.67 (0.24), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 308 HIS 0.005 0.001 HIS A 180 PHE 0.016 0.002 PHE D 307 TYR 0.009 0.002 TYR C 221 ARG 0.008 0.000 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 296 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8068 (mp) REVERT: A 377 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7396 (t) REVERT: A 427 MET cc_start: 0.7843 (ttt) cc_final: 0.7531 (ttm) REVERT: B 181 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6165 (mt-10) REVERT: B 296 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 427 MET cc_start: 0.7838 (ttt) cc_final: 0.7535 (ttm) REVERT: B 428 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: C 296 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8022 (mp) REVERT: C 377 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7442 (t) REVERT: C 427 MET cc_start: 0.7835 (ttt) cc_final: 0.7553 (ttm) REVERT: D 181 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: D 296 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8039 (mp) REVERT: D 427 MET cc_start: 0.7837 (ttt) cc_final: 0.7546 (ttm) outliers start: 30 outliers final: 12 residues processed: 312 average time/residue: 3.1352 time to fit residues: 1105.4967 Evaluate side-chains 308 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 287 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain G residue 309 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 195 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21672 Z= 0.218 Angle : 0.491 6.714 29356 Z= 0.256 Chirality : 0.038 0.139 3110 Planarity : 0.004 0.051 3790 Dihedral : 4.746 64.123 2886 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.85 % Allowed : 12.25 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2572 helix: 1.00 (0.13), residues: 1336 sheet: -1.68 (0.25), residues: 404 loop : 0.77 (0.25), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 308 HIS 0.003 0.001 HIS D 180 PHE 0.012 0.001 PHE D 307 TYR 0.009 0.001 TYR C 221 ARG 0.008 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 309 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 377 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7322 (t) REVERT: A 427 MET cc_start: 0.7875 (ttt) cc_final: 0.7568 (ttm) REVERT: B 296 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8046 (mp) REVERT: B 427 MET cc_start: 0.7840 (ttt) cc_final: 0.7543 (ttm) REVERT: C 296 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8006 (mp) REVERT: C 377 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7370 (t) REVERT: C 427 MET cc_start: 0.7826 (ttt) cc_final: 0.7518 (ttm) REVERT: D 181 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.5784 (mp0) REVERT: D 296 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8040 (mp) REVERT: D 427 MET cc_start: 0.7877 (ttt) cc_final: 0.7560 (ttm) outliers start: 19 outliers final: 5 residues processed: 317 average time/residue: 3.1507 time to fit residues: 1127.1593 Evaluate side-chains 319 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 307 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain G residue 309 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21672 Z= 0.271 Angle : 0.511 7.244 29356 Z= 0.267 Chirality : 0.039 0.136 3110 Planarity : 0.004 0.052 3790 Dihedral : 4.795 63.765 2886 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.94 % Allowed : 12.97 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2572 helix: 0.98 (0.13), residues: 1338 sheet: -1.64 (0.25), residues: 404 loop : 0.83 (0.25), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 308 HIS 0.004 0.001 HIS D 180 PHE 0.016 0.002 PHE A 307 TYR 0.008 0.001 TYR C 221 ARG 0.009 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 299 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 377 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7348 (t) REVERT: A 427 MET cc_start: 0.7852 (ttt) cc_final: 0.7548 (ttm) REVERT: B 296 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 427 MET cc_start: 0.7837 (ttt) cc_final: 0.7544 (ttm) REVERT: C 296 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8110 (mp) REVERT: C 377 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7341 (t) REVERT: C 427 MET cc_start: 0.7833 (ttt) cc_final: 0.7552 (ttm) REVERT: D 88 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7475 (mtmp) REVERT: D 181 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.5886 (mp0) REVERT: D 296 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8050 (mp) REVERT: D 427 MET cc_start: 0.7835 (ttt) cc_final: 0.7545 (ttm) outliers start: 21 outliers final: 7 residues processed: 309 average time/residue: 3.2505 time to fit residues: 1129.9405 Evaluate side-chains 306 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 292 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain G residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21672 Z= 0.326 Angle : 0.540 7.773 29356 Z= 0.284 Chirality : 0.040 0.155 3110 Planarity : 0.004 0.063 3790 Dihedral : 4.913 63.318 2886 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.94 % Allowed : 13.15 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2572 helix: 0.84 (0.13), residues: 1338 sheet: -1.63 (0.25), residues: 404 loop : 0.77 (0.25), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 308 HIS 0.005 0.001 HIS D 180 PHE 0.018 0.002 PHE D 307 TYR 0.008 0.002 TYR B 325 ARG 0.009 0.000 ARG A 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 288 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7507 (mtmp) REVERT: A 296 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 377 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7380 (t) REVERT: A 427 MET cc_start: 0.7842 (ttt) cc_final: 0.7545 (ttm) REVERT: B 296 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 427 MET cc_start: 0.7818 (ttt) cc_final: 0.7534 (ttm) REVERT: C 296 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8102 (mp) REVERT: C 377 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7379 (t) REVERT: C 427 MET cc_start: 0.7840 (ttt) cc_final: 0.7547 (ttm) REVERT: C 428 MET cc_start: 0.8492 (mtm) cc_final: 0.8277 (mtm) REVERT: D 88 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7459 (mtmp) REVERT: D 147 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6470 (mm-30) REVERT: D 181 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: D 296 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8121 (mp) REVERT: D 427 MET cc_start: 0.7820 (ttt) cc_final: 0.7537 (ttm) outliers start: 21 outliers final: 9 residues processed: 298 average time/residue: 3.2649 time to fit residues: 1093.0240 Evaluate side-chains 303 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain G residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.171718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142876 restraints weight = 54002.603| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.19 r_work: 0.3336 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21672 Z= 0.266 Angle : 0.514 8.111 29356 Z= 0.269 Chirality : 0.039 0.218 3110 Planarity : 0.004 0.058 3790 Dihedral : 4.802 63.847 2886 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.76 % Allowed : 13.37 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2572 helix: 0.95 (0.13), residues: 1338 sheet: -1.61 (0.25), residues: 404 loop : 0.84 (0.25), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 308 HIS 0.005 0.001 HIS B 180 PHE 0.014 0.002 PHE C 307 TYR 0.008 0.001 TYR C 221 ARG 0.009 0.000 ARG A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16604.34 seconds wall clock time: 290 minutes 39.87 seconds (17439.87 seconds total)