Starting phenix.real_space_refine on Fri Apr 12 02:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz7_41736/04_2024/8tz7_41736_trim_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.083 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 3 5.49 5 S 87 5.16 5 C 8187 2.51 5 N 1923 2.21 5 O 2139 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 11.38, per 1000 atoms: 0.47 Number of scatterers: 24408 At special positions: 0 Unit cell: (128.52, 128.52, 76.68, 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 87 16.00 P 3 15.00 O 2139 8.00 N 1923 7.00 C 8187 6.00 H 12069 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: 19.67 Conformation dependent library (CDL) restraints added in 2.7 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 Processing helix chain 'A' and resid 133 through 156 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 158 through 174 Proline residue: A 167 - end of helix Processing helix chain 'A' and resid 176 through 202 removed outlier: 4.728A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.516A pdb=" N SER A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'A' and resid 253 through 281 removed outlier: 3.513A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 289 through 292 No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.526A pdb=" N ILE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.859A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 Proline residue: A 351 - end of helix removed outlier: 4.557A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 380 through 388 removed outlier: 4.323A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.083A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 438 through 481 removed outlier: 3.706A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.590A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.274A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.846A pdb=" N GLY A 576 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.798A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 593 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 618 removed outlier: 3.548A pdb=" N LEU A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 Processing helix chain 'B' and resid 133 through 156 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 158 through 174 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.728A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.516A pdb=" N SER B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 251 Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.514A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 289 through 292 No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.526A pdb=" N ILE B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.860A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Proline residue: B 351 - end of helix removed outlier: 4.557A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 380 through 388 removed outlier: 4.323A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.083A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 438 through 481 removed outlier: 3.706A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.589A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 507 through 522 removed outlier: 4.274A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.847A pdb=" N GLY B 576 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 4.798A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 593 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 618 removed outlier: 3.548A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 Processing helix chain 'C' and resid 133 through 156 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 158 through 174 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 176 through 202 removed outlier: 4.728A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.516A pdb=" N SER C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'C' and resid 253 through 281 removed outlier: 3.513A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL C 280 " --> pdb=" O GLY C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 292 No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.525A pdb=" N ILE C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 329 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.860A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Proline residue: C 351 - end of helix removed outlier: 4.556A pdb=" N VAL C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 380 through 388 removed outlier: 4.323A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 413 removed outlier: 4.084A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 438 through 481 removed outlier: 3.706A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.590A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 507 through 522 removed outlier: 4.274A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 541 Processing helix chain 'C' and resid 556 through 565 Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.846A pdb=" N GLY C 576 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 4.798A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 593 " --> pdb=" O LYS C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 618 removed outlier: 3.548A pdb=" N LEU C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 602 " --> pdb=" O MET C 598 " (cutoff:3.500A) 831 hydrogen bonds defined for protein. 