Starting phenix.real_space_refine on Tue Nov 18 22:51:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pbf_20292/11_2025/6pbf_20292.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pbf_20292/11_2025/6pbf_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pbf_20292/11_2025/6pbf_20292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pbf_20292/11_2025/6pbf_20292.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pbf_20292/11_2025/6pbf_20292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pbf_20292/11_2025/6pbf_20292.map" } 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18484 Number of models: 1 Model: "" Number of chains: 5 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: "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} Restraints were copied for chains: C, D Time building chain proxies: 4.80, 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: 1.45 Conformation dependent library (CDL) restraints added in 764.1 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: 0.59 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: 3.07 Time building geometry restraints manager: 1.87 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: 0.670 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.090 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- 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 : 0.712 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: 0.8538 (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: 0.6411 (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: 0.6698 (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: 0.7318 (t0) cc_final: 0.7074 (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: 0.8489 (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: 0.1398 time to fit residues: 133.2588 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 : 0.582 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135152 restraints weight = 19923.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137194 restraints weight = 12833.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138586 restraints weight = 9455.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139511 restraints weight = 7656.908| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.680 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: 0.8853 (m) cc_final: 0.8626 (m) REVERT: A 253 THR cc_start: 0.8584 (p) cc_final: 0.8376 (p) REVERT: A 266 VAL cc_start: 0.9238 (t) cc_final: 0.8992 (p) REVERT: A 315 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 317 VAL cc_start: 0.8471 (t) cc_final: 0.8099 (p) REVERT: A 435 LEU cc_start: 0.8289 (tp) cc_final: 0.7921 (tp) REVERT: A 447 MET cc_start: 0.7294 (mmt) cc_final: 0.6699 (mmm) REVERT: A 495 TRP cc_start: 0.8429 (m100) cc_final: 0.8160 (m100) REVERT: A 592 LEU cc_start: 0.8954 (tp) cc_final: 0.8418 (tt) REVERT: B 54 LYS cc_start: 0.7869 (tttm) cc_final: 0.7587 (tmtt) REVERT: B 83 LEU cc_start: 0.8553 (mp) cc_final: 0.8003 (tt) REVERT: B 128 GLN cc_start: 0.7789 (tt0) cc_final: 0.7460 (tp40) REVERT: B 146 ARG cc_start: 0.6873 (ttp-110) cc_final: 0.5830 (mmt90) REVERT: B 178 ILE cc_start: 0.8172 (mm) cc_final: 0.7918 (mm) REVERT: B 435 LEU cc_start: 0.8183 (tp) cc_final: 0.7844 (tp) REVERT: B 497 MET cc_start: 0.8895 (ttt) cc_final: 0.8603 (ttp) REVERT: B 522 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6986 (tp30) REVERT: B 554 MET cc_start: 0.7184 (tpt) cc_final: 0.6639 (tpp) REVERT: B 603 MET cc_start: 0.7486 (tpt) cc_final: 0.6981 (tpp) REVERT: C 98 LEU cc_start: 0.8299 (mm) cc_final: 0.8047 (mm) REVERT: C 193 ASP cc_start: 0.6107 (p0) cc_final: 0.5859 (p0) REVERT: C 197 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6915 (p0) REVERT: C 202 ILE cc_start: 0.8735 (mm) cc_final: 0.8498 (mm) REVERT: C 315 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6789 (mm-30) REVERT: C 447 MET cc_start: 0.7444 (mmm) cc_final: 0.6879 (mmm) REVERT: D 130 LEU cc_start: 0.7967 (tp) cc_final: 0.7724 (mm) REVERT: D 146 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.6842 (ttm110) REVERT: D 370 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7340 (pt0) REVERT: D 435 LEU cc_start: 0.8317 (tp) cc_final: 0.8088 (tt) REVERT: D 633 VAL cc_start: 0.8564 (t) cc_final: 0.8262 (m) outliers start: 4 outliers final: 0 residues processed: 520 average time/residue: 0.1212 time to fit residues: 100.9170 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 : 0.688 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.151975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130821 restraints weight = 36152.