Starting phenix.real_space_refine on Wed Apr 10 15:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf4_41219/04_2024/8tf4_41219_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf4_41219/04_2024/8tf4_41219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf4_41219/04_2024/8tf4_41219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf4_41219/04_2024/8tf4_41219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf4_41219/04_2024/8tf4_41219_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tf4_41219/04_2024/8tf4_41219_neut_updated.pdb" } resolution = 2.86 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= 0.003 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Cl 12 4.86 5 C 13008 2.51 5 N 3268 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "D" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 150 Unusual residues: {'CPL': 2, 'ECN': 1, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 10.69, per 1000 atoms: 0.54 Number of scatterers: 19888 At special positions: 0 Unit cell: (136.95, 136.95, 121.18, 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) Cl 12 17.00 S 136 16.00 P 4 15.00 O 3460 8.00 N 3268 7.00 C 13008 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 62.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.679A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.660A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.741A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.622A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'A' and resid 373 through 376 No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.655A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 423 through 444 Processing helix chain 'A' and resid 450 through 471 removed outlier: 3.669A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.626A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 553 through 565 Processing helix chain 'A' and resid 569 through 607 removed outlier: 3.779A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'B' and resid 29 through 46 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.679A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.660A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.741A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.622A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'B' and resid 373 through 376 No H-bonds generated for 'chain 'B' and resid 373 through 376' Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.654A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 423 through 444 Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.669A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG B 470 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 Proline residue: B 477 - end of helix Processing helix chain 'B' and resid 489 through 512 removed outlier: 3.625A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 553 through 565 Processing helix chain 'B' and resid 569 through 607 removed outlier: 3.779A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.679A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.661A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.740A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.622A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 No H-bonds generated for 'chain 'C' and resid 281 through 284' Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'C' and resid 373 through 376 No H-bonds generated for 'chain 'C' and resid 373 through 376' Processing helix chain 'C' and resid 380 through 410 Proline residue: C 405 - end of helix removed outlier: 3.655A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 423 through 444 Processing helix chain 'C' and resid 450 through 471 removed outlier: 3.668A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY C 471 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 487 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 489 through 512 removed outlier: 3.626A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 553 through 565 Processing helix chain 'C' and resid 569 through 607 removed outlier: 3.779A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'D' and resid 29 through 46 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.679A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.660A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.741A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.621A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 284 No H-bonds generated for 'chain 'D' and resid 281 through 284' Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 325 through 348 Processing helix chain 'D' and resid 373 through 376 No H-bonds generated for 'chain 'D' and resid 373 through 376' Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.654A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 450 through 471 removed outlier: 3.669A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG D 470 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 487 Proline residue: D 477 - end of helix Processing helix chain 'D' and resid 489 through 512 removed outlier: 3.626A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 553 through 565 Processing helix chain 'D' and resid 569 through 607 removed outlier: 3.778A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing sheet with id= A, first strand: chain 'A' and resid 630 through 636 removed outlier: 3.504A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 630 through 636 removed outlier: 3.503A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 630 through 636 removed outlier: 3.503A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 630 through 636 removed outlier: 3.504A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 960 hydrogen bonds defined for protein. 