Starting phenix.real_space_refine on Thu Mar 5 01:48:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pbf_20292/03_2026/6pbf_20292.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pbf_20292/03_2026/6pbf_20292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pbf_20292/03_2026/6pbf_20292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pbf_20292/03_2026/6pbf_20292.map" model { file = "/net/cci-nas-00/data/ceres_data/6pbf_20292/03_2026/6pbf_20292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pbf_20292/03_2026/6pbf_20292.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12008 2.51 5 N 3140 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18484 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 11, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 11, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "C" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 11, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "D" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4588 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 24, 'TRANS': 573} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 11, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'O6V': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'O6V': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'O6V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.26 Number of scatterers: 18484 At special positions: 0 Unit cell: (131.936, 131.936, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3204 8.00 N 3140 7.00 C 12008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 833.2 milliseconds 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 65.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.710A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.954A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 119 through 128 removed outlier: 4.285A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 4.253A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.536A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.613A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.877A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.511A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.849A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 348 removed outlier: 4.950A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.722A pdb=" N GLU A 375 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 376' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.671A pdb=" N PHE A 408 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 422 through 446 removed outlier: 4.472A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.528A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.618A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 513 removed outlier: 4.080A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.571A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.641A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.711A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 81 through 90 removed outlier: 3.954A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 119 through 128 removed outlier: 4.285A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 4.253A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.536A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 222 removed outlier: 3.613A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.878A pdb=" N VAL B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.511A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 4.848A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 removed outlier: 4.950A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.722A pdb=" N GLU B 375 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 376' Processing helix chain 'B' and resid 382 through 404 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.671A pdb=" N PHE B 408 " --> pdb=" O PRO B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 422 through 446 removed outlier: 4.472A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.528A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.618A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 513 removed outlier: 4.079A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.571A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 587 through 608 removed outlier: 4.641A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.711A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.954A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 119 through 128 removed outlier: 4.285A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 4.252A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 4.536A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 222 removed outlier: 3.613A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 291 through 297 removed outlier: 3.878A pdb=" N VAL C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.511A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.849A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 removed outlier: 4.950A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.722A pdb=" N GLU C 375 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 376 " --> pdb=" O LEU C 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 376' Processing helix chain 'C' and resid 382 through 404 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.671A pdb=" N PHE C 408 " --> pdb=" O PRO C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 422 through 446 removed outlier: 4.472A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.529A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.618A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 513 removed outlier: 4.080A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.571A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 587 through 608 removed outlier: 4.641A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.711A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 81 through 90 removed outlier: 3.953A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 119 through 128 removed outlier: 4.285A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 4.253A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.535A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 222 removed outlier: 3.612A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 291 through 297 removed outlier: 