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133998 restraints weight = 19676.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136109 restraints weight = 12610.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137475 restraints weight = 9132.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138376 restraints weight = 7308.480| |-----------------------------------------------------------------------------| 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 : 0.709 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: 0.8287 (mmp) cc_final: 0.7983 (mmt) REVERT: A 105 LEU cc_start: 0.9147 (tp) cc_final: 0.8932 (tp) REVERT: A 161 TYR cc_start: 0.8103 (t80) cc_final: 0.7798 (t80) REVERT: A 266 VAL cc_start: 0.9189 (t) cc_final: 0.8920 (p) REVERT: A 280 LEU cc_start: 0.8930 (pp) cc_final: 0.8723 (pp) REVERT: A 315 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6934 (mm-30) REVERT: A 481 MET cc_start: 0.7836 (tpp) cc_final: 0.7574 (tpp) REVERT: A 495 TRP cc_start: 0.8654 (m100) cc_final: 0.8251 (m100) REVERT: A 592 LEU cc_start: 0.8901 (tp) cc_final: 0.8303 (tt) REVERT: B 54 LYS cc_start: 0.7890 (tttm) cc_final: 0.7576 (tmtt) REVERT: B 146 ARG cc_start: 0.7121 (ttp-110) cc_final: 0.6004 (mmt90) REVERT: B 415 TYR cc_start: 0.7409 (t80) cc_final: 0.7142 (t80) REVERT: B 435 LEU cc_start: 0.8865 (tp) cc_final: 0.8509 (tp) REVERT: B 554 MET cc_start: 0.7476 (tpt) cc_final: 0.7219 (tpp) REVERT: C 98 LEU cc_start: 0.8355 (mm) cc_final: 0.8056 (mm) REVERT: C 128 GLN cc_start: 0.7961 (tt0) cc_final: 0.7448 (tp40) REVERT: C 315 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6769 (mm-30) REVERT: C 390 LEU cc_start: 0.8816 (mp) cc_final: 0.8563 (tt) REVERT: C 432 TYR cc_start: 0.8849 (t80) cc_final: 0.8593 (t80) REVERT: C 447 MET cc_start: 0.7141 (mmm) cc_final: 0.6915 (mmm) REVERT: C 475 LEU cc_start: 0.8649 (tp) cc_final: 0.8389 (tt) REVERT: C 489 ASP cc_start: 0.7670 (m-30) cc_final: 0.7339 (m-30) REVERT: C 491 MET cc_start: 0.8789 (tpp) cc_final: 0.8500 (tpp) REVERT: D 130 LEU cc_start: 0.7910 (tp) cc_final: 0.7672 (mm) REVERT: D 146 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.6728 (ttm110) REVERT: D 370 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7182 (pt0) REVERT: D 554 MET cc_start: 0.8118 (tpt) cc_final: 0.7878 (tpp) REVERT: D 569 LEU cc_start: 0.8745 (mp) cc_final: 0.8314 (mp) REVERT: D 615 ARG cc_start: 0.8213 (tpt90) cc_final: 0.7630 (tpt-90) REVERT: D 633 VAL cc_start: 0.8843 (t) cc_final: 0.8476 (m) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.1149 time to fit residues: 94.0282 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 : 0.643 ------------------------------------------------------------------------------- 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: 7.9990 chunk 59 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 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: 0.9990 chunk 7 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.147760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126685 restraints weight = 36780.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129543 restraints weight = 20722.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131386 restraints weight = 13722.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132590 restraints weight = 10318.