Starting phenix.real_space_refine on Wed Nov 20 03:05:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fob_29344/11_2024/8fob_29344.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fob_29344/11_2024/8fob_29344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fob_29344/11_2024/8fob_29344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fob_29344/11_2024/8fob_29344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fob_29344/11_2024/8fob_29344.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fob_29344/11_2024/8fob_29344.cif" } resolution = 2.71 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= 0.031 sd= 0.128 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 Ca 2 9.91 5 P 8 5.49 5 S 156 5.16 5 C 13436 2.51 5 N 3232 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20390 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "C" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4766 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 26, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 320 Unusual residues: {' CA': 2, 'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 318 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 353 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 283 Unusual residues: {'PCW': 1, 'POV': 7, 'Y01': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4, 'POV:plan-1': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 12.20, per 1000 atoms: 0.60 Number of scatterers: 20390 At special positions: 0 Unit cell: (123.48, 125.16, 118.44, 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) Ca 2 19.99 S 156 16.00 P 8 15.00 O 3556 8.00 N 3232 7.00 C 13436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 2.4 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 62.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.515A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.808A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.636A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.519A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.969A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.592A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.671A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.709A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.950A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.513A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.780A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 removed outlier: 3.770A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.518A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.604A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 510 removed outlier: 5.267A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.524A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.642A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.515A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.807A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.636A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.518A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.970A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.591A pdb=" N ILE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.671A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.710A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.951A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.512A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.781A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.769A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 4.519A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.605A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 510 removed outlier: 5.267A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.523A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.643A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.515A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.807A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.636A pdb=" N LEU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.518A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.968A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.591A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.670A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.711A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.951A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.513A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.780A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.769A pdb=" N