3.878A pdb=" N VAL D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.511A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.849A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 348 removed outlier: 4.950A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 removed outlier: 3.722A pdb=" N GLU D 375 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 376 " --> pdb=" O LEU D 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 376' Processing helix chain 'D' and resid 382 through 404 Processing helix chain 'D' and resid 405 through 408 removed outlier: 3.671A pdb=" N PHE D 408 " --> pdb=" O PRO D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 422 through 446 removed outlier: 4.472A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.528A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.618A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 513 removed outlier: 4.080A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.572A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 587 through 608 removed outlier: 4.641A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 279 Processing sheet with id=AA2, first strand: chain 'B' and resid 273 through 279 Processing sheet with id=AA3, first strand: chain 'C' and resid 273 through 279 Processing sheet with id=AA4, first strand: chain 'D' and resid 273 through 279 984 hydrogen bonds defined for protein. 2916 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: 2.61 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5936 1.35 - 1.48: 4889 1.48 - 1.61: 7883 1.61 - 1.74: 0 1.74 - 1.87: 220 Bond restraints: 18928 Sorted by residual: bond pdb=" C16 O6V C1001 " pdb=" N15 O6V C1001 " ideal model delta sigma weight residual 1.357 1.464 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C16 O6V A1002 " pdb=" N15 O6V A1002 " ideal model delta sigma weight residual 1.357 1.464 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C16 O6V A1001 " pdb=" N15 O6V A1001 " ideal model delta sigma weight residual 1.357 1.464 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C16 O6V B1001 " pdb=" N15 O6V B1001 " ideal model delta sigma weight residual 1.357 1.464 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C14 O6V B1001 " pdb=" N15 O6V B1001 " ideal model delta sigma weight residual 1.394 1.476 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 18923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 25241 2.97 - 5.94: 435 5.94 - 8.91: 88 8.91 - 11.87: 0 11.87 - 14.84: 8 Bond angle restraints: 25772 Sorted by residual: angle pdb=" C06 O6V B1001 " pdb=" C04 O6V B1001 " pdb=" O03 O6V B1001 " ideal model delta sigma weight residual 110.66 125.50 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" C06 O6V A1002 " pdb=" C04 O6V A1002 " pdb=" O03 O6V A1002 " ideal model delta sigma weight residual 110.66 125.50 -14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" C06 O6V A1001 " pdb=" C04 O6V A1001 " pdb=" O03 O6V A1001 " ideal model delta sigma weight residual 110.66 125.47 -14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C06 O6V C1001 " pdb=" C04 O6V C1001 " pdb=" O03 O6V C1001 " ideal model delta sigma weight residual 110.66 125.45 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" N VAL B 313 " pdb=" CA VAL B 313 " pdb=" C VAL B 313 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.37e+01 ... (remaining 25767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 9786 17.72 - 35.44: 1114 35.44 - 53.16: 188 53.16 - 70.88: 64 70.88 - 88.60: 32 Dihedral angle restraints: 11184 sinusoidal: 4208 harmonic: 6976 Sorted by residual: dihedral pdb=" CA PRO B 424 " pdb=" C PRO B 424 " pdb=" N PHE B 425 " pdb=" CA PHE B 425 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO C 424 " pdb=" C PRO C 424 " pdb=" N PHE C 425 " pdb=" CA PHE C 425 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO D 424 " pdb=" C PRO D 424 " pdb=" N PHE D 425 " pdb=" CA PHE D 425 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 11181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2335 0.061 - 0.123: 533 0.123 - 0.184: 80 0.184 - 0.245: 12 0.245 - 0.306: 4 Chirality restraints: 2964 Sorted by residual: chirality pdb=" C07 O6V C1001 " pdb=" C06 O6V C1001 " pdb=" C16 O6V C1001 " pdb=" S08 O6V C1001 " both_signs ideal model delta sigma weight residual False -3.00 -3.30 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C07 O6V B1001 " pdb=" C06 O6V B1001 " pdb=" C16 O6V B1001 " pdb=" S08 O6V B1001 " both_signs ideal model delta sigma weight residual False -3.00 -3.30 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C07 O6V A1001 " pdb=" C06 O6V A1001 " pdb=" C16 O6V A1001 " pdb=" S08 O6V A1001 " both_signs ideal model delta sigma weight residual False -3.00 -3.30 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2961 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 486 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ILE D 486 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE D 486 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE D 487 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 486 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C ILE C 486 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE C 486 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE C 487 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 486 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C ILE A 486 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 486 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 487 " -0.017 2.00e-02 2.50e+03 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5607 2.82 - 3.34: 16800 3.34 - 3.86: 29975 3.86 - 4.38: 29857 4.38 - 4.90: 52466 Nonbonded interactions: 134705 Sorted by model distance: nonbonded pdb=" NH1 ARG B 470 " pdb=" OE1 GLN B 596 " model vdw 2.300 3.120 nonbonded pdb=" NH1 ARG A 470 " pdb=" OE1 GLN A 596 " model vdw 2.301 3.120 nonbonded pdb=" NH1 ARG D 470 " pdb=" OE1 GLN D 596 " model vdw 2.301 3.120 nonbonded pdb=" NH1 ARG C 470 " pdb=" OE1 GLN C 596 " model vdw 2.302 3.120 nonbonded pdb=" OG1 THR C 514 " pdb=" OE2 GLU C 515 " model vdw 2.305 3.040 ... (remaining 134700 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 637) selection = (chain 'B' and resid 29 through 637) selection = (chain 'C' and resid 29 through 637) selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 18928 Z= 0.292 Angle : 0.990 14.842 25772 Z= 0.515 Chirality : 0.054 0.306 2964 Planarity : 0.007 0.064 3252 Dihedral : 16.458 88.601 6672 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.22 % Allowed : 9.83 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.13), residues: 2368 helix: -2.30 (0.11), residues: 1376 sheet: -2.94 (0.48), residues: 56 loop : -3.75 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.016 0.002 TYR D 547 PHE 0.021 0.002 PHE A 244 TRP 0.023 0.002 TRP C 286 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00598 (18928) covalent geometry : angle 0.99032 (25772) hydrogen bonds : bond 0.08521 ( 984) hydrogen bonds : angle 4.19564 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 627 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.8537 (pt) cc_final: 0.7970 (pt) REVERT: A 242 THR cc_start: 0.8656 (m) cc_final: 0.8233 (m) REVERT: A 315 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 415 TYR cc_start: 0.7063 (t80) cc_final: 0.6412 (t80) REVERT: A 436 VAL cc_start: 0.9203 (t) cc_final: 0.8914 (p) REVERT: A 547 TYR cc_start: 0.8088 (m-80) cc_final: 0.7617 (m-10) REVERT: B 83 LEU cc_start: 0.8129 (mp) cc_final: 0.7643 (tt) REVERT: B 146 ARG cc_start: 0.6697 (ttp-110) cc_final: 0.5586 (mtt90) REVERT: B 283 ILE cc_start: 0.9132 (tt) cc_final: 0.8692 (tt) REVERT: B 435 LEU cc_start: 0.7939 (tp) cc_final: 0.7581 (tp) REVERT: B 440 MET cc_start: 0.7607 (tpt) cc_final: 0.7356 (tpt) REVERT: B 523 PHE cc_start: 0.6754 (m-80) cc_final: 0.6448 (m-80) REVERT: C 105 LEU cc_start: 0.8831 (tp) cc_final: 0.8624 (tp) REVERT: C 172 CYS cc_start: 0.7753 (p) cc_final: 0.7314 (m) REVERT: C 193 ASP cc_start: 0.6181 (p0) cc_final: 0.5876 (p0) REVERT: C 202 ILE cc_start: 0.8636 (mm) cc_final: 0.8413 (mm) REVERT: C 364 ASP cc_start: 0.7319 (t0) cc_final: 0.7075 (t0) REVERT: C 440 MET cc_start: 0.6896 (tpt) cc_final: 0.6461 (tpt) REVERT: D 42 GLU cc_start: 0.8852 (tp30) cc_final: 0.8488 (tp30) REVERT: D 55 GLU cc_start: 0.8165 (tp30) cc_final: 0.7770 (pt0) REVERT: D 146 ARG cc_start: 0.8255 (ttp-110) cc_final: 0.7134 (ttm170) REVERT: D 301 LYS cc_start: 0.8767 (mttp) cc_final: 0.8551 (ttpt) REVERT: D 370 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7349 (pt0) outliers start: 4 outliers final: 0 residues processed: 629 average time/residue: 0.1384 time to fit residues: 131.9074 Evaluate side-chains 410 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 84 HIS A 185 HIS A 197 ASN A 238 HIS A 267 GLN A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS B 84 HIS B 185 HIS B 238 HIS B 267 GLN B 370 GLN B 509 HIS C 37 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 206 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 HIS D 84 HIS ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D 267 GLN D 509 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131956 restraints weight = 36714.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135146 restraints weight = 19923.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137195 restraints weight = 12837.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138592 restraints weight = 9464.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139389 restraints weight = 7652.887| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18928 Z= 0.131 Angle : 0.639 9.547 25772 Z= 0.320 Chirality : 0.042 0.370 2964 Planarity : 0.005 0.069 3252 Dihedral : 8.676 67.425 2688 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.22 % Allowed : 4.80 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.16), residues: 2368 helix: -0.63 (0.13), residues: 1420 sheet: -2.11 (0.58), residues: 56 loop : -3.31 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 190 TYR 0.019 0.001 TYR A 339 PHE 0.023 0.002 PHE D 416 TRP 0.022 0.002 TRP C 462 HIS 0.004 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00289 (18928) covalent geometry : angle 0.63880 (25772) hydrogen bonds : bond 0.03660 ( 984) hydrogen bonds : angle 3.69652 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 518 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 THR cc_start: 0.8855 (m) cc_final: 0.8630 (m) REVERT: A 253 THR cc_start: 0.8584 (p) cc_final: 0.8375 (p) REVERT: A 266 VAL cc_start: 0.9238 (t) cc_final: 0.8991 (p) REVERT: A 315 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 317 VAL cc_start: 0.8471 (t) cc_final: 0.8100 (p) REVERT: A 435 LEU cc_start: 0.8285 (tp) cc_final: 0.7917 (tp) REVERT: A 447 MET cc_start: 0.7288 (mmt) cc_final: 0.6685 (mmm) REVERT: A 495 TRP cc_start: 0.8429 (m100) cc_final: 0.8159 (m100) REVERT: A 592 LEU cc_start: 0.8953 (tp) cc_final: 0.8418 (tt) REVERT: B 54 LYS cc_start: 0.7869 (tttm) cc_final: 0.7585 (tmtt) REVERT: B 83 LEU cc_start: 0.8544 (mp) cc_final: 0.7999 (tt) REVERT: B 128 GLN cc_start: 0.7792 (tt0) cc_final: 0.7460 (tp40) REVERT: B 146 ARG cc_start: 0.6876 (ttp-110) cc_final: 0.5828 (mmt90) REVERT: B 178 ILE cc_start: 0.8172 (mm) cc_final: 0.7920 (mm) REVERT: B 435 LEU cc_start: 0.8176 (tp) cc_final: 0.7838 (tp) REVERT: B 497 MET cc_start: 0.8892 (ttt) cc_final: 0.8600 (ttp) REVERT: B 522 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6984 (tp30) REVERT: B 554 MET cc_start: 0.7186 (tpt) cc_final: 0.6639 (tpp) REVERT: B 603 MET cc_start: 0.7484 (tpt) cc_final: 0.6980 (tpp) REVERT: C 98 LEU cc_start: 0.8295 (mm) cc_final: 0.8043 (mm) REVERT: C 193 ASP cc_start: 0.6120 (p0) cc_final: 0.5862 (p0) REVERT: C 197 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6918 (p0) REVERT: C 202 ILE cc_start: 0.8736 (mm) cc_final: 0.8499 (mm) REVERT: C 315 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6786 (mm-30) REVERT: C 447 MET cc_start: 0.7430 (mmm) cc_final: 0.6862 (mmm) REVERT: D 130 LEU cc_start: 0.7968 (tp) cc_final: 0.7725 (mm) REVERT: D 146 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.6842 (ttm110) REVERT: D 370 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7346 (pt0) REVERT: D 435 LEU cc_start: 0.8309 (tp) cc_final: 0.8079 (tt) REVERT: D 633 VAL cc_start: 0.8563 (t) cc_final: 0.8260 (m) outliers start: 4 outliers final: 0 residues processed: 520 average time/residue: 0.1221 time to fit residues: 101.3778 Evaluate side-chains 391 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 62 optimal weight: 0.0030 chunk 173 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 426 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS B 238 HIS B 370 GLN B 483 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 185 HIS D 267 GLN D 635 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130299 restraints weight = 36194.