2808 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: 6.53 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3423 1.31 - 1.44: 5105 1.44 - 1.57: 11572 1.57 - 1.70: 16 1.70 - 1.82: 236 Bond restraints: 20352 Sorted by residual: bond pdb=" C PRO C 544 " pdb=" O PRO C 544 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.13e-02 7.83e+03 1.64e+01 bond pdb=" C PRO A 544 " pdb=" O PRO A 544 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.13e-02 7.83e+03 1.64e+01 bond pdb=" C PRO D 544 " pdb=" O PRO D 544 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.13e-02 7.83e+03 1.62e+01 bond pdb=" C PRO B 544 " pdb=" O PRO B 544 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.13e-02 7.83e+03 1.59e+01 bond pdb=" CA SER D 291 " pdb=" CB SER D 291 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.55e-02 4.16e+03 1.24e+01 ... (remaining 20347 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.04: 432 105.04 - 112.53: 9159 112.53 - 120.02: 9700 120.02 - 127.51: 8143 127.51 - 135.00: 178 Bond angle restraints: 27612 Sorted by residual: angle pdb=" N GLN C 73 " pdb=" CA GLN C 73 " pdb=" C GLN C 73 " ideal model delta sigma weight residual 112.93 106.25 6.68 1.12e+00 7.97e-01 3.56e+01 angle pdb=" N GLN A 73 " pdb=" CA GLN A 73 " pdb=" C GLN A 73 " ideal model delta sigma weight residual 112.93 106.26 6.67 1.12e+00 7.97e-01 3.54e+01 angle pdb=" N GLN D 73 " pdb=" CA GLN D 73 " pdb=" C GLN D 73 " ideal model delta sigma weight residual 112.93 106.27 6.66 1.12e+00 7.97e-01 3.53e+01 angle pdb=" N GLN B 73 " pdb=" CA GLN B 73 " pdb=" C GLN B 73 " ideal model delta sigma weight residual 112.93 106.29 6.64 1.12e+00 7.97e-01 3.51e+01 angle pdb=" N PHE B 72 " pdb=" CA PHE B 72 " pdb=" C PHE B 72 " ideal model delta sigma weight residual 112.54 105.58 6.96 1.22e+00 6.72e-01 3.26e+01 ... (remaining 27607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 12222 32.85 - 65.70: 250 65.70 - 98.55: 48 98.55 - 131.39: 4 131.39 - 164.24: 12 Dihedral angle restraints: 12536 sinusoidal: 5508 harmonic: 7028 Sorted by residual: dihedral pdb=" C3 CPL B 801 " pdb=" C1 CPL B 801 " pdb=" C2 CPL B 801 " pdb=" O3P CPL B 801 " ideal model delta sinusoidal sigma weight residual 72.09 -123.67 -164.24 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 CPL A 805 " pdb=" C1 CPL A 805 " pdb=" C2 CPL A 805 " pdb=" O3P CPL A 805 " ideal model delta sinusoidal sigma weight residual 72.09 -123.68 -164.23 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 CPL C 801 " pdb=" C1 CPL C 801 " pdb=" C2 CPL C 801 " pdb=" O3P CPL C 801 " ideal model delta sinusoidal sigma weight residual 72.09 -123.68 -164.23 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 12533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1624 0.058 - 0.116: 977 0.116 - 0.174: 368 0.174 - 0.232: 111 0.232 - 0.290: 48 Chirality restraints: 3128 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3125 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 802 " -0.120 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" C22 ERG B 802 " 0.106 2.00e-02 2.50e+03 pdb=" C23 ERG B 802 " 0.141 2.00e-02 2.50e+03 pdb=" C24 ERG B 802 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG D 802 " 0.120 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" C22 ERG D 802 " -0.106 2.00e-02 2.50e+03 pdb=" C23 ERG D 802 " -0.141 2.00e-02 2.50e+03 pdb=" C24 ERG D 802 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 801 " -0.120 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" C22 ERG A 801 " 0.106 2.00e-02 2.50e+03 pdb=" C23 ERG A 801 " 0.141 2.00e-02 2.50e+03 pdb=" C24 ERG A 801 " -0.127 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4260 2.82 - 3.34: 19983 3.34 - 3.86: 34288 3.86 - 4.38: 42168 4.38 - 4.90: 70072 Nonbonded interactions: 170771 Sorted by model distance: nonbonded pdb=" O ALA C 563 " pdb=" OG1 THR C 567 " model vdw 2.302 2.440 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.302 2.440 nonbonded pdb=" O ALA B 563 " pdb=" OG1 THR B 567 " model vdw 2.302 2.440 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.302 2.440 nonbonded pdb=" NH2 ARG C 146 " pdb=" OE1 GLU C 164 " model vdw 2.482 2.520 ... (remaining 170766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 802)) selection = (chain 'B' and (resid 28 through 637 or resid 802)) selection = (chain 'C' and (resid 28 through 637 or resid 802)) selection = (chain 'D' and (resid 28 through 637 or resid 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.160 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 53.590 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.140 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.056 20352 Z= 0.766 Angle : 1.774 12.371 27612 Z= 1.198 Chirality : 0.086 0.290 3128 Planarity : 0.013 0.124 3424 Dihedral : 15.620 164.242 7992 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.58 % Allowed : 0.96 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2384 helix: -0.65 (0.12), residues: 1476 sheet: -0.04 (0.53), residues: 76 loop : 0.47 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.153 0.018 TRP C 593 HIS 0.009 0.003 HIS A 238 PHE 0.056 0.013 PHE C 256 TYR 0.108 0.022 TYR A 336 ARG 0.007 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 378 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6990 (ttt90) cc_final: 0.6437 (ttt90) REVERT: A 43 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6827 (mmm-85) REVERT: A 80 GLU cc_start: 0.7819 (pt0) cc_final: 0.7483 (pm20) REVERT: A 139 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7251 (mtt-85) REVERT: A 153 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7636 (mpt-90) REVERT: A 176 GLU cc_start: 0.6891 (mp0) cc_final: 0.6611 (tt0) REVERT: A 257 GLN cc_start: 0.7426 (pt0) cc_final: 0.6402 (tp40) REVERT: A 260 MET cc_start: 0.8349 (mmp) cc_final: 0.8143 (mmm) REVERT: A 261 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8110 (mm110) REVERT: A 262 LYS cc_start: 0.8282 (mttt) cc_final: 0.7664 (ptpt) REVERT: A 300 LYS cc_start: 0.8001 (pttm) cc_final: 0.7700 (ptpt) REVERT: A 302 ARG cc_start: 0.7795 (ptp90) cc_final: 0.7376 (ppp-140) REVERT: A 451 VAL cc_start: 0.8419 (t) cc_final: 0.8192 (p) REVERT: A 473 GLN cc_start: 0.8500 (tt0) cc_final: 0.8145 (tp40) REVERT: A 483 GLN cc_start: 0.8054 (tt0) cc_final: 0.7825 (tm-30) REVERT: A 491 MET cc_start: 0.8144 (mmm) cc_final: 0.7649 (tpp) REVERT: B 33 ARG cc_start: 0.6987 (ttt90) cc_final: 0.6439 (ttt90) REVERT: B 43 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6819 (mmm-85) REVERT: B 100 GLU cc_start: 0.7830 (tt0) cc_final: 0.7625 (mt-10) REVERT: B 139 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7232 (mtt-85) REVERT: B 176 GLU cc_start: 0.6910 (mp0) cc_final: 0.6610 (tt0) REVERT: B 184 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 260 MET cc_start: 0.8329 (mmp) cc_final: 0.8126 (mmm) REVERT: B 262 LYS cc_start: 0.8258 (mttt) cc_final: 0.7698 (ptpt) REVERT: B 300 LYS cc_start: 0.7991 (pttm) cc_final: 0.7703 (ptpt) REVERT: B 302 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7376 (ppp-140) REVERT: B 451 VAL cc_start: 0.8390 (t) cc_final: 0.8160 (p) REVERT: B 473 GLN cc_start: 0.8512 (tt0) cc_final: 0.8130 (tp40) REVERT: B 483 GLN cc_start: 0.8048 (tt0) cc_final: 0.7826 (tm-30) REVERT: B 491 MET cc_start: 0.8124 (mmm) cc_final: 0.7634 (tpp) REVERT: C 33 ARG cc_start: 0.7002 (ttt90) cc_final: 0.6464 (ttt90) REVERT: C 43 ARG cc_start: 0.7137 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: C 139 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7244 (mtt-85) REVERT: C 176 GLU cc_start: 0.6909 (mp0) cc_final: 0.6608 (tt0) REVERT: C 260 MET cc_start: 0.8331 (mmp) cc_final: 0.8129 (mmm) REVERT: C 261 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8101 (mm110) REVERT: C 262 LYS cc_start: 0.8260 (mttt) cc_final: 0.7697 (ptpt) REVERT: C 300 LYS cc_start: 0.7995 (pttm) cc_final: 0.7705 (ptpt) REVERT: C 302 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7377 (ppp-140) REVERT: C 451 VAL cc_start: 0.8398 (t) cc_final: 0.8168 (p) REVERT: C 473 GLN cc_start: 0.8513 (tt0) cc_final: 0.8129 (tp40) REVERT: C 483 GLN cc_start: 0.8047 (tt0) cc_final: 0.7826 (tm-30) REVERT: C 491 MET cc_start: 0.8127 (mmm) cc_final: 0.7636 (tpp) REVERT: D 33 ARG cc_start: 0.7032 (ttt90) cc_final: 0.6502 (ttt90) REVERT: D 43 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6831 (mmm-85) REVERT: D 139 ARG cc_start: 0.7503 (mtt90) cc_final: 0.7235 (mtt-85) REVERT: D 176 GLU cc_start: 0.6889 (mp0) cc_final: 0.6598 (tt0) REVERT: D 260 MET cc_start: 0.8332 (mmp) cc_final: 0.8129 (mmm) REVERT: D 261 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8099 (mm110) REVERT: D 262 LYS cc_start: 0.8257 (mttt) cc_final: 0.7691 (ptpt) REVERT: D 300 LYS cc_start: 0.7981 (pttm) cc_final: 0.7702 (ptpt) REVERT: D 302 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7375 (ppp-140) REVERT: D 451 VAL cc_start: 0.8395 (t) cc_final: 0.8165 (p) REVERT: D 473 GLN cc_start: 0.8505 (tt0) cc_final: 0.8117 (tp40) REVERT: D 483 GLN cc_start: 0.8049 (tt0) cc_final: 0.7831 (tm-30) REVERT: D 491 MET cc_start: 0.8126 (mmm) cc_final: 0.7634 (tpp) outliers start: 12 outliers final: 4 residues processed: 386 average time/residue: 1.5567 time to fit residues: 667.5203 Evaluate side-chains 278 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 274 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain D residue 315 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 473 GLN A 596 GLN B 74 GLN B 261 GLN B 473 GLN B 596 GLN C 74 GLN C 473 GLN C 596 GLN D 74 GLN D 473 GLN D 596 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20352 Z= 0.209 Angle : 0.546 6.367 27612 Z= 0.281 Chirality : 0.039 0.138 3128 Planarity : 0.004 0.036 3424 Dihedral : 13.068 164.144 3440 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.78 % Allowed : 6.30 % Favored : 91.92 % 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: 1.41 (0.17), residues: 2384 helix: 1.34 (0.13), residues: 1488 sheet: -0.98 (0.41), residues: 128 loop : 0.72 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 593 HIS 0.004 0.001 HIS A 201 PHE 0.019 0.002 PHE A 611 TYR 0.013 0.001 TYR A 89 ARG 0.004 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 2.271 Fit side-chains REVERT: A 80 GLU cc_start: 0.7745 (pt0) cc_final: 0.7400 (pm20) REVERT: A 176 GLU cc_start: 0.6959 (mp0) cc_final: 0.6643 (tt0) REVERT: A 257 GLN cc_start: 0.7253 (pt0) cc_final: 0.6369 (tp40) REVERT: A 261 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7953 (mm110) REVERT: A 262 LYS cc_start: 0.8329 (mttt) cc_final: 0.7768 (mttp) REVERT: A 300 LYS cc_start: 0.7930 (pttm) cc_final: 0.7655 (ptpt) REVERT: A 302 ARG cc_start: 0.7827 (ptp90) cc_final: 0.7440 (ptm-80) REVERT: A 354 LEU cc_start: 0.8462 (mt) cc_final: 0.8188 (mm) REVERT: A 364 ASP cc_start: 0.7442 (t0) cc_final: 0.7184 (t0) REVERT: A 382 ASP cc_start: 0.7757 (m-30) cc_final: 0.7521 (m-30) REVERT: A 491 MET cc_start: 0.7879 (mmm) cc_final: 0.7405 (tpp) REVERT: B 139 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7380 (mtt-85) REVERT: B 176 GLU cc_start: 0.6965 (mp0) cc_final: 0.6643 (tt0) REVERT: B 257 GLN cc_start: 0.7215 (pt0) cc_final: 0.6311 (tp40) REVERT: B 261 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7921 (mm110) REVERT: B 262 LYS cc_start: 0.8336 (mttt) cc_final: 0.7696 (ptpt) REVERT: B 300 LYS cc_start: 0.7911 (pttm) cc_final: 0.7647 (ptpt) REVERT: B 302 ARG cc_start: 0.7815 (ptp90) cc_final: 0.7433 (ptm-80) REVERT: B 354 LEU cc_start: 0.8454 (mt) cc_final: 0.8181 (mm) REVERT: B 382 ASP cc_start: 0.7673 (m-30) cc_final: 0.7423 (m-30) REVERT: B 491 MET cc_start: 0.7895 (mmm) cc_final: 0.7420 (tpp) REVERT: C 139 ARG cc_start: 0.7697 (mtt90) cc_final: 0.7363 (mtt-85) REVERT: C 176 GLU cc_start: 0.6959 (mp0) cc_final: 0.6638 (tt0) REVERT: C 257 GLN cc_start: 0.7247 (pt0) cc_final: 0.6387 (tp40) REVERT: C 262 LYS cc_start: 0.8298 (mttt) cc_final: 0.7682 (ptpt) REVERT: C 300 LYS cc_start: 0.7914 (pttm) cc_final: 0.7646 (ptpt) REVERT: C 302 ARG cc_start: 0.7812 (ptp90) cc_final: 0.7434 (ptm-80) REVERT: C 354 LEU cc_start: 0.8463 (mt) cc_final: 0.8185 (mm) REVERT: C 364 ASP cc_start: 0.7455 (t0) cc_final: 0.7199 (t0) REVERT: C 382 ASP cc_start: 0.7674 (m-30) cc_final: 0.7424 (m-30) REVERT: C 491 MET cc_start: 0.7884 (mmm) cc_final: 0.7406 (tpp) REVERT: D 139 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7467 (mtt-85) REVERT: D 176 GLU cc_start: 0.6971 (mp0) cc_final: 0.6648 (tt0) REVERT: D 193 ASP cc_start: 0.6891 (t0) cc_final: 0.6572 (t70) REVERT: D 257 GLN cc_start: 0.7251 (pt0) cc_final: 0.6364 (tp40) REVERT: D 262 LYS cc_start: 0.8297 (mttt) cc_final: 0.7730 (mppt) REVERT: D 300 LYS cc_start: 0.7901 (pttm) cc_final: 0.7640 (ptpt) REVERT: D 302 ARG cc_start: 0.7809 (ptp90) cc_final: 0.7433 (ptm-80) REVERT: D 354 LEU cc_start: 0.8462 (mt) cc_final: 0.8182 (mm) REVERT: D 382 ASP cc_start: 0.7694 (m-30) cc_final: 0.7445 (m-30) REVERT: D 491 MET cc_start: 0.7896 (mmm) cc_final: 0.7422 (tpp) outliers start: 37 outliers final: 4 residues processed: 312 average time/residue: 1.6642 time to fit residues: 573.5656 Evaluate side-chains 233 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain D residue 548 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 148 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN D 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20352 Z= 0.253 Angle : 0.538 8.998 27612 Z= 0.273 Chirality : 0.039 0.136 3128 Planarity : 0.004 0.034 3424 Dihedral : 12.492 165.440 3428 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.54 % Allowed : 7.64 % Favored : 90.82 % 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: 1.67 (0.17), residues: 2384 helix: 1.63 (0.13), residues: 1488 sheet: -1.08 (0.44), residues: 128 loop : 0.69 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 593 HIS 0.004 0.001 HIS D 201 PHE 0.012 0.002 PHE B 425 TYR 0.014 0.002 TYR D 89 ARG 0.006 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 2.407 Fit