2214 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: 9.63 Time building geometry restraints manager: 20.50 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: 12051 1.03 - 1.23: 31 1.23 - 1.42: 5345 1.42 - 1.62: 7149 1.62 - 1.81: 165 Bond restraints: 24741 Sorted by residual: bond pdb=" O4 LBN C 802 " pdb=" P1 LBN C 802 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" O4 LBN B 802 " pdb=" P1 LBN B 802 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O4 LBN A 802 " pdb=" P1 LBN A 802 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" O2 LBN A 802 " pdb=" P1 LBN A 802 " ideal model delta sigma weight residual 1.650 1.511 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O2 LBN C 802 " pdb=" P1 LBN C 802 " ideal model delta sigma weight residual 1.650 1.511 0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 24736 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 412 106.60 - 113.46: 28485 113.46 - 120.32: 8460 120.32 - 127.18: 7038 127.18 - 134.05: 164 Bond angle restraints: 44559 Sorted by residual: angle pdb=" O1 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O2 LBN C 802 " ideal model delta sigma weight residual 93.45 109.34 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O1 LBN B 802 " pdb=" P1 LBN B 802 " pdb=" O2 LBN B 802 " ideal model delta sigma weight residual 93.45 109.32 -15.87 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O1 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O2 LBN A 802 " ideal model delta sigma weight residual 93.45 109.30 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 103.85 4.34 1.29e+00 6.01e-01 1.13e+01 angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 103.89 4.30 1.29e+00 6.01e-01 1.11e+01 ... (remaining 44554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 11260 26.60 - 53.21: 394 53.21 - 79.81: 109 79.81 - 106.41: 6 106.41 - 133.02: 3 Dihedral angle restraints: 11772 sinusoidal: 6042 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 802 " pdb=" C2 LBN A 802 " pdb=" C3 LBN A 802 " pdb=" O7 LBN A 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.31 -133.02 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O5 LBN C 802 " pdb=" C2 LBN C 802 " pdb=" C3 LBN C 802 " pdb=" O7 LBN C 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.35 -132.98 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O5 LBN B 802 " pdb=" C2 LBN B 802 " pdb=" C3 LBN B 802 " pdb=" O7 LBN B 802 " ideal model delta sinusoidal sigma weight residual 62.67 -164.36 -132.97 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 11769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1208 0.026 - 0.052: 433 0.052 - 0.078: 217 0.078 - 0.104: 116 0.104 - 0.130: 15 Chirality restraints: 1989 Sorted by residual: chirality pdb=" CA VAL A 550 " pdb=" N VAL A 550 " pdb=" C VAL A 550 " pdb=" CB VAL A 550 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL C 550 " pdb=" N VAL C 550 " pdb=" C VAL C 550 " pdb=" CB VAL C 550 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA VAL B 550 " pdb=" N VAL B 550 " pdb=" C VAL B 550 " pdb=" CB VAL B 550 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1986 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO C 296 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 296 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 296 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.024 5.00e-02 4.00e+02 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 589 2.13 - 2.75: 42962 2.75 - 3.36: 69993 3.36 - 3.98: 86194 3.98 - 4.60: 139382 Nonbonded interactions: 339120 Sorted by model distance: nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.511 1.850 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.513 1.850 nonbonded pdb=" O LEU C 248 " pdb=" HG1 THR C 252 " model vdw 1.513 1.850 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.559 1.850 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.560 1.850 ... (remaining 339115 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' selection = chain 'C' } 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: 0.840 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: 0.360 Extract box with map and model: 4.980 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 80.980 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 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:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 0.149 12672 Z= 0.332 Angle : 0.643 15.886 17241 Z= 0.321 Chirality : 0.038 0.130 1989 Planarity : 0.003 0.044 2091 Dihedral : 12.678 133.018 4302 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.48 % Allowed : 3.12 % Favored : 96.39 % 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: 3.50 (0.21), residues: 1593 helix: 2.94 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.001 PHE B 488 TYR 0.007 0.001 TYR B 519 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.6891 (tp) cc_final: 0.6669 (mt) REVERT: A 307 MET cc_start: 0.8471 (mtm) cc_final: 0.8098 (mtp) REVERT: A 497 MET cc_start: 0.7792 (tmt) cc_final: 0.6777 (tmt) REVERT: A 598 MET cc_start: 0.8202 (tpp) cc_final: 0.7635 (tpt) REVERT: B 307 MET cc_start: 0.8419 (mtm) cc_final: 0.8215 (mtp) REVERT: B 329 MET cc_start: 0.8462 (mtp) cc_final: 0.8238 (mtm) REVERT: C 329 MET cc_start: 0.8538 (mtp) cc_final: 0.8160 (mtm) REVERT: C 344 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p90) REVERT: C 430 MET cc_start: 0.8057 (mtt) cc_final: 0.7540 (mtt) REVERT: C 497 MET cc_start: 0.7517 (tmt) cc_final: 0.7170 (tmt) outliers start: 6 outliers final: 2 residues processed: 239 average time/residue: 1.6425 time to fit residues: 448.4523 Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain C residue 344 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS B 394 HIS B 508 GLN C 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12672 Z= 0.277 Angle : 0.535 5.702 17241 Z= 0.297 Chirality : 0.038 0.125 1989 Planarity : 0.005 0.059 2091 Dihedral : 9.892 145.711 1797 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.76 % Allowed : 9.78 % Favored : 88.46 % 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: 2.18 (0.21), residues: 1593 helix: 1.93 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.79 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 323 HIS 0.004 0.001 HIS B 226 PHE 0.019 0.002 PHE A 523 TYR 0.007 0.001 TYR A 119 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8521 (mtm) cc_final: 0.8192 (mtp) REVERT: A 497 MET cc_start: 0.7866 (tmt) cc_final: 0.6867 (tmt) REVERT: A 583 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 598 MET cc_start: 0.8205 (tpp) cc_final: 0.7633 (tpt) REVERT: B 284 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8048 (mtpp) REVERT: B 482 ASP cc_start: 0.8043 (t0) cc_final: 0.7714 (m-30) REVERT: C 344 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8105 (p90) REVERT: C 470 MET cc_start: 0.7703 (ttm) cc_final: 0.7493 (ttm) REVERT: C 497 MET cc_start: 0.7936 (tmt) cc_final: 0.6996 (tmt) outliers start: 22 outliers final: 11 residues processed: 210 average time/residue: 1.9102 time to fit residues: 451.7735 Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12672 Z= 0.225 Angle : 0.473 4.485 17241 Z= 0.256 Chirality : 0.035 0.117 1989 Planarity : 0.005 0.055 2091 Dihedral : 9.185 141.987 1797 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.56 % Allowed : 12.50 % Favored : 84.94 % 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: 1.96 (0.21), residues: 1593 helix: 1.75 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -0.91 (0.32), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.003 0.001 HIS C 226 PHE 0.014 0.001 PHE B 413 TYR 0.007 0.001 TYR C 494 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 2.261 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8468 (mtm) cc_final: 0.8180 (mtp) REVERT: A 497 MET cc_start: 0.7834 (tmt) cc_final: 0.6785 (tmt) REVERT: A 583 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8228 (t) REVERT: A 598 MET cc_start: 0.8318 (tpp) cc_final: 0.7575 (tpt) REVERT: B 482 ASP cc_start: 0.8166 (t0) cc_final: 0.7683 (m-30) REVERT: B 583 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7971 (t) REVERT: C 189 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8168 (tm) REVERT: C 344 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8321 (p90) REVERT: C 480 MET cc_start: 0.8011 (mmm) cc_final: 0.7796 (mtt) REVERT: C 497 MET cc_start: 0.7943 (tmt) cc_final: 0.6946 (tmt) outliers start: 32 outliers final: 12 residues processed: 199 average time/residue: 1.8252 time to fit residues: 411.3338 Evaluate side-chains 190 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 394 HIS C 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12672 Z= 0.275 Angle : 0.498 4.603 17241 Z= 0.271 Chirality : 0.037 0.115 1989 Planarity : 0.005 0.060 2091 Dihedral : 9.132 146.063 1795 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.72 % Allowed : 12.90 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1593 helix: 1.51 (0.15), residues: 1308 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 323 HIS 0.003 0.001 HIS C 226 PHE 0.015 0.002 PHE A 413 TYR 0.008 0.001 TYR A 119 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8535 (mtm) cc_final: 0.8285 (mtp) REVERT: A 344 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8282 (p90) REVERT: A 497 MET cc_start: 0.7872 (tmt) cc_final: 0.6764 (tmt) REVERT: A 583 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8307 (t) REVERT: A 598 MET cc_start: 0.8380 (tpp) cc_final: 0.7661 (tpt) REVERT: A 620 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7321 (t0) REVERT: B 189 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8286 (tt) REVERT: B 482 ASP cc_start: 0.8105 (t0) cc_final: 0.7762 (m-30) REVERT: B 583 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.7992 (t) REVERT: C 141 THR cc_start: 0.7164 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 189 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8261 (tm) REVERT: C 418 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7051 (pt0) REVERT: C 497 MET cc_start: 0.7947 (tmt) cc_final: 0.6848 (tmt) outliers start: 34 outliers final: 17 residues processed: 197 average time/residue: 1.8279 time to fit residues: 407.3233 Evaluate side-chains 194 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 