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133452 restraints weight = 19753.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135554 restraints weight = 12668.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136934 restraints weight = 9187.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137854 restraints weight = 7350.795| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18928 Z= 0.132 Angle : 0.622 9.104 25772 Z= 0.311 Chirality : 0.042 0.349 2964 Planarity : 0.004 0.056 3252 Dihedral : 8.058 77.443 2688 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2368 helix: 0.23 (0.14), residues: 1400 sheet: -1.37 (0.65), residues: 56 loop : -3.06 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 470 TYR 0.019 0.001 TYR A 547 PHE 0.018 0.001 PHE B 115 TRP 0.020 0.002 TRP D 286 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00296 (18928) covalent geometry : angle 0.62241 (25772) hydrogen bonds : bond 0.03614 ( 984) hydrogen bonds : angle 3.62379 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8286 (mmp) cc_final: 0.7982 (mmt) REVERT: A 105 LEU cc_start: 0.9145 (tp) cc_final: 0.8931 (tp) REVERT: A 161 TYR cc_start: 0.8104 (t80) cc_final: 0.7797 (t80) REVERT: A 266 VAL cc_start: 0.9189 (t) cc_final: 0.8920 (p) REVERT: A 280 LEU cc_start: 0.8934 (pp) cc_final: 0.8728 (pp) REVERT: A 315 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6939 (mm-30) REVERT: A 481 MET cc_start: 0.7837 (tpp) cc_final: 0.7573 (tpp) REVERT: A 495 TRP cc_start: 0.8655 (m100) cc_final: 0.8252 (m100) REVERT: A 592 LEU cc_start: 0.8902 (tp) cc_final: 0.8305 (tt) REVERT: B 54 LYS cc_start: 0.7891 (tttm) cc_final: 0.7577 (tmtt) REVERT: B 146 ARG cc_start: 0.7121 (ttp-110) cc_final: 0.6005 (mmt90) REVERT: B 415 TYR cc_start: 0.7411 (t80) cc_final: 0.7144 (t80) REVERT: B 435 LEU cc_start: 0.8866 (tp) cc_final: 0.8510 (tp) REVERT: B 554 MET cc_start: 0.7477 (tpt) cc_final: 0.7218 (tpp) REVERT: C 98 LEU cc_start: 0.8354 (mm) cc_final: 0.8055 (mm) REVERT: C 128 GLN cc_start: 0.7960 (tt0) cc_final: 0.7449 (tp40) REVERT: C 315 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6771 (mm-30) REVERT: C 390 LEU cc_start: 0.8817 (mp) cc_final: 0.8564 (tt) REVERT: C 432 TYR cc_start: 0.8850 (t80) cc_final: 0.8593 (t80) REVERT: C 447 MET cc_start: 0.7140 (mmm) cc_final: 0.6916 (mmm) REVERT: C 475 LEU cc_start: 0.8649 (tp) cc_final: 0.8388 (tt) REVERT: C 489 ASP cc_start: 0.7671 (m-30) cc_final: 0.7338 (m-30) REVERT: C 491 MET cc_start: 0.8789 (tpp) cc_final: 0.8502 (tpp) REVERT: D 130 LEU cc_start: 0.7910 (tp) cc_final: 0.7672 (mm) REVERT: D 146 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.6729 (ttm110) REVERT: D 370 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7181 (pt0) REVERT: D 554 MET cc_start: 0.8115 (tpt) cc_final: 0.7875 (tpp) REVERT: D 569 LEU cc_start: 0.8742 (mp) cc_final: 0.8311 (mp) REVERT: D 615 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7631 (tpt-90) REVERT: D 633 VAL cc_start: 0.8842 (t) cc_final: 0.8475 (m) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.1113 time to fit residues: 91.0086 Evaluate side-chains 386 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 2 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 230 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 426 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 238 HIS B 267 GLN B 370 GLN C 37 ASN C 185 HIS C 267 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125244 restraints weight = 36918.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128347 restraints weight = 20107.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130356 restraints weight = 12964.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131660 restraints weight = 9531.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132509 restraints weight = 7739.892| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18928 Z= 0.192 Angle : 0.705 9.110 25772 Z= 0.355 Chirality : 0.045 0.340 2964 Planarity : 0.004 0.043 3252 Dihedral : 7.796 72.642 2688 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 2368 helix: 0.47 (0.14), residues: 1396 sheet: -1.08 (0.67), residues: 56 loop : -2.97 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 35 TYR 0.022 0.002 TYR A 547 PHE 0.022 0.002 PHE A 244 TRP 0.025 0.002 TRP D 286 HIS 0.010 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00435 (18928) covalent geometry : angle 0.70493 (25772) hydrogen bonds : bond 0.04380 ( 984) hydrogen bonds : angle 3.99155 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8411 (tt0) cc_final: 0.7931 (tp40) REVERT: A 134 ARG cc_start: 0.8671 (tpp80) cc_final: 0.7927 (tpp-160) REVERT: A 202 ILE cc_start: 0.8916 (mm) cc_final: 0.8431 (mm) REVERT: A 315 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6976 (mm-30) REVERT: A 317 VAL cc_start: 0.8628 (t) cc_final: 0.8314 (p) REVERT: A 420 ILE cc_start: 0.9251 (tt) cc_final: 0.8947 (tp) REVERT: A 442 MET cc_start: 0.8097 (tpp) cc_final: 0.7866 (tpp) REVERT: A 447 MET cc_start: 0.7435 (mmm) cc_final: 0.7106 (mmm) REVERT: A 481 MET cc_start: 0.8182 (tpp) cc_final: 0.7729 (tpp) REVERT: A 592 LEU cc_start: 0.8963 (tp) cc_final: 0.8268 (tt) REVERT: B 54 LYS cc_start: 0.7835 (tttm) cc_final: 0.7516 (tmtt) REVERT: B 146 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.6173 (mmt90) REVERT: B 364 ASP cc_start: 0.8009 (t70) cc_final: 0.7802 (t0) REVERT: B 435 LEU cc_start: 0.8970 (tp) cc_final: 0.8706 (tp) REVERT: B 466 MET cc_start: 0.8608 (mtm) cc_final: 0.8402 (mtt) REVERT: B 554 MET cc_start: 0.8020 (tpt) cc_final: 0.7724 (tpp) REVERT: C 128 GLN cc_start: 0.8080 (tt0) cc_final: 0.7697 (tp40) REVERT: C 161 TYR cc_start: 0.8229 (t80) cc_final: 0.7952 (t80) REVERT: C 315 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6934 (mm-30) REVERT: C 415 TYR cc_start: 0.8006 (t80) cc_final: 0.7779 (t80) REVERT: C 475 LEU cc_start: 0.8698 (tp) cc_final: 0.8388 (tt) REVERT: C 497 MET cc_start: 0.8530 (ttp) cc_final: 0.8234 (ttp) REVERT: C 591 GLU cc_start: 0.8040 (tt0) cc_final: 0.7779 (tt0) REVERT: D 84 HIS cc_start: 0.8233 (m90) cc_final: 0.8013 (m90) REVERT: D 146 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.6649 (ttm110) REVERT: D 554 MET cc_start: 0.8482 (tpt) cc_final: 0.8122 (tpp) REVERT: D 635 ASN cc_start: 0.8386 (t0) cc_final: 0.8136 (t0) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1122 time to fit residues: 84.3749 Evaluate side-chains 355 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 203 optimal weight: 0.4980 chunk 123 optimal weight: 0.0970 chunk 117 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132886 restraints weight = 35786.