side-chains REVERT: A 33 ARG cc_start: 0.6787 (tpt-90) cc_final: 0.6261 (ttp80) REVERT: A 35 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7065 (ttt90) REVERT: A 80 GLU cc_start: 0.7722 (pt0) cc_final: 0.7425 (pm20) REVERT: A 176 GLU cc_start: 0.7062 (mp0) cc_final: 0.6686 (tt0) REVERT: A 257 GLN cc_start: 0.7194 (pt0) cc_final: 0.6405 (tp40) REVERT: A 262 LYS cc_start: 0.8249 (mttt) cc_final: 0.7743 (mttp) REVERT: A 300 LYS cc_start: 0.7937 (pttm) cc_final: 0.7654 (ptpt) REVERT: A 302 ARG cc_start: 0.7831 (ptp90) cc_final: 0.7453 (ptm160) REVERT: A 354 LEU cc_start: 0.8495 (mt) cc_final: 0.8258 (mm) REVERT: A 364 ASP cc_start: 0.7606 (t0) cc_final: 0.7332 (t0) REVERT: A 382 ASP cc_start: 0.7807 (m-30) cc_final: 0.7528 (m-30) REVERT: A 491 MET cc_start: 0.7919 (mmm) cc_final: 0.7469 (tpp) REVERT: B 33 ARG cc_start: 0.6791 (tpt-90) cc_final: 0.6263 (ttp80) REVERT: B 139 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7440 (mtt-85) REVERT: B 176 GLU cc_start: 0.7074 (mp0) cc_final: 0.6680 (tt0) REVERT: B 257 GLN cc_start: 0.7136 (pt0) cc_final: 0.6508 (tp40) REVERT: B 262 LYS cc_start: 0.8282 (mttt) cc_final: 0.7761 (mttp) REVERT: B 300 LYS cc_start: 0.7927 (pttm) cc_final: 0.7656 (ptpt) REVERT: B 302 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7455 (ptm160) REVERT: B 354 LEU cc_start: 0.8490 (mt) cc_final: 0.8253 (mm) REVERT: B 382 ASP cc_start: 0.7761 (m-30) cc_final: 0.7486 (m-30) REVERT: B 491 MET cc_start: 0.7918 (mmm) cc_final: 0.7468 (tpp) REVERT: C 33 ARG cc_start: 0.6790 (tpt-90) cc_final: 0.6264 (ttp80) REVERT: C 139 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7432 (mtt-85) REVERT: C 176 GLU cc_start: 0.7073 (mp0) cc_final: 0.6681 (tt0) REVERT: C 257 GLN cc_start: 0.7195 (pt0) cc_final: 0.6321 (tp40) REVERT: C 261 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7869 (mm110) REVERT: C 262 LYS cc_start: 0.8288 (mttt) cc_final: 0.7750 (mttp) REVERT: C 300 LYS cc_start: 0.7916 (pttm) cc_final: 0.7647 (ptpt) REVERT: C 302 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7456 (ptm160) REVERT: C 354 LEU cc_start: 0.8486 (mt) cc_final: 0.8250 (mm) REVERT: C 364 ASP cc_start: 0.7627 (t0) cc_final: 0.7362 (t0) REVERT: C 382 ASP cc_start: 0.7785 (m-30) cc_final: 0.7494 (m-30) REVERT: C 491 MET cc_start: 0.7920 (mmm) cc_final: 0.7470 (tpp) REVERT: D 33 ARG cc_start: 0.6789 (tpt-90) cc_final: 0.6265 (ttp80) REVERT: D 139 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7565 (mtt-85) REVERT: D 176 GLU cc_start: 0.7080 (mp0) cc_final: 0.6684 (tt0) REVERT: D 257 GLN cc_start: 0.7193 (pt0) cc_final: 0.6325 (tp40) REVERT: D 261 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7868 (mm110) REVERT: D 262 LYS cc_start: 0.8287 (mttt) cc_final: 0.7748 (mttp) REVERT: D 300 LYS cc_start: 0.7916 (pttm) cc_final: 0.7646 (ptpt) REVERT: D 302 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7452 (ptm160) REVERT: D 354 LEU cc_start: 0.8485 (mt) cc_final: 0.8248 (mm) REVERT: D 382 ASP cc_start: 0.7741 (m-30) cc_final: 0.7482 (m-30) REVERT: D 491 MET cc_start: 0.7921 (mmm) cc_final: 0.7471 (tpp) outliers start: 32 outliers final: 8 residues processed: 257 average time/residue: 1.6042 time to fit residues: 458.4002 Evaluate side-chains 240 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 231 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20352 Z= 0.155 Angle : 0.474 6.488 27612 Z= 0.235 Chirality : 0.036 0.126 3128 Planarity : 0.004 0.034 3424 Dihedral : 11.669 164.415 3428 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.30 % Allowed : 8.56 % Favored : 90.14 % 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: 1.92 (0.17), residues: 2384 helix: 1.86 (0.13), residues: 1480 sheet: -1.17 (0.44), residues: 128 loop : 0.74 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.021 0.001 PHE A 611 TYR 0.009 0.001 TYR D 216 ARG 0.006 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 2.348 Fit side-chains REVERT: A 33 ARG cc_start: 0.6736 (tpt-90) cc_final: 0.6238 (mtm180) REVERT: A 43 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7346 (mmm-85) REVERT: A 80 GLU cc_start: 0.7685 (pt0) cc_final: 0.7422 (pm20) REVERT: A 176 GLU cc_start: 0.7060 (mp0) cc_final: 0.6685 (tt0) REVERT: A 257 GLN cc_start: 0.7074 (pt0) cc_final: 0.6465 (tp40) REVERT: A 260 MET cc_start: 0.8207 (tpt) cc_final: 0.7915 (mmm) REVERT: A 262 LYS cc_start: 0.8295 (mttt) cc_final: 0.7798 (mttp) REVERT: A 300 LYS cc_start: 0.7934 (pttm) cc_final: 0.7607 (ptpt) REVERT: A 302 ARG cc_start: 0.7724 (ptp90) cc_final: 0.7350 (ptm160) REVERT: A 354 LEU cc_start: 0.8466 (mt) cc_final: 0.8263 (mm) REVERT: A 364 ASP cc_start: 0.7532 (t0) cc_final: 0.7213 (t0) REVERT: A 382 ASP cc_start: 0.7810 (m-30) cc_final: 0.7545 (m-30) REVERT: A 491 MET cc_start: 0.7891 (mmm) cc_final: 0.7417 (tpp) REVERT: B 33 ARG cc_start: 0.6721 (tpt-90) cc_final: 0.6230 (mtm180) REVERT: B 35 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7071 (ttt90) REVERT: B 43 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7401 (mmm-85) REVERT: B 139 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7482 (mtt-85) REVERT: B 176 GLU cc_start: 0.7082 (mp0) cc_final: 0.6684 (tt0) REVERT: B 257 GLN cc_start: 0.7045 (pt0) cc_final: 0.6510 (tp40) REVERT: B 262 LYS cc_start: 0.8210 (mttt) cc_final: 0.7753 (mttp) REVERT: B 300 LYS cc_start: 0.7954 (pttm) cc_final: 0.7607 (ptpt) REVERT: B 302 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7349 (ptm160) REVERT: B 354 LEU cc_start: 0.8488 (mt) cc_final: 0.8273 (mm) REVERT: B 382 ASP cc_start: 0.7725 (m-30) cc_final: 0.7496 (m-30) REVERT: B 491 MET cc_start: 0.7891 (mmm) cc_final: 0.7417 (tpp) REVERT: C 33 ARG cc_start: 0.6731 (tpt-90) cc_final: 0.6241 (mtm180) REVERT: C 35 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7070 (ttt90) REVERT: C 43 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: C 139 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7493 (mtt-85) REVERT: C 176 GLU cc_start: 0.7080 (mp0) cc_final: 0.6685 (tt0) REVERT: C 257 GLN cc_start: 0.7111 (pt0) cc_final: 0.6417 (tp40) REVERT: C 262 LYS cc_start: 0.8252 (mttt) cc_final: 0.7770 (mttp) REVERT: C 300 LYS cc_start: 0.7936 (pttm) cc_final: 0.7602 (ptpt) REVERT: C 302 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7350 (ptm160) REVERT: C 354 LEU cc_start: 0.8480 (mt) cc_final: 0.8274 (mm) REVERT: C 364 ASP cc_start: 0.7536 (t0) cc_final: 0.7242 (t0) REVERT: C 382 ASP cc_start: 0.7752 (m-30) cc_final: 0.7501 (m-30) REVERT: C 491 MET cc_start: 0.7892 (mmm) cc_final: 0.7416 (tpp) REVERT: D 33 ARG cc_start: 0.6730 (tpt-90) cc_final: 