205 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12672 Z= 0.387 Angle : 0.553 5.136 17241 Z= 0.301 Chirality : 0.039 0.127 1989 Planarity : 0.006 0.066 2091 Dihedral : 9.319 148.331 1793 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.29 % Allowed : 13.78 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1593 helix: 1.12 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.004 0.001 HIS C 226 PHE 0.015 0.002 PHE C 413 TYR 0.010 0.002 TYR C 119 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8536 (mtm) cc_final: 0.8305 (mtp) REVERT: A 325 MET cc_start: 0.8313 (mtp) cc_final: 0.8098 (mtp) REVERT: A 344 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8266 (p90) REVERT: A 497 MET cc_start: 0.7890 (tmt) cc_final: 0.6876 (tmt) REVERT: A 577 ILE cc_start: 0.8077 (pt) cc_final: 0.7807 (pt) REVERT: A 583 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8252 (t) REVERT: A 598 MET cc_start: 0.8302 (tpp) cc_final: 0.7767 (tpt) REVERT: B 205 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: B 482 ASP cc_start: 0.8069 (t0) cc_final: 0.7742 (m-30) REVERT: B 583 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8015 (t) REVERT: C 141 THR cc_start: 0.7149 (OUTLIER) cc_final: 0.6930 (p) REVERT: C 189 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8269 (tm) REVERT: C 418 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: C 497 MET cc_start: 0.7923 (tmt) cc_final: 0.6847 (tmt) outliers start: 41 outliers final: 15 residues processed: 198 average time/residue: 1.8499 time to fit residues: 415.0657 Evaluate side-chains 184 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 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 508 GLN C 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12672 Z= 0.224 Angle : 0.475 7.610 17241 Z= 0.255 Chirality : 0.035 0.111 1989 Planarity : 0.005 0.059 2091 Dihedral : 9.024 144.563 1793 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 15.71 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1593 helix: 1.35 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -1.12 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.002 0.001 HIS C 288 PHE 0.013 0.001 PHE B 413 TYR 0.006 0.001 TYR C 119 ARG 0.001 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8516 (mtm) cc_final: 0.8266 (mtp) REVERT: A 344 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8243 (p90) REVERT: A 430 MET cc_start: 0.8414 (mtt) cc_final: 0.8169 (mtt) REVERT: A 497 MET cc_start: 0.7843 (tmt) cc_final: 0.6823 (tmt) REVERT: A 577 ILE cc_start: 0.7993 (pt) cc_final: 0.7724 (pt) REVERT: A 583 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8179 (t) REVERT: A 585 MET cc_start: 0.8384 (mtt) cc_final: 0.7993 (mtt) REVERT: A 598 MET cc_start: 0.8372 (tpp) cc_final: 0.7796 (tpt) REVERT: B 482 ASP cc_start: 0.8064 (t0) cc_final: 0.7741 (m-30) REVERT: B 554 MET cc_start: 0.8938 (ptt) cc_final: 0.8679 (ptt) REVERT: B 583 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7989 (t) REVERT: C 189 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8267 (tm) REVERT: C 418 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7074 (pt0) REVERT: C 497 MET cc_start: 0.7860 (tmt) cc_final: 0.6762 (tmt) REVERT: C 571 ASN cc_start: 0.8127 (p0) cc_final: 0.7890 (p0) outliers start: 26 outliers final: 16 residues processed: 183 average time/residue: 1.9510 time to fit residues: 402.2320 Evaluate side-chains 185 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12672 Z= 0.246 Angle : 0.477 7.206 17241 Z= 0.256 Chirality : 0.036 0.112 1989 Planarity : 0.005 0.059 2091 Dihedral : 8.966 143.971 1793 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 15.38 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1593 helix: 1.35 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -1.11 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 181 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.001 PHE B 413 TYR 0.007 0.001 TYR C 119 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8262 (p90) REVERT: A 430 MET cc_start: 0.8438 (mtt) cc_final: 0.8233 (mtt) REVERT: A 497 MET cc_start: 0.7852 (tmt) cc_final: 0.6833 (tmt) REVERT: A 577 ILE cc_start: 0.8025 (pt) cc_final: 0.7748 (pt) REVERT: A 583 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8172 (t) REVERT: A 585 MET cc_start: 0.8392 (mtt) cc_final: 0.7980 (mtt) REVERT: A 598 MET cc_start: 0.8363 (tpp) cc_final: 0.7778 (tpt) REVERT: B 482 ASP cc_start: 0.8063 (t0) cc_final: 0.7754 (m-30) REVERT: B 583 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7983 (t) REVERT: C 141 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.7018 (p) REVERT: C 189 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8275 (tm) REVERT: C 418 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: C 497 MET cc_start: 0.7867 (tmt) cc_final: 0.6782 (tmt) REVERT: C 571 ASN cc_start: 0.8107 (p0) cc_final: 0.7876 (p0) outliers start: 31 outliers final: 18 residues processed: 188 average time/residue: 1.8401 time to fit residues: 391.6362 Evaluate side-chains 190 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12672 Z= 0.217 Angle : 0.463 7.545 17241 Z= 0.247 Chirality : 0.035 0.113 1989 Planarity : 0.005 0.056 2091 Dihedral : 8.840 143.313 1793 