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135977 restraints weight = 19553.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137995 restraints weight = 12591.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139324 restraints weight = 9228.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140117 restraints weight = 7464.689| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18928 Z= 0.113 Angle : 0.606 8.501 25772 Z= 0.299 Chirality : 0.042 0.341 2964 Planarity : 0.004 0.043 3252 Dihedral : 7.321 78.910 2688 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2368 helix: 0.86 (0.14), residues: 1396 sheet: -1.21 (0.64), residues: 56 loop : -2.76 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.009 0.001 TYR A 222 PHE 0.018 0.001 PHE C 523 TRP 0.016 0.001 TRP B 286 HIS 0.011 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00248 (18928) covalent geometry : angle 0.60570 (25772) hydrogen bonds : bond 0.03398 ( 984) hydrogen bonds : angle 3.68491 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8249 (tt0) cc_final: 0.7869 (tp40) REVERT: A 134 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8037 (tpp-160) REVERT: A 202 ILE cc_start: 0.8846 (mm) cc_final: 0.8619 (mm) REVERT: A 245 LYS cc_start: 0.8453 (mttp) cc_final: 0.8157 (mtpp) REVERT: A 266 VAL cc_start: 0.9211 (t) cc_final: 0.8931 (p) REVERT: A 315 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6978 (mm-30) REVERT: A 317 VAL cc_start: 0.8584 (t) cc_final: 0.8335 (p) REVERT: A 415 TYR cc_start: 0.6882 (t80) cc_final: 0.6676 (t80) REVERT: A 481 MET cc_start: 0.8023 (tpp) cc_final: 0.7621 (tpp) REVERT: A 592 LEU cc_start: 0.8845 (tp) cc_final: 0.8135 (tt) REVERT: B 33 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7955 (mpp80) REVERT: B 54 LYS cc_start: 0.7854 (tttm) cc_final: 0.7561 (tmtt) REVERT: B 93 GLU cc_start: 0.8421 (pp20) cc_final: 0.8114 (pp20) REVERT: B 128 GLN cc_start: 0.7867 (tt0) cc_final: 0.7602 (tp40) REVERT: B 146 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.6198 (mmt90) REVERT: B 197 ASN cc_start: 0.8088 (t0) cc_final: 0.7488 (t0) REVERT: B 435 LEU cc_start: 0.8996 (tp) cc_final: 0.8681 (tp) REVERT: B 554 MET cc_start: 0.7858 (tpt) cc_final: 0.7606 (tpp) REVERT: C 128 GLN cc_start: 0.7996 (tt0) cc_final: 0.7639 (tp40) REVERT: C 202 ILE cc_start: 0.8904 (mm) cc_final: 0.8617 (mm) REVERT: C 219 LEU cc_start: 0.9295 (mm) cc_final: 0.8940 (mt) REVERT: C 260 MET cc_start: 0.9059 (mmt) cc_final: 0.8858 (tpp) REVERT: C 315 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6878 (mm-30) REVERT: C 317 VAL cc_start: 0.8898 (m) cc_final: 0.8635 (p) REVERT: C 432 TYR cc_start: 0.8867 (t80) cc_final: 0.8548 (t80) REVERT: C 481 MET cc_start: 0.8458 (tpp) cc_final: 0.7811 (tpp) REVERT: C 497 MET cc_start: 0.8549 (ttp) cc_final: 0.8326 (ttp) REVERT: C 592 LEU cc_start: 0.8799 (tp) cc_final: 0.8343 (tt) REVERT: D 146 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.6634 (ttm110) REVERT: D 266 VAL cc_start: 0.8826 (t) cc_final: 0.8505 (p) REVERT: D 324 TYR cc_start: 0.7994 (m-80) cc_final: 0.7538 (m-10) REVERT: D 370 GLN cc_start: 0.7514 (tp40) cc_final: 0.6726 (tt0) REVERT: D 554 MET cc_start: 0.8540 (tpt) cc_final: 0.8239 (tpp) REVERT: D 635 ASN cc_start: 0.8390 (t0) cc_final: 0.8109 (t0) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.1113 time to fit residues: 87.9382 Evaluate side-chains 376 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 84 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 370 GLN C 238 HIS C 418 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123589 restraints weight = 38373.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126476 restraints weight = 21587.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128392 restraints weight = 14292.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129607 restraints weight = 10684.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130501 restraints weight = 8794.333| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18928 Z= 0.192 Angle : 0.720 11.154 25772 Z= 0.359 Chirality : 0.045 0.318 2964 Planarity : 0.004 0.047 3252 Dihedral : 7.442 76.742 2688 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2368 helix: 0.80 (0.14), residues: 1396 sheet: -0.90 (0.71), residues: 56 loop : -2.81 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 470 TYR 0.025 0.002 TYR C 415 PHE 0.025 0.002 PHE D 512 TRP 0.023 0.002 TRP B 286 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00440 (18928) covalent geometry : angle 0.72048 (25772) hydrogen bonds : bond 0.04371 ( 984) hydrogen bonds : angle 4.01618 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8958 (tt) cc_final: 0.8665 (tt) REVERT: A 105 LEU cc_start: 0.9370 (tp) cc_final: 0.9062 (tp) REVERT: A 128 GLN cc_start: 0.8455 (tt0) cc_final: 0.7996 (tp40) REVERT: A 198 THR cc_start: 0.6712 (t) cc_final: 0.6136 (t) REVERT: A 202 ILE cc_start: 0.8847 (mm) cc_final: 0.8432 (mm) REVERT: A 315 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6981 (mm-30) REVERT: A 317 VAL cc_start: 0.8836 (t) cc_final: 0.8601 (p) REVERT: A 481 MET cc_start: 0.8299 (tpp) cc_final: 0.7807 (tpp) REVERT: A 592 LEU cc_start: 0.8896 (tp) cc_final: 0.8018 (tt) REVERT: B 54 LYS cc_start: 0.7869 (tttm) cc_final: 0.7518 (tmtt) REVERT: B 93 GLU cc_start: 0.8624 (pp20) cc_final: 0.8418 (pp20) REVERT: B 146 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.6272 (mmt90) REVERT: B 364 ASP cc_start: 0.8181 (t70) cc_final: 0.7978 (t0) REVERT: B 435 LEU cc_start: 0.9000 (tp) cc_final: 0.8743 (tp) REVERT: B 466 MET cc_start: 0.8885 (mtm) cc_final: 0.8657 (mtt) REVERT: B 491 MET cc_start: 0.8825 (mmm) cc_final: 0.8475 (tpp) REVERT: B 501 ILE cc_start: 0.9064 (tt) cc_final: 0.8747 (tp) REVERT: B 554 MET cc_start: 0.8317 (tpt) cc_final: 0.7983 (tpp) REVERT: B 578 MET cc_start: 0.8214 (ttm) cc_final: 0.7770 (ttm) REVERT: B 592 LEU cc_start: 0.8980 (tp) cc_final: 0.8611 (tt) REVERT: B 608 MET cc_start: 0.7951 (tpp) cc_final: 0.7628 (tpp) REVERT: C 38 MET cc_start: 0.8903 (mmm) cc_final: 0.8692 (mmp) REVERT: C 128 GLN cc_start: 0.8134 (tt0) cc_final: 0.7800 (tp40) REVERT: C 178 ILE cc_start: 0.8608 (mm) cc_final: 0.8226 (mm) REVERT: C 315 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6851 (mm-30) REVERT: C 317 VAL cc_start: 0.9028 (m) cc_final: 0.8751 (p) REVERT: C 485 MET cc_start: 0.8029 (tpt) cc_final: 0.7577 (tpp) REVERT: C 497 MET cc_start: 0.8536 (ttp) cc_final: 0.8282 (ttp) REVERT: C 592 LEU cc_start: 0.8982 (tp) cc_final: 0.8407 (tt) REVERT: D 146 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.6608 (ttm110) REVERT: D 268 TRP cc_start: 0.7954 (p-90) cc_final: 0.7551 (p-90) REVERT: D 324 TYR cc_start: 0.7995 (m-80) cc_final: 0.7530 (m-10) REVERT: D 415 TYR cc_start: 0.7934 (t80) cc_final: 0.7316 (t80) REVERT: D 481 MET cc_start: 0.8277 (tpp) cc_final: 0.7899 (tpp) REVERT: D 495 TRP cc_start: 0.8352 (m100) cc_final: 0.8132 (m100) REVERT: D 554 MET cc_start: 0.8658 (tpt) cc_final: 0.8369 (tpp) REVERT: D 635 ASN cc_start: 0.8323 (t0) cc_final: 0.8047 (t0) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1133 time to fit residues: 83.2084 Evaluate side-chains 354 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 446 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN C 37 ASN C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 238 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123576 restraints weight = 36725.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126461 restraints weight = 20735.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128362 restraints weight = 13759.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129627 restraints weight = 10293.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130446 restraints weight = 8434.445| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18928 Z= 0.190 Angle : 0.715 12.088 25772 Z= 0.352 Chirality : 0.045 0.321 2964 Planarity : 0.004 0.092 3252 Dihedral : 7.392 77.637 2688 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2368 helix: 0.75 (0.14), residues: 1408 sheet: -0.93 (0.72), residues: 56 loop : -2.76 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 584 TYR 0.021 0.002 TYR C 415 PHE 0.020 0.002 PHE C 244 TRP 0.028 0.002 TRP D 286 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00436 (18928) covalent geometry : angle 0.71460 (25772) hydrogen bonds : bond 0.04126 ( 984) hydrogen bonds : angle 4.02169 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.669 Fit side-chains REVERT: A 54 LYS cc_start: 0.7941 (tttm) cc_final: 0.7363 (tmtt) REVERT: A 105 LEU cc_start: 0.9414 (tp) cc_final: 0.8963 (tp) REVERT: A 128 GLN cc_start: 0.8416 (tt0) cc_final: 0.7660 (tm-30) REVERT: A 130 LEU cc_start: 0.7799 (tp) cc_final: 0.7396 (mp) REVERT: A 315 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 317 VAL cc_start: 0.8765 (t) cc_final: 0.8533 (p) REVERT: A 432 TYR cc_start: 0.8826 (t80) cc_final: 0.8481 (t80) REVERT: A 435 LEU cc_start: 0.9012 (tp) cc_final: 0.8724 (tt) REVERT: A 447 MET cc_start: 0.6890 (mmm) cc_final: 0.6640 (mmm) REVERT: A 481 MET cc_start: 0.8352 (tpp) cc_final: 0.8112 (tpp) REVERT: A 570 MET cc_start: 0.7698 (tpp) cc_final: 0.7142 (tpp) REVERT: A 592 LEU cc_start: 0.8911 (tp) cc_final: 0.8083 (tt) REVERT: B 33 ARG cc_start: 0.8306 (mpp80) cc_final: 0.8042 (mpp80) REVERT: B 54 LYS cc_start: 0.7930 (tttm) cc_final: 0.7582 (tmtt) REVERT: B 84 HIS cc_start: 0.8664 (m90) cc_final: 0.8396 (m90) REVERT: B 128 GLN cc_start: 0.8051 (tt0) cc_final: 0.7746 (tp40) REVERT: B 146 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.6343 (mmt90) REVERT: B 364 ASP cc_start: 0.8310 (t70) cc_final: 0.8075 (t0) REVERT: B 435 LEU cc_start: 0.9026 (tp) cc_final: 0.8722 (tp) REVERT: B 466 MET cc_start: 0.8918 (mtm) cc_final: 0.8699 (mtt) REVERT: B 481 MET cc_start: 0.8300 (tpp) cc_final: 0.7690 (tpp) REVERT: B 491 MET cc_start: 0.8809 (mmm) cc_final: 0.8546 (tpp) REVERT: B 501 ILE cc_start: 0.9022 (tt) cc_final: 0.8793 (tp) REVERT: B 554 MET cc_start: 0.8572 (tpt) cc_final: 0.8207 (tpp) REVERT: B 608 MET cc_start: 0.7986 (tpp) cc_final: 0.7702 (tpp) REVERT: C 128 GLN cc_start: 0.8096 (tt0) cc_final: 0.7794 (tp40) REVERT: C 161 TYR cc_start: 0.7978 (t80) cc_final: 0.7525 (t80) REVERT: C 219 LEU cc_start: 0.9088 (mm) cc_final: 0.8795 (mt) REVERT: C 315 GLU cc_start: 0.7647 (mm-30) cc_final: 0.6677 (mm-30) REVERT: C 317 VAL cc_start: 0.8989 (m) cc_final: 0.8698 (p) REVERT: C 435 LEU cc_start: 0.8986 (tp) cc_final: 0.8639 (tt) REVERT: C 481 MET cc_start: 0.8488 (tpp) cc_final: 0.7933 (tmm) REVERT: C 497 MET cc_start: 0.8529 (ttp) cc_final: 0.8258 (ttp) REVERT: C 592 LEU cc_start: 0.8944 (tp) cc_final: 0.8377 (tt) REVERT: D 146 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.6600 (ttm110) REVERT: D 268 TRP cc_start: 0.7954 (p-90) cc_final: 0.7612 (p-90) REVERT: D 481 MET cc_start: 0.8304 (tpp) cc_final: 0.8032 (ttp) REVERT: D 554 MET cc_start: 0.8706 (tpt) cc_final: 0.8440 (tpp) REVERT: D 635 ASN cc_start: 0.8386 (t0) cc_final: 0.8147 (t0) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1114 time to fit residues: 80.6571 Evaluate side-chains 358 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 446 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124010 restraints weight = 38205.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126902 restraints weight = 21316.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128804 restraints weight = 13997.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130060 restraints weight = 10407.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130812 restraints weight = 8487.314| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18928 Z= 0.180 Angle : 0.713 9.329 25772 Z= 0.352 Chirality : 0.045 0.327 2964 Planarity : 0.004 0.049 3252 Dihedral : 7.321 77.810 2688 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2368 helix: 0.78 (0.14), residues: 1404 sheet: -1.01 (0.71), residues: 56 loop : -2.75 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.020 0.002 TYR C 555 PHE 0.022 0.002 PHE D 512 TRP 0.026 0.002 TRP D 286 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00415 (18928) covalent geometry : angle 0.71279 (25772) hydrogen bonds : bond 0.04109 ( 984) hydrogen bonds : angle 4.01489 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 0.684 Fit side-chains REVERT: A 54 LYS cc_start: 0.8003 (tttm) cc_final: 0.7441 (tmtt) REVERT: A 105 LEU cc_start: 0.9417 (tp) cc_final: 0.8969 (tp) REVERT: A 128 GLN cc_start: 0.8423 (tt0) cc_final: 0.7750 (tm-30) REVERT: A 130 LEU