0.6241 (mtm180) REVERT: D 35 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7071 (ttt90) REVERT: D 43 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7331 (mmm-85) REVERT: D 139 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7488 (mtt-85) REVERT: D 176 GLU cc_start: 0.7079 (mp0) cc_final: 0.6682 (tt0) REVERT: D 257 GLN cc_start: 0.7110 (pt0) cc_final: 0.6399 (tp40) REVERT: D 262 LYS cc_start: 0.8253 (mttt) cc_final: 0.7769 (mttp) REVERT: D 300 LYS cc_start: 0.7933 (pttm) cc_final: 0.7600 (ptpt) REVERT: D 302 ARG cc_start: 0.7718 (ptp90) cc_final: 0.7346 (ptm160) REVERT: D 354 LEU cc_start: 0.8474 (mt) cc_final: 0.8265 (mm) REVERT: D 491 MET cc_start: 0.7901 (mmm) cc_final: 0.7427 (tpp) outliers start: 27 outliers final: 8 residues processed: 292 average time/residue: 1.5626 time to fit residues: 507.9834 Evaluate side-chains 254 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 243 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 51 GLN C 51 GLN C 261 GLN D 51 GLN D 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20352 Z= 0.244 Angle : 0.490 5.684 27612 Z= 0.247 Chirality : 0.038 0.135 3128 Planarity : 0.004 0.035 3424 Dihedral : 11.800 168.334 3428 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.39 % Allowed : 9.52 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2384 helix: 1.74 (0.13), residues: 1484 sheet: -1.43 (0.42), residues: 128 loop : 0.65 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 593 HIS 0.004 0.001 HIS C 201 PHE 0.012 0.001 PHE A 425 TYR 0.011 0.001 TYR A 89 ARG 0.008 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 2.242 Fit side-chains REVERT: A 33 ARG cc_start: 0.6725 (tpt-90) cc_final: 0.6246 (ttp-170) REVERT: A 35 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7087 (ttt90) REVERT: A 80 GLU cc_start: 0.7658 (pt0) cc_final: 0.7409 (pm20) REVERT: A 176 GLU cc_start: 0.7015 (mp0) cc_final: 0.6568 (tt0) REVERT: A 257 GLN cc_start: 0.7114 (pt0) cc_final: 0.6544 (tp40) REVERT: A 262 LYS cc_start: 0.8311 (mttt) cc_final: 0.7794 (mttp) REVERT: A 300 LYS cc_start: 0.7954 (pttm) cc_final: 0.7659 (ptpt) REVERT: A 302 ARG cc_start: 0.7793 (ptp90) cc_final: 0.7385 (ptm160) REVERT: A 354 LEU cc_start: 0.8484 (mt) cc_final: 0.8268 (mm) REVERT: A 364 ASP cc_start: 0.7660 (t0) cc_final: 0.7377 (t0) REVERT: A 382 ASP cc_start: 0.7754 (m-30) cc_final: 0.7509 (m-30) REVERT: A 491 MET cc_start: 0.7931 (mmm) cc_final: 0.7479 (tpp) REVERT: B 33 ARG cc_start: 0.6753 (tpt-90) cc_final: 0.6275 (ttp-170) REVERT: B 35 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7091 (ttt90) REVERT: B 139 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7487 (mtt-85) REVERT: B 176 GLU cc_start: 0.7015 (mp0) cc_final: 0.6565 (tt0) REVERT: B 257 GLN cc_start: 0.7170 (pt0) cc_final: 0.6595 (tp40) REVERT: B 262 LYS cc_start: 0.8284 (mttt) cc_final: 0.7777 (mttp) REVERT: B 300 LYS cc_start: 0.7953 (pttm) cc_final: 0.7658 (ptpt) REVERT: B 302 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7413 (ptm160) REVERT: B 354 LEU cc_start: 0.8483 (mt) cc_final: 0.8264 (mm) REVERT: B 491 MET cc_start: 0.7932 (mmm) cc_final: 0.7478 (tpp) REVERT: B 522 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: C 33 ARG cc_start: 0.6749 (tpt-90) cc_final: 0.6271 (ttp-170) REVERT: C 35 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7090 (ttt90) REVERT: C 139 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7503 (mtt-85) REVERT: C 176 GLU cc_start: 0.7013 (mp0) cc_final: 0.6566 (tt0) REVERT: C 257 GLN cc_start: 0.7169 (pt0) cc_final: 0.6562 (tp40) REVERT: C 262 LYS cc_start: 0.8301 (mttt) cc_final: 0.7770 (mttp) REVERT: C 300 LYS cc_start: 0.7955 (pttm) cc_final: 0.7656 (ptpt) REVERT: C 302 ARG cc_start: 0.7786 (ptp90) cc_final: 0.7413 (ptm160) REVERT: C 354 LEU cc_start: 0.8461 (mt) cc_final: 0.8246 (mm) REVERT: C 364 ASP cc_start: 0.7670 (t0) cc_final: 0.7391 (t0) REVERT: C 491 MET cc_start: 0.7933 (mmm) cc_final: 0.7479 (tpp) REVERT: D 33 ARG cc_start: 0.6748 (tpt-90) cc_final: 0.6270 (ttp-170) REVERT: D 35 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7092 (ttt90) REVERT: D 139 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7499 (mtt-85) REVERT: D 176 GLU cc_start: 0.7011 (mp0) cc_final: 0.6561 (tt0) REVERT: D 257 GLN cc_start: 0.7168 (pt0) cc_final: 0.6484 (tp40) REVERT: D 262 LYS cc_start: 0.8300 (mttt) cc_final: 0.7768 (mttp) REVERT: D 300 LYS cc_start: 0.7953 (pttm) cc_final: 0.7656 (ptpt) REVERT: D 302 ARG cc_start: 0.7784 (ptp90) cc_final: 0.7412 (ptm160) REVERT: D 354 LEU cc_start: 0.8459 (mt) cc_final: 0.8244 (mm) REVERT: D 491 MET cc_start: 0.7921 (mmm) cc_final: 0.7475 (tpp) outliers start: 29 outliers final: 8 residues processed: 252 average time/residue: 1.6950 time to fit residues: 472.9763 Evaluate side-chains 240 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 227 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 0.0040 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 261 GLN B 51 GLN C 51 GLN C 261 GLN D 51 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20352 Z= 0.189 Angle : 0.465 5.563 27612 Z= 0.234 Chirality : 0.037 0.131 3128 Planarity : 0.004 0.038 3424 Dihedral : 11.671 168.250 3428 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.11 % Allowed : 9.71 % Favored : 89.18 % 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: 1.81 (0.17), residues: 2384 helix: 1.83 (0.13), residues: 1484 sheet: -1.50 (0.41), residues: 128 loop : 0.62 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 593 HIS 0.003 0.001 HIS C 201 PHE 0.024 0.001 PHE A 611 TYR 0.009 0.001 TYR A 89 ARG 0.009 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 233 time to evaluate : 2.230 Fit side-chains REVERT: A 33 ARG cc_start: 0.6724 (tpt-90) cc_final: 0.6284 (mtm180) REVERT: A 35 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7105 (ttt90) REVERT: A 80 GLU cc_start: 0.7660 (pt0) cc_final: 0.7416 (pm20) REVERT: A 176 GLU cc_start: 0.7047 (mp0) cc_final: 0.6596 (tt0) REVERT: A 257 GLN cc_start: 0.7042 (pt0) cc_final: 0.6483 (tp40) REVERT: A 262 LYS cc_start: 0.8312 (mttt) cc_final: 0.7757 (mttp) REVERT: A 294 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6981 (mt-10) REVERT: A 300 LYS cc_start: 0.7948 (pttm) cc_final: 0.7623 (ptpt) REVERT: A 302 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7325 (ptm160) REVERT: A 354 LEU cc_start: 0.8473 (mt) cc_final: 0.8262 (mm) REVERT: A 364 ASP cc_start: 0.7621 (t0) cc_final: 0.7319 (t0) REVERT: A 491 MET cc_start: 0.7906 (mmm) cc_final: 0.7453 (tpp) REVERT: B 33 ARG cc_start: 0.6701 (tpt-90) cc_final: 