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 15.87 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1593 helix: 1.44 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -1.05 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 181 HIS 0.002 0.001 HIS C 226 PHE 0.012 0.001 PHE B 413 TYR 0.006 0.001 TYR C 119 ARG 0.001 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8287 (p90) REVERT: A 497 MET cc_start: 0.7838 (tmt) cc_final: 0.6814 (tmt) REVERT: A 583 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8175 (t) REVERT: A 585 MET cc_start: 0.8384 (mtt) cc_final: 0.7973 (mtt) REVERT: A 598 MET cc_start: 0.8376 (tpp) cc_final: 0.7755 (tpt) REVERT: B 482 ASP cc_start: 0.8063 (t0) cc_final: 0.7759 (m-30) REVERT: B 554 MET cc_start: 0.8944 (ptt) cc_final: 0.8716 (ptt) REVERT: B 583 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7967 (t) REVERT: C 141 THR cc_start: 0.7145 (OUTLIER) cc_final: 0.6874 (p) REVERT: C 189 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8276 (tm) REVERT: C 418 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: C 497 MET cc_start: 0.7846 (tmt) cc_final: 0.6761 (tmt) REVERT: C 571 ASN cc_start: 0.8058 (p0) cc_final: 0.7838 (p0) outliers start: 25 outliers final: 17 residues processed: 187 average time/residue: 1.9492 time to fit residues: 413.3165 Evaluate side-chains 193 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12672 Z= 0.247 Angle : 0.478 7.387 17241 Z= 0.256 Chirality : 0.036 0.114 1989 Planarity : 0.005 0.057 2091 Dihedral : 8.839 143.733 1793 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.84 % Allowed : 16.11 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.22), residues: 1593 helix: 1.37 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 181 HIS 0.003 0.001 HIS C 226 PHE 0.012 0.001 PHE B 413 TYR 0.007 0.001 TYR C 119 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.7849 (tmt) cc_final: 0.6831 (tmt) REVERT: A 583 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8185 (t) REVERT: A 585 MET cc_start: 0.8389 (mtt) cc_final: 0.7979 (mtt) REVERT: A 598 MET cc_start: 0.8354 (tpp) cc_final: 0.7776 (tpt) REVERT: B 482 ASP cc_start: 0.8074 (t0) cc_final: 0.7783 (m-30) REVERT: B 554 MET cc_start: 0.8956 (ptt) cc_final: 0.8708 (ptt) REVERT: B 583 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7942 (t) REVERT: C 189 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8280 (tm) REVERT: C 204 GLN cc_start: 0.8152 (tt0) cc_final: 0.7918 (tt0) REVERT: C 418 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7039 (pt0) REVERT: C 497 MET cc_start: 0.7856 (tmt) cc_final: 0.6773 (tmt) REVERT: C 571 ASN cc_start: 0.8081 (p0) cc_final: 0.7873 (p0) outliers start: 23 outliers final: 18 residues processed: 181 average time/residue: 1.8954 time to fit residues: 386.8453 Evaluate side-chains 189 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 443 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 GLN B 508 GLN C 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12672 Z= 0.173 Angle : 0.441 7.586 17241 Z= 0.233 Chirality : 0.034 0.111 1989 Planarity : 0.004 0.054 2091 Dihedral : 8.552 141.513 1791 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 16.51 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1593 helix: 1.59 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 181 HIS 0.002 0.001 HIS A 288 PHE 0.010 0.001 PHE C 413 TYR 0.004 0.001 TYR B 216 ARG 0.001 0.000 ARG C 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.7810 (tmt) cc_final: 0.6779 (tmt) REVERT: A 583 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8144 (t) REVERT: A 585 MET cc_start: 0.8431 (mtt) cc_final: 0.8024 (mtt) REVERT: A 598 MET cc_start: 0.8392 (tpp) cc_final: 0.7784 (tpt) REVERT: B 482 ASP cc_start: 0.8092 (t0) cc_final: 0.7819 (m-30) REVERT: B 554 MET cc_start: 0.8984 (ptt) cc_final: 0.8761 (ptt) REVERT: B 583 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7851 (t) REVERT: C 189 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8265 (tm) REVERT: C 204 GLN cc_start: 0.8167 (tt0) cc_final: 0.7926 (tt0) REVERT: C 497 MET cc_start: 0.7824 (tmt) cc_final: 0.6716 (tmt) REVERT: C 571 ASN cc_start: 0.7934 (p0) cc_final: 0.7701 (p0) outliers start: 19 outliers final: 14 residues processed: 183 average time/residue: 1.8513 time to fit residues: 382.5960 Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 0.0270 chunk 7 optimal weight: 7.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN C 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099143 restraints weight = 37252.578| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.46 r_work: 0.2860 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12672 Z= 0.169 Angle : 0.440 7.409 17241 Z= 0.232 Chirality : 0.034 0.112 1989 Planarity : 0.004 0.053 2091 Dihedral : 8.437 140.350 1791 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.44 % Allowed : 16.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.22), residues: 1593 helix: 1.69 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 181 HIS 0.002 0.001 HIS A 288 PHE 0.010 0.001 PHE C 413 TYR 0.004 0.001 TYR B 216 ARG 0.001 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.08 seconds wall clock time: 140 minutes 48.26 seconds (8448.26 seconds total)