cc_start: 0.8007 (tp) cc_final: 0.7719 (mt) REVERT: A 198 THR cc_start: 0.6859 (t) cc_final: 0.6318 (t) REVERT: A 202 ILE cc_start: 0.8843 (mm) cc_final: 0.8437 (mm) REVERT: A 315 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 317 VAL cc_start: 0.8844 (t) cc_final: 0.8597 (p) REVERT: A 435 LEU cc_start: 0.8962 (tp) cc_final: 0.8666 (tt) REVERT: A 481 MET cc_start: 0.8325 (tpp) cc_final: 0.7913 (tpp) REVERT: A 570 MET cc_start: 0.7667 (tpp) cc_final: 0.7144 (tpp) REVERT: B 54 LYS cc_start: 0.7962 (tttm) cc_final: 0.7482 (tmtt) REVERT: B 84 HIS cc_start: 0.8652 (m90) cc_final: 0.8363 (m90) REVERT: B 128 GLN cc_start: 0.8079 (tt0) cc_final: 0.7792 (tp40) REVERT: B 146 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.6376 (mmt90) REVERT: B 364 ASP cc_start: 0.8529 (t70) cc_final: 0.8310 (t0) REVERT: B 435 LEU cc_start: 0.8995 (tp) cc_final: 0.8676 (tp) REVERT: B 442 MET cc_start: 0.8042 (tpp) cc_final: 0.7762 (tpp) REVERT: B 466 MET cc_start: 0.8895 (mtm) cc_final: 0.8669 (mtt) REVERT: B 481 MET cc_start: 0.8265 (tpp) cc_final: 0.7733 (tpp) REVERT: B 491 MET cc_start: 0.8778 (mmm) cc_final: 0.8392 (tpp) REVERT: B 501 ILE cc_start: 0.9091 (tt) cc_final: 0.8808 (tp) REVERT: B 570 MET cc_start: 0.7702 (tpp) cc_final: 0.7387 (tpp) REVERT: B 603 MET cc_start: 0.7351 (tpt) cc_final: 0.6864 (tpp) REVERT: B 608 MET cc_start: 0.8025 (tpp) cc_final: 0.7741 (tpp) REVERT: C 128 GLN cc_start: 0.8128 (tt0) cc_final: 0.7830 (tp40) REVERT: C 161 TYR cc_start: 0.7982 (t80) cc_final: 0.7597 (t80) REVERT: C 219 LEU cc_start: 0.9169 (mm) cc_final: 0.8855 (mt) REVERT: C 315 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7187 (mm-30) REVERT: C 317 VAL cc_start: 0.8966 (m) cc_final: 0.8681 (p) REVERT: C 415 TYR cc_start: 0.7739 (t80) cc_final: 0.7258 (t80) REVERT: C 435 LEU cc_start: 0.8980 (tp) cc_final: 0.8593 (tt) REVERT: C 481 MET cc_start: 0.8473 (tpp) cc_final: 0.7691 (tpp) REVERT: C 497 MET cc_start: 0.8518 (ttp) cc_final: 0.7861 (ttp) REVERT: D 42 GLU cc_start: 0.8807 (tp30) cc_final: 0.8472 (tp30) REVERT: D 146 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.6573 (ttm110) REVERT: D 268 TRP cc_start: 0.7994 (p-90) cc_final: 0.7719 (p-90) REVERT: D 415 TYR cc_start: 0.7931 (t80) cc_final: 0.7363 (t80) REVERT: D 460 LEU cc_start: 0.9017 (mt) cc_final: 0.8771 (mt) REVERT: D 481 MET cc_start: 0.8310 (tpp) cc_final: 0.8006 (tpp) REVERT: D 554 MET cc_start: 0.8754 (tpt) cc_final: 0.8431 (tpp) REVERT: D 596 GLN cc_start: 0.8255 (pt0) cc_final: 0.8036 (pt0) REVERT: D 635 ASN cc_start: 0.8333 (t0) cc_final: 0.8124 (t0) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.1068 time to fit residues: 76.7197 Evaluate side-chains 361 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 370 GLN A 446 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 370 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128162 restraints weight = 37960.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131179 restraints weight = 21018.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133142 restraints weight = 13672.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134428 restraints weight = 10115.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135286 restraints weight = 8221.239| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18928 Z= 0.131 Angle : 0.668 10.430 25772 Z= 0.324 Chirality : 0.043 0.320 2964 Planarity : 0.004 0.036 3252 Dihedral : 7.117 79.786 2688 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2368 helix: 0.93 (0.14), residues: 1408 sheet: -1.20 (0.69), residues: 56 loop : -2.68 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.018 0.001 TYR B 432 PHE 0.028 0.002 PHE D 523 TRP 0.018 0.002 TRP D 286 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00301 (18928) covalent geometry : angle 0.66826 (25772) hydrogen bonds : bond 0.03574 ( 984) hydrogen bonds : angle 3.83429 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.723 Fit side-chains REVERT: A 54 LYS cc_start: 0.8049 (tttm) cc_final: 0.7539 (tmtt) REVERT: A 105 LEU cc_start: 0.9409 (tp) cc_final: 0.9062 (tp) REVERT: A 128 GLN cc_start: 0.8325 (tt0) cc_final: 0.7607 (tm-30) REVERT: A 130 LEU cc_start: 0.7913 (tp) cc_final: 0.7623 (mp) REVERT: A 198 THR cc_start: 0.7069 (t) cc_final: 0.6617 (t) REVERT: A 202 ILE cc_start: 0.8801 (mm) cc_final: 0.8397 (mm) REVERT: A 315 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 317 VAL cc_start: 0.8804 (t) cc_final: 0.8583 (p) REVERT: A 432 TYR cc_start: 0.8805 (t80) cc_final: 0.8509 (t80) REVERT: A 435 LEU cc_start: 0.8953 (tp) cc_final: 0.8660 (tt) REVERT: A 481 MET cc_start: 0.8342 (tpp) cc_final: 0.7877 (tpp) REVERT: B 54 LYS cc_start: 0.7985 (tttm) cc_final: 0.7514 (tmtt) REVERT: B 84 HIS cc_start: 0.8596 (m90) cc_final: 0.8336 (m90) REVERT: B 98 LEU cc_start: 0.8671 (mt) cc_final: 0.8237 (mt) REVERT: B 128 GLN cc_start: 0.8058 (tt0) cc_final: 0.7766 (tp40) REVERT: B 146 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.6416 (mmt90) REVERT: B 279 ASP cc_start: 0.7770 (t70) cc_final: 0.7501 (t0) REVERT: B 294 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7533 (tt0) REVERT: B 435 LEU cc_start: 0.8967 (tp) cc_final: 0.8704 (tp) REVERT: B 442 MET cc_start: 0.8029 (tpp) cc_final: 0.7805 (tpp) REVERT: B 481 MET cc_start: 0.8227 (tpp) cc_final: 0.7742 (tpp) REVERT: B 491 MET cc_start: 0.8785 (mmm) cc_final: 0.8542 (tpp) REVERT: B 501 ILE cc_start: 0.9042 (tt) cc_final: 0.8794 (tp) REVERT: B 570 MET cc_start: 0.7608 (tpp) cc_final: 0.7293 (mmm) REVERT: B 603 MET cc_start: 0.7333 (tpt) cc_final: 0.6711 (tpp) REVERT: B 608 MET cc_start: 0.7980 (tpp) cc_final: 0.7757 (tpp) REVERT: C 128 GLN cc_start: 0.8001 (tt0) cc_final: 0.7761 (tp40) REVERT: C 161 TYR cc_start: 0.7926 (t80) cc_final: 0.7646 (t80) REVERT: C 219 LEU cc_start: 0.9176 (mm) cc_final: 0.8945 (mt) REVERT: C 315 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7202 (mm-30) REVERT: C 317 VAL cc_start: 0.8903 (m) cc_final: 0.8619 (p) REVERT: C 415 TYR cc_start: 0.7688 (t80) cc_final: 0.7242 (t80) REVERT: C 435 LEU cc_start: 0.8941 (tp) cc_final: 0.8529 (tt) REVERT: C 481 MET cc_start: 0.8470 (tpp) cc_final: 0.7722 (tpp) REVERT: C 489 ASP cc_start: 0.7214 (m-30) cc_final: 0.5897 (m-30) REVERT: C 496 LEU cc_start: 0.9104 (tp) cc_final: 0.8886 (tt) REVERT: C 592 LEU cc_start: 0.8841 (tp) cc_final: 0.8588 (tt) REVERT: D 42 GLU cc_start: 0.8762 (tp30) cc_final: 0.8452 (tp30) REVERT: D 146 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.6581 (mmt90) REVERT: D 268 TRP cc_start: 0.7969 (p-90) cc_final: 0.7701 (p-90) REVERT: D 415 TYR cc_start: 0.7891 (t80) cc_final: 0.7358 (t80) REVERT: D 481 MET cc_start: 0.8360 (tpp) cc_final: 0.8089 (tpp) REVERT: D 554 MET cc_start: 0.8718 (tpt) cc_final: 0.8379 (tpp) REVERT: D 596 GLN cc_start: 0.8310 (pt0) cc_final: 0.8101 (pt0) REVERT: D 635 ASN cc_start: 0.8225 (t0) cc_final: 0.8010 (t0) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1077 time to fit residues: 78.7533 Evaluate side-chains 363 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 215 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 7 optimal weight: 0.