VAL C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 4.519A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 472 removed outlier: 3.605A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 510 removed outlier: 5.267A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.524A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.642A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.515A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.807A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.635A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.518A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.970A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.591A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.672A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.710A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.757A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.951A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.650A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.512A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.781A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 removed outlier: 3.770A pdb=" N VAL D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.614A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 4.519A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.605A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 510 removed outlier: 5.268A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.523A pdb=" N PHE D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.183A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 588 removed outlier: 3.629A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.642A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.499A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.498A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 353 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.498A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 268 removed outlier: 6.499A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 353 949 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 3144 1.29 - 1.45: 5428 1.45 - 1.60: 11832 1.60 - 1.76: 76 1.76 - 1.91: 288 Bond restraints: 20768 Sorted by residual: bond pdb=" CAV Y01 B 804 " pdb=" CAZ Y01 B 804 " ideal model delta sigma weight residual 1.507 1.912 -0.405 2.00e-02 2.50e+03 4.11e+02 bond pdb=" CAV Y01 D 805 " pdb=" CAZ Y01 D 805 " ideal model delta sigma weight residual 1.507 1.912 -0.405 2.00e-02 2.50e+03 4.10e+02 bond pdb=" CAV Y01 C 804 " pdb=" CAZ Y01 C 804 " ideal model delta sigma weight residual 1.507 1.911 -0.404 2.00e-02 2.50e+03 4.07e+02 bond pdb=" CAV Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 1.507 1.910 -0.403 2.00e-02 2.50e+03 4.06e+02 bond pdb=" CAV Y01 B 803 " pdb=" CAZ Y01 B 803 " ideal model delta sigma weight residual 1.507 1.910 -0.403 2.00e-02 2.50e+03 4.05e+02 ... (remaining 20763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 26798 3.26 - 6.52: 902 6.52 - 9.78: 205 9.78 - 13.04: 80 13.04 - 16.30: 15 Bond angle restraints: 28000 Sorted by residual: angle pdb=" C SER D 175 " pdb=" N GLU D 176 " pdb=" CA GLU D 176 " ideal model delta sigma weight residual 120.82 129.18 -8.36 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C SER A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 120.82 129.17 -8.35 1.50e+00 4.44e-01 3.10e+01 angle pdb=" C SER B 175 " pdb=" N GLU B 176 " pdb=" CA GLU B 176 " ideal model delta sigma weight residual 120.82 129.14 -8.32 1.50e+00 4.44e-01 3.08e+01 angle pdb=" C SER C 175 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 120.82 129.13 -8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" C28 POV D 810 " pdb=" C29 POV D 810 " pdb="C210 POV D 810 " ideal model delta sigma weight residual 127.79 111.49 16.30 3.00e+00 1.11e-01 2.95e+01 ... (remaining 27995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 12342 32.69 - 65.39: 661 65.39 - 98.08: 132 98.08 - 130.77: 49 130.77 - 163.46: 16 Dihedral angle restraints: 13200 sinusoidal: 6236 harmonic: 6964 Sorted by residual: dihedral pdb=" CA GLU C 519 " pdb=" C GLU C 519 " pdb=" N LEU C 520 " pdb=" CA LEU C 520 " ideal model delta harmonic sigma weight residual -180.00 -146.74 -33.26 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA GLU A 519 " pdb=" C GLU A 519 " pdb=" N LEU A 520 " pdb=" CA LEU A 520 " ideal model delta harmonic sigma weight residual 180.00 -146.80 -33.20 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA GLU B 519 " pdb=" C GLU B 519 " pdb=" N LEU B 520 " pdb=" CA LEU B 520 " ideal model delta harmonic sigma weight residual -180.00 -146.82 -33.18 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 13197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.992: 3068 0.992 - 1.984: 0 1.984 - 2.976: 0 2.976 - 3.968: 4 3.968 - 4.959: 44 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CBC Y01 D 804 " pdb=" CAR Y01 D 804 " pdb=" CAV Y01 D 804 " pdb=" OAW Y01 D 804 " both_signs ideal model delta sigma weight residual False -2.54 2.42 -4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" CBC Y01 C 803 " pdb=" CAR Y01 C 803 " pdb=" CAV Y01 C 803 " pdb=" OAW Y01 C 803 " both_signs ideal model delta sigma weight residual False -2.54 2.36 -4.91 2.00e-01 2.50e+01 6.02e+02 chirality pdb=" CBC Y01 A 801 " pdb=" CAR Y01 A 801 " pdb=" CAV Y01 A 801 " pdb=" OAW Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.54 2.35 -4.89 2.00e-01 2.50e+01 5.99e+02 ... (remaining 3113 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 810 " 0.324 2.00e-02 2.50e+03 3.21e-01 1.03e+03 pdb=" C29 POV C 810 " -0.329 2.00e-02 2.50e+03 pdb="C210 POV C 810 " -0.314 2.00e-02 2.50e+03 pdb="C211 POV C 810 " 0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 807 " 0.314 2.00e-02 2.50e+03 3.13e-01 9.78e+02 pdb=" C29 POV A 807 " -0.317 2.00e-02 2.50e+03 pdb="C210 POV A 807 " -0.309 2.00e-02 2.50e+03 pdb="C211 POV A 807 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 810 " 0.278 2.00e-02 2.50e+03 2.81e-01 7.89e+02 pdb=" C29 POV D 810 " -0.271 2.00e-02 2.50e+03 pdb="C210 POV D 810 " -0.291 2.00e-02 2.50e+03 pdb="C211 POV D 810 " 0.283 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 310 2.64 - 3.20: 17165 3.20 - 3.77: 30968 3.77 - 4.33: 44446 4.33 - 4.90: 70428 Nonbonded interactions: 163317 Sorted by model distance: nonbonded pdb="CA CA A 812 " pdb="CA CA A 813 " model vdw 2.073 1.980 nonbonded pdb=" OH TYR C 547 " pdb=" O HOH C 901 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR C 524 " pdb=" O TYR D 547 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 547 " pdb=" O HOH A 901 " model vdw 2.232 3.040 nonbonded pdb=" O PRO D 544 " pdb=" O HOH D 901 " model vdw 2.237 3.040 ... (remaining 163312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) selection = (chain 'B' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 808 and (name C210 or name C211 o \ r name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or \ name C218)) or (resid 809 and (name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 6.150 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.380 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.024 0.405 20768 Z= 1.433 Angle : 1.572 16.303 28000 Z= 0.769 Chirality : 0.539 4.959 3116 Planarity : 0.013 0.321 3416 Dihedral : 21.836 163.463 8696 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.39 % Allowed : 5.81 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -5.44 (0.13), residues: 2360 helix: -3.77 (0.08), residues: 1448 sheet: -3.07 (0.59), residues: 68 loop : -2.96 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 629 HIS 0.014 0.003 HIS C 426 PHE 0.023 0.003 PHE D 508 TYR 0.044 0.003 TYR B 547 ARG 0.011 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 470 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5577 (m-10) cc_final: 0.5356 (m-10) REVERT: A 99 MET cc_start: 0.6952 (mtt) cc_final: 0.6704 (mtt) REVERT: A 110 MET cc_start: 0.7046 (ttm) cc_final: 0.6766 (ttt) REVERT: A 222 TYR cc_start: 0.7335 (m-10) cc_final: 0.7045 (m-80) REVERT: A 497 MET cc_start: 0.7186 (mtt) cc_final: 0.6982 (mtt) REVERT: A 637 GLN cc_start: 0.7186 (mp-120) cc_final: 0.6632 (mm-40) REVERT: B 96 MET cc_start: 0.7863 (mtm) cc_final: 0.7578 (mmm) REVERT: B 110 MET cc_start: 0.6970 (ttm) cc_final: 0.6289 (ttt) REVERT: B 222 TYR cc_start: 0.7153 (m-10) cc_final: 0.6831 (m-80) REVERT: B 294 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7380 (mt-10) REVERT: B 497 MET cc_start: 0.7220 (mtt) cc_final: 0.6998 (mtt) REVERT: B 637 GLN cc_start: 0.7235 (mp-120) cc_final: 0.6742 (mm-40) REVERT: C 96 MET cc_start: 0.7839 (mtm) cc_final: 0.7530 (mmp) REVERT: C 110 MET cc_start: 0.6982 (ttm) cc_final: 0.6434 (ttt) REVERT: C 222 TYR cc_start: 0.7152 (m-10) cc_final: 0.6934 (m-80) REVERT: C 637 GLN cc_start: 0.7060 (mp-120) cc_final: 0.6281 (mm-40) REVERT: D 96 MET cc_start: 0.7786 (mtm) cc_final: 0.7488 (mmp) REVERT: D 110 MET cc_start: 0.6960 (ttm) cc_final: 0.6405 (ttt) REVERT: D 114 LEU cc_start: 0.7232 (tt) cc_final: 0.6934 (tp) REVERT: D 