0.6251 (mtm180) REVERT: B 35 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7091 (ttt90) REVERT: B 139 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7498 (mtt-85) REVERT: B 176 GLU cc_start: 0.7060 (mp0) cc_final: 0.6613 (tt0) REVERT: B 257 GLN cc_start: 0.7115 (pt0) cc_final: 0.6646 (tp40) REVERT: B 262 LYS cc_start: 0.8272 (mttt) cc_final: 0.7781 (mttp) REVERT: B 300 LYS cc_start: 0.7936 (pttm) cc_final: 0.7612 (ptpt) REVERT: B 302 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7324 (ptm160) REVERT: B 354 LEU cc_start: 0.8473 (mt) cc_final: 0.8258 (mm) REVERT: B 364 ASP cc_start: 0.7672 (t0) cc_final: 0.7469 (t70) REVERT: B 491 MET cc_start: 0.7893 (mmm) cc_final: 0.7442 (tpp) REVERT: C 33 ARG cc_start: 0.6697 (tpt-90) cc_final: 0.6254 (mtm180) REVERT: C 35 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7076 (ttt90) REVERT: C 139 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7496 (mtt-85) REVERT: C 176 GLU cc_start: 0.7051 (mp0) cc_final: 0.6608 (tt0) REVERT: C 257 GLN cc_start: 0.7110 (pt0) cc_final: 0.6531 (tp40) REVERT: C 262 LYS cc_start: 0.8297 (mttt) cc_final: 0.7793 (mttp) REVERT: C 294 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6983 (mt-10) REVERT: C 300 LYS cc_start: 0.7927 (pttm) cc_final: 0.7605 (ptpt) REVERT: C 302 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7324 (ptm160) REVERT: C 354 LEU cc_start: 0.8485 (mt) cc_final: 0.8277 (mm) REVERT: C 364 ASP cc_start: 0.7639 (t0) cc_final: 0.7343 (t0) REVERT: C 491 MET cc_start: 0.7894 (mmm) cc_final: 0.7443 (tpp) REVERT: D 33 ARG cc_start: 0.6698 (tpt-90) cc_final: 0.6249 (mtm180) REVERT: D 35 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7078 (ttt90) REVERT: D 139 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7494 (mtt-85) REVERT: D 176 GLU cc_start: 0.7051 (mp0) cc_final: 0.6605 (tt0) REVERT: D 257 GLN cc_start: 0.7089 (pt0) cc_final: 0.6485 (tp40) REVERT: D 262 LYS cc_start: 0.8299 (mttt) cc_final: 0.7794 (mttp) REVERT: D 300 LYS cc_start: 0.7927 (pttm) cc_final: 0.7605 (ptpt) REVERT: D 302 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7324 (ptm160) REVERT: D 354 LEU cc_start: 0.8482 (mt) cc_final: 0.8274 (mm) REVERT: D 364 ASP cc_start: 0.7672 (t0) cc_final: 0.7471 (t70) REVERT: D 491 MET cc_start: 0.7900 (mmm) cc_final: 0.7455 (tpp) outliers start: 23 outliers final: 12 residues processed: 249 average time/residue: 1.5791 time to fit residues: 436.8142 Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 261 GLN B 51 GLN C 51 GLN C 261 GLN D 51 GLN D 261 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20352 Z= 0.216 Angle : 0.477 5.586 27612 Z= 0.240 Chirality : 0.037 0.135 3128 Planarity : 0.004 0.040 3424 Dihedral : 11.656 168.865 3428 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.25 % Allowed : 10.29 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2384 helix: 1.80 (0.13), residues: 1484 sheet: -1.58 (0.41), residues: 128 loop : 0.59 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 593 HIS 0.003 0.001 HIS C 201 PHE 0.010 0.001 PHE A 425 TYR 0.009 0.001 TYR D 89 ARG 0.011 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 2.437 Fit side-chains REVERT: A 33 ARG cc_start: 0.6698 (tpt-90) cc_final: 0.6245 (mtm180) REVERT: A 35 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7110 (ttt90) REVERT: A 80 GLU cc_start: 0.7655 (pt0) cc_final: 0.7397 (pm20) REVERT: A 176 GLU cc_start: 0.7102 (mp0) cc_final: 0.6643 (tt0) REVERT: A 257 GLN cc_start: 0.7007 (pt0) cc_final: 0.6524 (tp40) REVERT: A 262 LYS cc_start: 0.8344 (mttt) cc_final: 0.7785 (mttp) REVERT: A 300 LYS cc_start: 0.7945 (pttm) cc_final: 0.7623 (ptpt) REVERT: A 302 ARG cc_start: 0.7663 (ptp90) cc_final: 0.7320 (ptm160) REVERT: A 354 LEU cc_start: 0.8476 (mt) cc_final: 0.8266 (mm) REVERT: A 364 ASP cc_start: 0.7735 (t0) cc_final: 0.7476 (t0) REVERT: A 491 MET cc_start: 0.7924 (mmm) cc_final: 0.7469 (tpp) REVERT: B 33 ARG cc_start: 0.6676 (tpt-90) cc_final: 0.6234 (mtm180) REVERT: B 35 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7076 (ttt90) REVERT: B 139 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7493 (mtt-85) REVERT: B 176 GLU cc_start: 0.7088 (mp0) cc_final: 0.6615 (tt0) REVERT: B 257 GLN cc_start: 0.7151 (pt0) cc_final: 0.6534 (tp40) REVERT: B 262 LYS cc_start: 0.8260 (mttt) cc_final: 0.7777 (mttp) REVERT: B 300 LYS cc_start: 0.7945 (pttm) cc_final: 0.7622 (ptpt) REVERT: B 302 ARG cc_start: 0.7662 (ptp90) cc_final: 0.7319 (ptm160) REVERT: B 354 LEU cc_start: 0.8476 (mt) cc_final: 0.8263 (mm) REVERT: B 364 ASP cc_start: 0.7737 (t0) cc_final: 0.7509 (t70) REVERT: B 491 MET cc_start: 0.7914 (mmm) cc_final: 0.7461 (tpp) REVERT: C 33 ARG cc_start: 0.6713 (tpt-90) cc_final: 0.6267 (mtm180) REVERT: C 35 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7080 (ttt90) REVERT: C 139 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7491 (mtt-85) REVERT: C 176 GLU cc_start: 0.7086 (mp0) cc_final: 0.6615 (tt0) REVERT: C 257 GLN cc_start: 0.7122 (pt0) cc_final: 0.6577 (tp40) REVERT: C 262 LYS cc_start: 0.8305 (mttt) cc_final: 0.7741 (mttp) REVERT: C 300 LYS cc_start: 0.7947 (pttm) cc_final: 0.7623 (ptpt) REVERT: C 302 ARG cc_start: 0.7662 (ptp90) cc_final: 0.7321 (ptm160) REVERT: C 354 LEU cc_start: 0.8471 (mt) cc_final: 0.8261 (mm) REVERT: C 364 ASP cc_start: 0.7725 (t0) cc_final: 0.7439 (t0) REVERT: C 491 MET cc_start: 0.7912 (mmm) cc_final: 0.7459 (tpp) REVERT: D 33 ARG cc_start: 0.6688 (tpt-90) cc_final: 0.6242 (mtm180) REVERT: D 35 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7082 (ttt90) REVERT: D 139 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7487 (mtt-85) REVERT: D 176 GLU cc_start: 0.7087 (mp0) cc_final: 0.6612 (tt0) REVERT: D 257 GLN cc_start: 0.7082 (pt0) cc_final: 0.6522 (tp40) REVERT: D 262 LYS cc_start: 0.8299 (mttt) cc_final: 0.7740 (mttp) REVERT: D 300 LYS cc_start: 0.7946 (pttm) cc_final: 0.7621 (ptpt) REVERT: D 302 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7319 (ptm160) REVERT: D 354 LEU cc_start: 0.8469 (mt) cc_final: 0.8259 (mm) REVERT: D 364 ASP cc_start: 0.7738 (t0) cc_final: 0.7512 (t70) REVERT: D 491 MET cc_start: 0.7919 (mmm) cc_final: 0.7471 (tpp) outliers start: 26 outliers final: 12 residues processed: 239 average time/residue: 1.7065 time to fit residues: 454.7660 Evaluate side-chains 233 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 261 GLN B 51 GLN B 261 GLN C 51 GLN C 261 GLN D 51 GLN D 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20352 Z= 0.181 Angle : 0.462 6.602 27612 Z= 0.231 Chirality : 0.036 0.128 3128 Planarity : 0.004 0.049 3424 