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 446 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130681 restraints weight = 35992.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133750 restraints weight = 19699.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135743 restraints weight = 12734.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137064 restraints weight = 9364.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137855 restraints weight = 7576.271| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.7105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18928 Z= 0.122 Angle : 0.660 9.866 25772 Z= 0.318 Chirality : 0.043 0.317 2964 Planarity : 0.004 0.046 3252 Dihedral : 6.974 80.532 2688 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2368 helix: 1.00 (0.14), residues: 1396 sheet: -1.28 (0.67), residues: 56 loop : -2.63 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.019 0.001 TYR B 432 PHE 0.043 0.002 PHE C 523 TRP 0.022 0.002 TRP B 286 HIS 0.003 0.001 HIS D 509 Details of bonding type rmsd covalent geometry : bond 0.00278 (18928) covalent geometry : angle 0.65976 (25772) hydrogen bonds : bond 0.03427 ( 984) hydrogen bonds : angle 3.75972 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.699 Fit side-chains REVERT: A 54 LYS cc_start: 0.8055 (tttm) cc_final: 0.7562 (tmtt) REVERT: A 105 LEU cc_start: 0.9417 (tp) cc_final: 0.9101 (tp) REVERT: A 128 GLN cc_start: 0.8271 (tt0) cc_final: 0.7583 (tm-30) REVERT: A 130 LEU cc_start: 0.7911 (tp) cc_final: 0.7603 (mp) REVERT: A 198 THR cc_start: 0.6963 (t) cc_final: 0.6478 (t) REVERT: A 202 ILE cc_start: 0.8726 (mm) cc_final: 0.8300 (mm) REVERT: A 245 LYS cc_start: 0.8439 (mttp) cc_final: 0.7990 (mtpt) REVERT: A 315 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6645 (mm-30) REVERT: A 317 VAL cc_start: 0.8742 (t) cc_final: 0.8503 (p) REVERT: A 432 TYR cc_start: 0.8705 (t80) cc_final: 0.8461 (t80) REVERT: A 435 LEU cc_start: 0.8907 (tp) cc_final: 0.8585 (tt) REVERT: A 481 MET cc_start: 0.8350 (tpp) cc_final: 0.7945 (tpp) REVERT: B 54 LYS cc_start: 0.8082 (tttm) cc_final: 0.7646 (tmtt) REVERT: B 84 HIS cc_start: 0.8548 (m90) cc_final: 0.8315 (m90) REVERT: B 128 GLN cc_start: 0.8060 (tt0) cc_final: 0.7761 (tp40) REVERT: B 146 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.6485 (mmt90) REVERT: B 294 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7522 (tt0) REVERT: B 435 LEU cc_start: 0.9006 (tp) cc_final: 0.8693 (tp) REVERT: B 442 MET cc_start: 0.7992 (tpp) cc_final: 0.7782 (tpp) REVERT: B 453 PRO cc_start: 0.9111 (Cg_exo) cc_final: 0.8910 (Cg_endo) REVERT: B 481 MET cc_start: 0.8237 (tpp) cc_final: 0.7693 (tpp) REVERT: B 491 MET cc_start: 0.8769 (mmm) cc_final: 0.8495 (tpp) REVERT: B 501 ILE cc_start: 0.9068 (tt) cc_final: 0.8814 (tp) REVERT: B 536 LEU cc_start: 0.8796 (mm) cc_final: 0.8595 (mm) REVERT: B 570 MET cc_start: 0.7587 (tpp) cc_final: 0.7325 (mmm) REVERT: B 603 MET cc_start: 0.7345 (tpt) cc_final: 0.6689 (tpp) REVERT: C 128 GLN cc_start: 0.7962 (tt0) cc_final: 0.7710 (tp40) REVERT: C 260 MET cc_start: 0.9066 (mmt) cc_final: 0.8839 (tpp) REVERT: C 315 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6807 (mm-30) REVERT: C 317 VAL cc_start: 0.8855 (m) cc_final: 0.8543 (p) REVERT: C 318 SER cc_start: 0.8703 (m) cc_final: 0.8216 (t) REVERT: C 415 TYR cc_start: 0.7678 (t80) cc_final: 0.7384 (t80) REVERT: C 481 MET cc_start: 0.8400 (tpp) cc_final: 0.7875 (tpp) REVERT: C 501 ILE cc_start: 0.8890 (tt) cc_final: 0.8605 (tp) REVERT: C 554 MET cc_start: 0.8890 (tpp) cc_final: 0.8582 (tpp) REVERT: C 570 MET cc_start: 0.7574 (tpp) cc_final: 0.6633 (mmm) REVERT: C 592 LEU cc_start: 0.8854 (tp) cc_final: 0.8602 (tt) REVERT: D 42 GLU cc_start: 0.8697 (tp30) cc_final: 0.8433 (tp30) REVERT: D 128 GLN cc_start: 0.7987 (tt0) cc_final: 0.7752 (tp40) REVERT: D 146 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.6426 (mmt90) REVERT: D 268 TRP cc_start: 0.7885 (p-90) cc_final: 0.7640 (p-90) REVERT: D 324 TYR cc_start: 0.8047 (m-80) cc_final: 0.7610 (m-10) REVERT: D 415 TYR cc_start: 0.7900 (t80) cc_final: 0.7292 (t80) REVERT: D 481 MET cc_start: 0.8329 (tpp) cc_final: 0.8072 (tpp) REVERT: D 554 MET cc_start: 0.8681 (tpt) cc_final: 0.8449 (tpp) REVERT: D 635 ASN cc_start: 0.8220 (t0) cc_final: 0.8018 (t0) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1041 time to fit residues: 76.0250 Evaluate side-chains 372 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 48 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 446 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127795 restraints weight = 36203.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130792 restraints weight = 20107.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132728 restraints weight = 13170.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133991 restraints weight = 9784.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134743 restraints weight = 7999.093| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18928 Z= 0.162 Angle : 0.708 10.515 25772 Z= 0.343 Chirality : 0.045 0.316 2964 Planarity : 0.004 0.036 3252 Dihedral : 7.038 78.924 2688 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2368 helix: 0.84 (0.14), residues: 1420 sheet: -1.20 (0.70), residues: 56 loop : -2.74 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.020 0.002 TYR B 555 PHE 0.038 0.002 PHE C 523 TRP 0.024 0.002 TRP D 286 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00376 (18928) covalent geometry : angle 0.70763 (25772) hydrogen bonds : bond 0.03893 ( 984) hydrogen bonds : angle 3.89204 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.18 seconds wall clock time: 51 minutes 23.80 seconds (3083.80 seconds total)