116 GLU cc_start: 0.7771 (tt0) cc_final: 0.7145 (pm20) REVERT: D 222 TYR cc_start: 0.7136 (m-10) cc_final: 0.6879 (m-80) REVERT: D 294 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7426 (mt-10) REVERT: D 637 GLN cc_start: 0.7229 (mp-120) cc_final: 0.6713 (mm-40) outliers start: 8 outliers final: 1 residues processed: 474 average time/residue: 1.3692 time to fit residues: 733.6846 Evaluate side-chains 265 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 174 ASN A 206 GLN A 217 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 258 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN B 174 ASN B 206 GLN B 217 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 258 HIS B 267 GLN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 174 ASN C 206 GLN C 217 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 258 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 174 ASN D 206 GLN D 217 ASN D 257 GLN D 258 HIS ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20768 Z= 0.303 Angle : 0.766 7.173 28000 Z= 0.391 Chirality : 0.047 0.308 3116 Planarity : 0.006 0.052 3416 Dihedral : 17.294 148.027 4109 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.22 % Allowed : 12.45 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.13 (0.16), residues: 2360 helix: -1.60 (0.12), residues: 1444 sheet: -2.63 (0.55), residues: 68 loop : -2.67 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 268 HIS 0.004 0.001 HIS B 426 PHE 0.026 0.002 PHE A 537 TYR 0.027 0.002 TYR D 547 ARG 0.007 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 278 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.5821 (m-10) cc_final: 0.5403 (m-10) REVERT: A 215 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7676 (ttm) REVERT: A 222 TYR cc_start: 0.7377 (m-10) cc_final: 0.7123 (m-80) REVERT: A 263 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7162 (mtt90) REVERT: B 96 MET cc_start: 0.7818 (mtm) cc_final: 0.7616 (mmp) REVERT: B 110 MET cc_start: 0.6748 (ttm) cc_final: 0.6149 (ttt) REVERT: B 215 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: B 222 TYR cc_start: 0.7243 (m-10) cc_final: 0.7000 (m-80) REVERT: B 294 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 485 MET cc_start: 0.8789 (mtt) cc_final: 0.8486 (mtt) REVERT: C 74 GLN cc_start: 0.6214 (tp-100) cc_final: 0.5490 (pm20) REVERT: C 110 MET cc_start: 0.6683 (ttm) cc_final: 0.6061 (ttt) REVERT: C 263 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7245 (mtt90) REVERT: D 74 GLN cc_start: 0.6249 (tp-100) cc_final: 0.5739 (pm20) REVERT: D 96 MET cc_start: 0.7696 (mtm) cc_final: 0.7401 (mtp) REVERT: D 110 MET cc_start: 0.6700 (ttm) cc_final: 0.6292 (ttt) REVERT: D 222 TYR cc_start: 0.7227 (m-10) cc_final: 0.7018 (m-80) REVERT: D 263 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7084 (mtt90) REVERT: D 294 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 309 ASP cc_start: 0.7744 (p0) cc_final: 0.7495 (p0) outliers start: 87 outliers final: 24 residues processed: 341 average time/residue: 0.9486 time to fit residues: 373.5898 Evaluate side-chains 277 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 365 ASN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN D 217 ASN D 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20768 Z= 0.307 Angle : 0.722 8.408 28000 Z= 0.364 Chirality : 0.046 0.379 3116 Planarity : 0.006 0.054 3416 Dihedral : 15.472 126.669 4109 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.17 % Allowed : 14.49 % Favored : 81.35 % 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: -2.32 (0.17), residues: 2360 helix: -0.84 (0.13), residues: 1452 sheet: -2.65 (0.50), residues: 76 loop : -2.58 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 268 HIS 0.005 0.001 HIS A 122 PHE 0.019 0.002 PHE A 537 TYR 0.024 0.002 TYR A 547 ARG 0.006 0.001 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 257 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6825 (mp) REVERT: A 45 TRP cc_start: 0.5767 (m-10) cc_final: 0.5397 (m-10) REVERT: A 222 TYR cc_start: 0.7258 (m-10) cc_final: 0.7009 (m-80) REVERT: A 263 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7250 (mtt90) REVERT: A 435 MET cc_start: 0.7060 (tpp) cc_final: 0.6210 (mmm) REVERT: B 51 LEU cc_start: 0.7414 (tm) cc_final: 0.6561 (mp) REVERT: B 110 MET cc_start: 0.6720 (ttm) cc_final: 0.6282 (ttt) REVERT: B 435 MET cc_start: 0.6981 (tpp) cc_final: 0.6057 (mmm) REVERT: B 485 MET cc_start: 0.8805 (mtt) cc_final: 0.8421 (mtt) REVERT: C 33 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.5750 (ttt-90) REVERT: C 99 MET cc_start: 0.7025 (mmt) cc_final: 0.5975 (ppp) REVERT: C 110 MET cc_start: 0.6816 (ttm) cc_final: 0.6395 (ttt) REVERT: C 263 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7304 (mtt90) REVERT: D 38 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6814 (mp) REVERT: D 99 MET cc_start: 0.6044 (mmt) cc_final: 0.5807 (mmt) REVERT: D 100 GLU cc_start: 0.7777 (mp0) cc_final: 0.7243 (pt0) REVERT: D 222 TYR cc_start: 0.7175 (m-10) cc_final: 0.6974 (m-80) REVERT: D 263 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7384 (mtt90) REVERT: D 485 MET cc_start: 0.8653 (mtt) cc_final: 0.8447 (mtt) outliers start: 86 outliers final: 33 residues processed: 310 average time/residue: 1.1637 time to fit residues: 416.3292 Evaluate side-chains 271 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20768 Z= 0.291 Angle : 0.690 7.558 28000 Z= 0.347 Chirality : 0.045 0.338 3116 Planarity : 0.005 0.053 3416 Dihedral : 14.972 123.356 4109 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.89 % Allowed : 14.83 % Favored : 80.28 % 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 (0.17), residues: 2360 helix: -0.41 (0.14), residues: 1416 sheet: -2.53 (0.52), residues: 76 loop : -2.39 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 268 HIS 0.004 0.001 HIS D 582 PHE 0.019 0.002 PHE D 456 TYR 0.018 0.002 TYR D 547 ARG 0.004 0.001 ARG C 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 240 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6720 (mp) REVERT: A 45 TRP cc_start: 0.5745 (m-10) cc_final: 0.5480 (m-10) REVERT: A 215 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7484 (ttm) REVERT: A 222 TYR cc_start: 0.7186 (m-10) cc_final: 0.6972 (m-80) REVERT: A 263 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7285 (mtt90) REVERT: A 435 MET cc_start: 0.7059 (tpp) cc_final: 0.6155 (mmm) REVERT: B 38 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6828 (mp) REVERT: B 51 LEU cc_start: 0.7430 (tm) cc_final: 0.6596 (mp) REVERT: B 99 MET cc_start: 0.7207 (mmt) cc_final: 0.6285 (ppp) REVERT: B 183 ILE cc_start: 0.7687 (pp) cc_final: 0.7450 (pt) REVERT: B 294 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: B 435 MET cc_start: 0.6994 (tpp) cc_final: 0.6147 (mmm) REVERT: C 33 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.5717 (ttt-90) REVERT: C 51 LEU cc_start: 0.7517 (tm) cc_final: 0.6663 (mp) REVERT: C 99 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6595 (mtt) REVERT: C 100 GLU cc_start: 0.7800 (mp0) cc_final: 0.7298 (pt0) REVERT: C 263 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7177 (mtt90) REVERT: C 294 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: D 38 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6722 (mp) REVERT: D 99 MET cc_start: 0.6108 (mmt) cc_final: 0.5836 (mmt) REVERT: D 222 TYR cc_start: 0.7184 (m-10) cc_final: 0.6983 (m-80) REVERT: D 229 LEU cc_start: 0.7993 (mt) cc_final: 0.7691 (pp) REVERT: D 294 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: D 625 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6171 (mm) REVERT: D 636 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7177 (ttp-170) outliers start: 101 outliers final: 44 residues processed: 313 average time/residue: 1.1262 time to fit residues: 407.5628 Evaluate side-chains 283 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20768 Z= 0.322 Angle : 0.707 8.722 28000 Z= 0.355 Chirality : 0.046 0.356 3116 Planarity : 0.006 0.054 3416 Dihedral : 14.882 124.561 4109 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.75 % Allowed : 15.46 % Favored : 79.80 % 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: -1.68 (0.17), residues: 2360 helix: -0.29 (0.14), residues: 1380 sheet: -2.46 (0.53), residues: 76 loop : -2.24 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 268 HIS 0.004 0.001 HIS B 582 PHE 0.017 0.002 PHE D 456 TYR 0.018 0.002 TYR D 547 ARG 0.004 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 236 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 215 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7657 (ttm) REVERT: A 222 TYR cc_start: 0.7118 (m-10) cc_final: 0.6907 (m-80) REVERT: A 263 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7244 (mtt90) REVERT: A 435 MET cc_start: 0.7045 (tpp) cc_final: 0.6154 (mmm) REVERT: B 38 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6823 (mp) REVERT: B 51 LEU cc_start: 0.7416 (tm) cc_final: 0.6592 (mp) REVERT: B 99 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6291 (ppp) REVERT: B 183 ILE cc_start: 0.7680 (pp) cc_final: 0.7456 (pt) REVERT: B 294 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 435 MET cc_start: 0.7026 (tpp) cc_final: 0.6159 (mmm) REVERT: C 33 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.5657 (ttt-90) REVERT: C 51 LEU cc_start: 0.7516 (tm) cc_final: 0.6654 (mp) REVERT: C 99 MET cc_start: 0.7000 (mmt) cc_final: 0.5909 (ppp) REVERT: C 229 LEU cc_start: 0.7971 (mt) cc_final: 0.7715 (pp) REVERT: C 294 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: C 555 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6210 (t80) REVERT: D 38 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6719 (mp) REVERT: D 45 TRP cc_start: 0.6110 (m-10) cc_final: 0.5856 (m100) REVERT: D 99 MET cc_start: 0.6006 (mmt) cc_final: 0.5681 (mmt) REVERT: D 222 TYR cc_start: 0.7124 (m-10) cc_final: 0.6912 (m-80) REVERT: D 229 LEU cc_start: 0.7962 (mt) cc_final: 0.7684 (pp) REVERT: D 294 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: D 625 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6259 (mm) REVERT: D 636 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7220 (ttp-170) outliers start: 98 outliers final: 51 residues processed: 310 average time/residue: 1.2079 time to fit residues: 435.8207 Evaluate side-chains 291 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 227 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 0.4980 chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20768 Z= 0.218 Angle : 0.640 8.536 28000 Z= 0.322 Chirality : 0.043 0.307 3116 Planarity : 0.005 0.052 3416 Dihedral : 14.207 108.826 4109 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.55 % Allowed : 16.47 % Favored : 78.97 % 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: -1.31 (0.18), residues: 2360 helix: -0.12 (0.14), residues: 1436 sheet: -2.40 (0.53), residues: 76 loop : -1.92 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 268 HIS 0.003 0.001 HIS B 582 PHE 0.015 0.002 PHE B 456 TYR 0.015 0.001 TYR B 547 ARG 0.004 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 244 time to evaluate : 2.418 Fit side-chains REVERT: A 38 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6700 (mp) REVERT: A 215 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7588 (ttm) REVERT: A 222 TYR cc_start: 0.7061 (m-10) cc_final: 0.6814 (m-80) REVERT: A 435 MET cc_start: 0.6952 (tpp) cc_final: 0.6119 (mmm) REVERT: B 38 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6811 (mp) REVERT: B 51 LEU cc_start: 0.7422 (tm) cc_final: 0.6596 (mp) REVERT: B 99 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6302 (ppp) REVERT: B 229 LEU cc_start: 0.7885 (mt) cc_final: 0.7668 (pp) REVERT: B 294 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: B 435 MET cc_start: 0.6983 (tpp) cc_final: 0.6156 (mmm) REVERT: B 555 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 636 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7289 (ttp-170) REVERT: C 33 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5590 (ttt-90) REVERT: C 51 LEU cc_start: 0.7474 (tm) cc_final: 0.6623 (mp) REVERT: C 99 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6423 (mtt) REVERT: C 555 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.6114 (t80) REVERT: D 38 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6540 (mp) REVERT: D 45 TRP cc_start: 0.6161 (m-10) cc_final: 0.5862 (m100) REVERT: D 100 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7112 (pt0) REVERT: D 294 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: D 625 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6236 (mm) REVERT: D 636 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7220 (ttp-170) outliers start: 94 outliers final: 45 residues processed: 314 average time/residue: 1.1617 time to fit residues: 420.0974 Evaluate side-chains 291 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN C 228 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20768 Z= 0.222 Angle : 0.666 16.055 28000 Z= 0.327 Chirality : 0.043 0.305 3116 Planarity : 0.005 0.051 3416 Dihedral : 13.800 103.047 4109 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.41 % Allowed : 17.34 % Favored : 78.25 % 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: -1.19 (0.18), residues: 2360 helix: -0.04 (0.14), residues: 1436 sheet: -2.38 (0.54), residues: 76 loop : -1.84 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 268 HIS 0.003 0.001 HIS D 582 PHE 0.018 0.002 PHE D 456 TYR 0.016 0.002 TYR B 547 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 243 