Dihedral : 11.513 168.453 3428 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.11 % Allowed : 10.77 % Favored : 88.12 % 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: 1.87 (0.17), residues: 2384 helix: 1.89 (0.13), residues: 1484 sheet: -1.57 (0.41), residues: 128 loop : 0.63 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 593 HIS 0.003 0.001 HIS C 201 PHE 0.029 0.001 PHE A 611 TYR 0.008 0.001 TYR A 216 ARG 0.012 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 2.300 Fit side-chains REVERT: A 33 ARG cc_start: 0.6704 (tpt-90) cc_final: 0.6266 (mtm180) REVERT: A 35 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7099 (ttt90) REVERT: A 176 GLU cc_start: 0.7110 (mp0) cc_final: 0.6645 (tt0) REVERT: A 257 GLN cc_start: 0.6943 (pt0) cc_final: 0.6650 (tp40) REVERT: A 262 LYS cc_start: 0.8351 (mttt) cc_final: 0.7755 (mttp) REVERT: A 300 LYS cc_start: 0.7946 (pttm) cc_final: 0.7602 (ptpt) REVERT: A 302 ARG cc_start: 0.7649 (ptp90) cc_final: 0.7313 (ptm160) REVERT: A 354 LEU cc_start: 0.8488 (mt) cc_final: 0.8276 (mm) REVERT: A 364 ASP cc_start: 0.7722 (t0) cc_final: 0.7448 (t0) REVERT: A 491 MET cc_start: 0.7901 (mmm) cc_final: 0.7451 (tpp) REVERT: B 33 ARG cc_start: 0.6673 (tpt-90) cc_final: 0.6251 (mtm180) REVERT: B 35 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7079 (ttt90) REVERT: B 139 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7460 (mtt-85) REVERT: B 176 GLU cc_start: 0.7130 (mp0) cc_final: 0.6652 (tt0) REVERT: B 257 GLN cc_start: 0.7072 (pt0) cc_final: 0.6576 (tp40) REVERT: B 262 LYS cc_start: 0.8282 (mttt) cc_final: 0.7781 (mttp) REVERT: B 300 LYS cc_start: 0.7947 (pttm) cc_final: 0.7602 (ptpt) REVERT: B 302 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7308 (ptm160) REVERT: B 354 LEU cc_start: 0.8491 (mt) cc_final: 0.8277 (mm) REVERT: B 364 ASP cc_start: 0.7767 (t0) cc_final: 0.7540 (t70) REVERT: B 382 ASP cc_start: 0.7900 (m-30) cc_final: 0.7664 (m-30) REVERT: B 491 MET cc_start: 0.7894 (mmm) cc_final: 0.7441 (tpp) REVERT: C 33 ARG cc_start: 0.6693 (tpt-90) cc_final: 0.6282 (mtm180) REVERT: C 35 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7076 (ttt90) REVERT: C 139 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7454 (mtt-85) REVERT: C 176 GLU cc_start: 0.7128 (mp0) cc_final: 0.6652 (tt0) REVERT: C 257 GLN cc_start: 0.7055 (pt0) cc_final: 0.6686 (tp40) REVERT: C 262 LYS cc_start: 0.8292 (mttt) cc_final: 0.7739 (mttp) REVERT: C 300 LYS cc_start: 0.7948 (pttm) cc_final: 0.7601 (ptpt) REVERT: C 302 ARG cc_start: 0.7647 (ptp90) cc_final: 0.7312 (ptm160) REVERT: C 354 LEU cc_start: 0.8478 (mt) cc_final: 0.8274 (mm) REVERT: C 364 ASP cc_start: 0.7723 (t0) cc_final: 0.7445 (t0) REVERT: C 382 ASP cc_start: 0.7920 (m-30) cc_final: 0.7713 (m-30) REVERT: C 491 MET cc_start: 0.7899 (mmm) cc_final: 0.7449 (tpp) REVERT: D 33 ARG cc_start: 0.6670 (tpt-90) cc_final: 0.6260 (mtm180) REVERT: D 35 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7079 (ttt90) REVERT: D 139 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7463 (mtt-85) REVERT: D 176 GLU cc_start: 0.7129 (mp0) cc_final: 0.6651 (tt0) REVERT: D 257 GLN cc_start: 0.7018 (pt0) cc_final: 0.6663 (tp40) REVERT: D 262 LYS cc_start: 0.8281 (mttt) cc_final: 0.7722 (mttp) REVERT: D 300 LYS cc_start: 0.7947 (pttm) cc_final: 0.7601 (ptpt) REVERT: D 302 ARG cc_start: 0.7648 (ptp90) cc_final: 0.7311 (ptm160) REVERT: D 354 LEU cc_start: 0.8478 (mt) cc_final: 0.8273 (mm) REVERT: D 364 ASP cc_start: 0.7827 (t0) cc_final: 0.7585 (t70) REVERT: D 382 ASP cc_start: 0.7774 (m-30) cc_final: 0.7469 (m-30) REVERT: D 491 MET cc_start: 0.7900 (mmm) cc_final: 0.7430 (tpp) outliers start: 23 outliers final: 12 residues processed: 242 average time/residue: 1.5244 time to fit residues: 412.0915 Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 203 optimal weight: 0.4980 chunk 214 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN B 261 GLN C 51 GLN D 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20352 Z= 0.247 Angle : 0.493 7.089 27612 Z= 0.247 Chirality : 0.038 0.138 3128 Planarity : 0.004 0.055 3424 Dihedral : 11.583 168.812 3428 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.06 % Allowed : 10.77 % Favored : 88.17 % 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: 1.74 (0.17), residues: 2384 helix: 1.78 (0.13), residues: 1484 sheet: -1.66 (0.40), residues: 128 loop : 0.59 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 593 HIS 0.004 0.001 HIS A 201 PHE 0.011 0.001 PHE A 425 TYR 0.010 0.001 TYR A 89 ARG 0.015 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 225 time to evaluate : 2.303 Fit side-chains REVERT: A 33 ARG cc_start: 0.6684 (tpt-90) cc_final: 0.6254 (ttp-170) REVERT: A 35 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7108 (ttt90) REVERT: A 80 GLU cc_start: 0.7631 (pt0) cc_final: 0.7333 (pm20) REVERT: A 176 GLU cc_start: 0.7166 (mp0) cc_final: 0.6657 (tt0) REVERT: A 257 GLN cc_start: 0.6962 (pt0) cc_final: 0.6549 (tp40) REVERT: A 262 LYS cc_start: 0.8344 (mttt) cc_final: 0.7758 (mttp) REVERT: A 300 LYS cc_start: 0.7982 (pttm) cc_final: 0.7643 (ptpt) REVERT: A 302 ARG cc_start: 0.7676 (ptp90) cc_final: 0.7327 (ptm160) REVERT: A 354 LEU cc_start: 0.8483 (mt) cc_final: 0.8261 (mm) REVERT: A 491 MET cc_start: 0.7944 (mmm) cc_final: 0.7479 (tpp) REVERT: B 33 ARG cc_start: 0.6702 (tpt-90) cc_final: 0.6261 (ttp-170) REVERT: B 35 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7088 (ttt90) REVERT: B 139 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7374 (mtt-85) REVERT: B 176 GLU cc_start: 0.7176 (mp0) cc_final: 0.6657 (tt0) REVERT: B 257 GLN cc_start: 0.7118 (pt0) cc_final: 0.6678 (tp40) REVERT: B 262 LYS cc_start: 0.8313 (mttt) cc_final: 0.7751 (mttp) REVERT: B 300 LYS cc_start: 0.7985 (pttm) cc_final: 0.7640 (ptpt) REVERT: B 302 ARG cc_start: 0.7676 (ptp90) cc_final: 0.7328 (ptm160) REVERT: B 354 LEU cc_start: 0.8486 (mt) cc_final: 0.8262 (mm) REVERT: B 364 ASP cc_start: 0.7860 (t0) cc_final: 0.7619 (t70) REVERT: B 382 ASP cc_start: 0.7898 (m-30) cc_final: 0.7626 (m-30) REVERT: B 491 MET cc_start: 0.7942 (mmm) cc_final: 0.7478 (tpp) REVERT: C 33 ARG cc_start: 0.6699 (tpt-90) cc_final: 0.6259 (ttp-170) REVERT: C 35 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7090 (ttt90) REVERT: C 139 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7369 (mtt-85) REVERT: C 176 GLU cc_start: 0.7175 (mp0) cc_final: 0.6657 (tt0) REVERT: C 257 GLN cc_start: 0.7043 (pt0) cc_final: 0.6577 (tp40) REVERT: C 262 LYS cc_start: 0.8301 (mttt) cc_final: 0.7773 (mttp) REVERT: C 300 LYS cc_start: 