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6763 (mp) REVERT: A 215 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7661 (ttm) REVERT: A 222 TYR cc_start: 0.7052 (m-10) cc_final: 0.6835 (m-80) REVERT: A 229 LEU cc_start: 0.7911 (mt) cc_final: 0.7675 (pp) REVERT: A 435 MET cc_start: 0.6952 (tpp) cc_final: 0.6104 (mmm) REVERT: A 555 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.6070 (t80) REVERT: B 38 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6573 (mp) REVERT: B 99 MET cc_start: 0.7161 (mmt) cc_final: 0.6897 (mtt) REVERT: B 435 MET cc_start: 0.6990 (tpp) cc_final: 0.6173 (mmm) REVERT: B 555 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.6055 (t80) REVERT: B 636 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7284 (ttp-170) REVERT: C 51 LEU cc_start: 0.7456 (tm) cc_final: 0.6613 (mp) REVERT: C 99 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.5885 (ppp) REVERT: C 294 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: C 555 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.6119 (t80) REVERT: D 33 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5645 (ttt-90) REVERT: D 45 TRP cc_start: 0.6177 (m-10) cc_final: 0.5907 (m100) REVERT: D 99 MET cc_start: 0.5803 (mtt) cc_final: 0.5046 (tpp) REVERT: D 100 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7173 (pt0) REVERT: D 555 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5990 (t80) REVERT: D 636 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7232 (ttp-170) outliers start: 91 outliers final: 46 residues processed: 308 average time/residue: 1.1719 time to fit residues: 415.1446 Evaluate side-chains 295 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20768 Z= 0.264 Angle : 0.706 16.910 28000 Z= 0.343 Chirality : 0.045 0.323 3116 Planarity : 0.005 0.051 3416 Dihedral : 13.667 100.433 4109 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.12 % Allowed : 18.17 % Favored : 77.71 % 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: -1.29 (0.18), residues: 2360 helix: -0.13 (0.14), residues: 1436 sheet: -2.39 (0.54), residues: 76 loop : -1.86 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 268 HIS 0.004 0.001 HIS D 582 PHE 0.015 0.002 PHE D 523 TYR 0.016 0.002 TYR B 547 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 241 time to evaluate : 2.188 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6755 (mp) REVERT: A 215 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7676 (ttm) REVERT: A 222 TYR cc_start: 0.7038 (m-10) cc_final: 0.6823 (m-80) REVERT: A 555 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 99 MET cc_start: 0.7237 (mmt) cc_final: 0.6188 (ppp) REVERT: B 555 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.6117 (t80) REVERT: B 636 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7322 (ttp-170) REVERT: C 51 LEU cc_start: 0.7442 (tm) cc_final: 0.6607 (mp) REVERT: C 99 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6400 (mtt) REVERT: C 294 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: C 555 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6186 (t80) REVERT: D 33 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5630 (ttt-90) REVERT: D 99 MET cc_start: 0.5927 (mtt) cc_final: 0.5130 (tpp) REVERT: D 100 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7126 (pt0) REVERT: D 183 ILE cc_start: 0.7634 (pp) cc_final: 0.7353 (pt) REVERT: D 636 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7168 (ttp-170) outliers start: 85 outliers final: 46 residues processed: 302 average time/residue: 1.1352 time to fit residues: 397.6385 Evaluate side-chains 294 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.0570 chunk 198 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 0.0470 chunk 224 optimal weight: 8.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20768 Z= 0.188 Angle : 0.673 17.420 28000 Z= 0.323 Chirality : 0.043 0.276 3116 Planarity : 0.005 0.050 3416 Dihedral : 13.110 93.696 4109 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.00 % Allowed : 19.