0.7986 (pttm) cc_final: 0.7640 (ptpt) REVERT: C 302 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7329 (ptm160) REVERT: C 354 LEU cc_start: 0.8481 (mt) cc_final: 0.8259 (mm) REVERT: C 382 ASP cc_start: 0.7942 (m-30) cc_final: 0.7694 (m-30) REVERT: C 491 MET cc_start: 0.7942 (mmm) cc_final: 0.7479 (tpp) REVERT: D 33 ARG cc_start: 0.6702 (tpt-90) cc_final: 0.6267 (ttp-170) REVERT: D 35 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7091 (ttt90) REVERT: D 139 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7366 (mtt-85) REVERT: D 176 GLU cc_start: 0.7168 (mp0) cc_final: 0.6652 (tt0) REVERT: D 257 GLN cc_start: 0.7016 (pt0) cc_final: 0.6570 (tp40) REVERT: D 262 LYS cc_start: 0.8299 (mttt) cc_final: 0.7771 (mttp) REVERT: D 300 LYS cc_start: 0.7986 (pttm) cc_final: 0.7637 (ptpt) REVERT: D 302 ARG cc_start: 0.7672 (ptp90) cc_final: 0.7326 (ptm160) REVERT: D 354 LEU cc_start: 0.8480 (mt) cc_final: 0.8259 (mm) REVERT: D 364 ASP cc_start: 0.7841 (t0) cc_final: 0.7568 (t70) REVERT: D 382 ASP cc_start: 0.7819 (m-30) cc_final: 0.7548 (m-30) REVERT: D 491 MET cc_start: 0.7928 (mmm) cc_final: 0.7474 (tpp) outliers start: 22 outliers final: 12 residues processed: 241 average time/residue: 1.6249 time to fit residues: 434.9655 Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 524 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.6980 chunk 227 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN C 51 GLN D 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20352 Z= 0.163 Angle : 0.462 7.162 27612 Z= 0.231 Chirality : 0.036 0.125 3128 Planarity : 0.004 0.059 3424 Dihedral : 11.367 167.964 3428 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.77 % Allowed : 11.20 % Favored : 88.03 % 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: 1.95 (0.17), residues: 2384 helix: 1.96 (0.13), residues: 1484 sheet: -1.57 (0.41), residues: 128 loop : 0.65 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 593 HIS 0.003 0.001 HIS A 201 PHE 0.032 0.001 PHE A 611 TYR 0.009 0.001 TYR D 216 ARG 0.014 0.000 ARG A 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.584 Fit side-chains REVERT: A 33 ARG cc_start: 0.6697 (tpt-90) cc_final: 0.6307 (ttp-170) REVERT: A 35 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7075 (ttt90) REVERT: A 74 GLN cc_start: 0.7202 (mt0) cc_final: 0.6998 (mt0) REVERT: A 80 GLU cc_start: 0.7619 (pt0) cc_final: 0.7362 (pm20) REVERT: A 176 GLU cc_start: 0.7149 (mp0) cc_final: 0.6654 (tt0) REVERT: A 257 GLN cc_start: 0.6896 (pt0) cc_final: 0.6504 (tp40) REVERT: A 260 MET cc_start: 0.8119 (tpt) cc_final: 0.7837 (mmm) REVERT: A 262 LYS cc_start: 0.8305 (mttt) cc_final: 0.7743 (mttp) REVERT: A 300 LYS cc_start: 0.7943 (pttm) cc_final: 0.7599 (ptpt) REVERT: A 302 ARG cc_start: 0.7657 (ptp90) cc_final: 0.7313 (ptm160) REVERT: A 354 LEU cc_start: 0.8469 (mt) cc_final: 0.8265 (mm) REVERT: A 491 MET cc_start: 0.7908 (mmm) cc_final: 0.7463 (tpp) REVERT: B 33 ARG cc_start: 0.6696 (tpt-90) cc_final: 0.6274 (mtm180) REVERT: B 35 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7064 (ttt90) REVERT: B 139 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7463 (mtt-85) REVERT: B 176 GLU cc_start: 0.7152 (mp0) cc_final: 0.6655 (tt0) REVERT: B 257 GLN cc_start: 0.6991 (pt0) cc_final: 0.6555 (tp40) REVERT: B 262 LYS cc_start: 0.8288 (mttt) cc_final: 0.7773 (mttp) REVERT: B 300 LYS cc_start: 0.7943 (pttm) cc_final: 0.7598 (ptpt) REVERT: B 302 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7314 (ptm160) REVERT: B 354 LEU cc_start: 0.8475 (mt) cc_final: 0.8271 (mm) REVERT: B 364 ASP cc_start: 0.7779 (t0) cc_final: 0.7551 (t70) REVERT: B 382 ASP cc_start: 0.7885 (m-30) cc_final: 0.7625 (m-30) REVERT: B 491 MET cc_start: 0.7906 (mmm) cc_final: 0.7458 (tpp) REVERT: C 33 ARG cc_start: 0.6693 (tpt-90) cc_final: 0.6272 (mtm180) REVERT: C 35 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7077 (ttt90) REVERT: C 139 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7463 (mtt-85) REVERT: C 176 GLU cc_start: 0.7150 (mp0) cc_final: 0.6655 (tt0) REVERT: C 257 GLN cc_start: 0.6996 (pt0) cc_final: 0.6564 (tp40) REVERT: C 262 LYS cc_start: 0.8253 (mttt) cc_final: 0.7761 (mttp) REVERT: C 300 LYS cc_start: 0.7944 (pttm) cc_final: 0.7598 (ptpt) REVERT: C 302 ARG cc_start: 0.7654 (ptp90) cc_final: 0.7315 (ptm160) REVERT: C 354 LEU cc_start: 0.8472 (mt) cc_final: 0.8263 (mm) REVERT: C 382 ASP cc_start: 0.7863 (m-30) cc_final: 0.7641 (m-30) REVERT: C 491 MET cc_start: 0.7907 (mmm) cc_final: 0.7461 (tpp) REVERT: D 33 ARG cc_start: 0.6692 (tpt-90) cc_final: 0.6275 (mtm180) REVERT: D 35 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7079 (ttt90) REVERT: D 139 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7461 (mtt-85) REVERT: D 176 GLU cc_start: 0.7154 (mp0) cc_final: 0.6653 (tt0) REVERT: D 257 GLN cc_start: 0.6960 (pt0) cc_final: 0.6546 (tp40) REVERT: D 262 LYS cc_start: 0.8264 (mttt) cc_final: 0.7767 (mttp) REVERT: D 300 LYS cc_start: 0.7945 (pttm) cc_final: 0.7596 (ptpt) REVERT: D 302 ARG cc_start: 0.7655 (ptp90) cc_final: 0.7313 (ptm160) REVERT: D 354 LEU cc_start: 0.8474 (mt) cc_final: 0.8264 (mm) REVERT: D 364 ASP cc_start: 0.7835 (t0) cc_final: 0.7604 (t70) REVERT: D 382 ASP cc_start: 0.7783 (m-30) cc_final: 0.7527 (m-30) REVERT: D 491 MET cc_start: 0.7905 (mmm) cc_final: 0.7428 (tpp) REVERT: D 497 MET cc_start: 0.8044 (ttm) cc_final: 0.7819 (ttp) outliers start: 16 outliers final: 8 residues processed: 231 average time/residue: 1.6239 time to fit residues: 417.8937 Evaluate side-chains 226 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.0980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN C 51 GLN C 635 ASN D 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113536 restraints weight = 22536.252| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.63 r_work: 0.3156 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20352 Z= 0.144 Angle : 0.448 5.853 27612 Z= 0.223 Chirality : 0.035 0.122 3128 Planarity : 0.004 0.058 3424 Dihedral : 11.060 166.107 3428 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.53 % Allowed : 12.02 % Favored : 87.45 % 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: 2.10 (0.17), residues: 2384 helix: 2.09 (0.13), residues: 1484 sheet: -1.52 (0.41), residues: 128 loop : 0.69 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 593 HIS 0.002 0.001 HIS B 201 PHE 0.007 0.001 PHE A 537 TYR 0.007 0.001 TYR A 339 ARG 0.014 0.000 ARG D 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7557.68 seconds wall clock time: 136 minutes 13.37 seconds (8173.37 seconds total)