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2360 helix: 0.20 (0.14), residues: 1424 sheet: -2.35 (0.54), residues: 76 loop : -1.70 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 268 HIS 0.006 0.001 HIS A 228 PHE 0.014 0.001 PHE A 434 TYR 0.018 0.001 TYR B 524 ARG 0.006 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6723 (mp) REVERT: A 215 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (ttm) REVERT: A 222 TYR cc_start: 0.7074 (m-10) cc_final: 0.6855 (m-80) REVERT: A 555 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.6013 (t80) REVERT: B 45 TRP cc_start: 0.6234 (m-10) cc_final: 0.5817 (m100) REVERT: B 99 MET cc_start: 0.7161 (mmt) cc_final: 0.6050 (ppp) REVERT: B 555 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.6093 (t80) REVERT: B 636 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7269 (ttp-170) REVERT: C 45 TRP cc_start: 0.6233 (m-10) cc_final: 0.5817 (m100) REVERT: C 99 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6388 (mtt) REVERT: C 215 MET cc_start: 0.7868 (mtt) cc_final: 0.7648 (ptm) REVERT: C 294 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: C 555 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.6153 (t80) REVERT: D 33 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.5597 (ttt-90) REVERT: D 45 TRP cc_start: 0.6182 (m-10) cc_final: 0.5797 (m100) REVERT: D 99 MET cc_start: 0.5957 (mtt) cc_final: 0.5167 (tpp) REVERT: D 100 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7104 (pt0) REVERT: D 183 ILE cc_start: 0.7601 (pp) cc_final: 0.7336 (pt) REVERT: D 555 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5969 (t80) REVERT: D 636 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7168 (ttp-170) outliers start: 62 outliers final: 33 residues processed: 306 average time/residue: 1.1966 time to fit residues: 421.0481 Evaluate side-chains 285 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 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 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20768 Z= 0.192 Angle : 0.685 17.704 28000 Z= 0.325 Chirality : 0.043 0.270 3116 Planarity : 0.005 0.050 3416 Dihedral : 12.841 89.175 4109 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.33 % Allowed : 20.54 % Favored : 77.13 % 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: -0.70 (0.18), residues: 2360 helix: 0.36 (0.14), residues: 1420 sheet: -2.04 (0.52), residues: 84 loop : -1.62 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.002 0.001 HIS A 228 PHE 0.021 0.002 PHE B 434 TYR 0.018 0.001 TYR B 524 ARG 0.005 0.000 ARG A 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.7618 (pp) cc_final: 0.7402 (pp) REVERT: A 555 TYR cc_start: 0.6411 (OUTLIER) cc_final: 0.6064 (t80) REVERT: B 45 TRP cc_start: 0.6226 (m-10) cc_final: 0.5807 (m100) REVERT: B 99 MET cc_start: 0.7201 (mmt) cc_final: 0.5972 (ppp) REVERT: B 555 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.6105 (t80) REVERT: B 636 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7238 (ttp-170) REVERT: C 45 TRP cc_start: 0.6245 (m-10) cc_final: 0.5888 (m100) REVERT: C 51 LEU cc_start: 0.7419 (tm) cc_final: 0.6687 (mp) REVERT: C 99 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6392 (mtt) REVERT: C 294 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: C 555 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.6198 (t80) REVERT: D 45 TRP cc_start: 0.6143 (m-10) cc_final: 0.5763 (m100) REVERT: D 99 MET cc_start: 0.5993 (mtt) cc_final: 0.5210 (tpp) REVERT: D 100 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7081 (pt0) REVERT: D 183 ILE cc_start: 0.7627 (pp) cc_final: 0.7400 (pt) REVERT: D 555 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5953 (t80) REVERT: D 636 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7158 (ttp-170) outliers start: 48 outliers final: 30 residues processed: 294 average time/residue: 1.1234 time to fit residues: 384.3074 Evaluate side-chains 289 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 555 TYR Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 636 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 HIS C 358 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.210326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177908 restraints weight = 28555.486| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.28 r_work: 0.3879 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20768 Z= 0.208 Angle : 0.701 17.803 28000 Z= 0.332 Chirality : 0.044 0.278 3116 Planarity : 0.005 0.049 3416 Dihedral : 12.805 88.648 4109 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.33 % Allowed : 20.83 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2360 helix: 0.38 (0.14), residues: 1416 sheet: -2.02 (0.52), residues: 84 loop : -1.63 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 268 HIS 0.003 0.001 HIS B 426 PHE 0.016 0.002 PHE B 456 TYR 0.019 0.001 TYR D 349 ARG 0.005 0.000 ARG A 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7058.29 seconds wall clock time: 220 minutes 32.58 seconds (13232.58 seconds total)