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133141 restraints weight = 8491.214| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18928 Z= 0.188 Angle : 0.709 9.046 25772 Z= 0.357 Chirality : 0.045 0.342 2964 Planarity : 0.004 0.043 3252 Dihedral : 7.748 72.081 2688 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.24 (0.17), residues: 2368 helix: 0.48 (0.14), residues: 1396 sheet: -1.06 (0.67), residues: 56 loop : -2.96 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 632 TYR 0.024 0.002 TYR A 547 PHE 0.025 0.002 PHE A 456 TRP 0.026 0.002 TRP D 286 HIS 0.009 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00425 (18928) covalent geometry : angle 0.70950 (25772) hydrogen bonds : bond 0.04426 ( 984) hydrogen bonds : angle 4.02104 ( 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 454 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8386 (tt0) cc_final: 0.7941 (tp40) REVERT: A 134 ARG cc_start: 0.8645 (tpp80) cc_final: 0.7897 (tpp-160) REVERT: A 202 ILE cc_start: 0.8862 (mm) cc_final: 0.8411 (mm) REVERT: A 315 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6935 (mm-30) REVERT: A 317 VAL cc_start: 0.8656 (t) cc_final: 0.8351 (p) REVERT: A 420 ILE cc_start: 0.9239 (tt) cc_final: 0.8943 (tp) REVERT: A 481 MET cc_start: 0.8293 (tpp) cc_final: 0.7842 (tpp) REVERT: A 570 MET cc_start: 0.7854 (tpp) cc_final: 0.7540 (tpp) REVERT: A 592 LEU cc_start: 0.8848 (tp) cc_final: 0.8165 (tt) REVERT: B 54 LYS cc_start: 0.7850 (tttm) cc_final: 0.7527 (tmtt) REVERT: B 146 ARG cc_start: 0.7543 (ttp-110) cc_final: 0.6209 (mmt90) REVERT: B 435 LEU cc_start: 0.9034 (tp) cc_final: 0.8772 (tp) REVERT: B 554 MET cc_start: 0.8131 (tpt) cc_final: 0.7865 (tpp) REVERT: C 128 GLN cc_start: 0.8114 (tt0) cc_final: 0.7736 (tp40) REVERT: C 315 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6884 (mm-30) REVERT: C 317 VAL cc_start: 0.8993 (m) cc_final: 0.8726 (p) REVERT: C 415 TYR cc_start: 0.7988 (t80) cc_final: 0.7771 (t80) REVERT: C 475 LEU cc_start: 0.8695 (tp) cc_final: 0.8409 (tt) REVERT: C 497 MET cc_start: 0.8491 (ttp) cc_final: 0.8150 (ttp) REVERT: C 591 GLU cc_start: 0.7979 (tt0) cc_final: 0.7768 (tt0) REVERT: D 146 ARG cc_start: 0.8065 (ttp-110) cc_final: 0.6638 (ttm110) REVERT: D 324 TYR cc_start: 0.8122 (m-80) cc_final: 0.7455 (m-10) REVERT: D 554 MET cc_start: 0.8677 (tpt) cc_final: 0.8366 (tpp) REVERT: D 635 ASN cc_start: 0.8379 (t0) cc_final: 0.8107 (t0) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1139 time to fit residues: 84.7852 Evaluate side-chains 353 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 0.8980 chunk 123 optimal weight: 0.3980 chunk 117 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN B 370 GLN ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 158 ASN D 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133867 restraints weight = 35611.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137027 restraints weight = 19333.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139115 restraints weight = 12419.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140492 restraints weight = 9015.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141331 restraints weight = 7219.802| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18928 Z= 0.111 Angle : 0.597 9.074 25772 Z= 0.292 Chirality : 0.041 0.339 2964 Planarity : 0.004 0.044 3252 Dihedral : 7.194 81.809 2688 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.74 (0.17), residues: 2368 helix: 0.86 (0.14), residues: 1400 sheet: -1.20 (0.63), residues: 56 loop : -2.71 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.009 0.001 TYR C 547 PHE 0.016 0.001 PHE D 115 TRP 0.015 0.001 TRP A 286 HIS 0.009 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00230 (18928) covalent geometry : angle 0.59703 (25772) hydrogen bonds : bond 0.03076 ( 984) hydrogen bonds : angle 3.62847 ( 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 482 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8170 (tt0) cc_final: 0.7825 (tp40) REVERT: A 134 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8018 (tpp-160) REVERT: A 202 ILE cc_start: 0.8826 (mm) cc_final: 0.8491 (mm) REVERT: A 245 LYS cc_start: 0.8406 (mttp) cc_final: 0.8165 (mtpt) REVERT: A 266 VAL cc_start: 0.9193 (t) cc_final: 0.8959 (p) REVERT: A 315 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 317 VAL cc_start: 0.8583 (t) cc_final: 0.8364 (p) REVERT: A 340 MET cc_start: 0.8537 (tpp) cc_final: 0.8261 (tpp) REVERT: A 415 TYR cc_start: 0.6698 (t80) cc_final: 0.6292 (t80) REVERT: A 420 ILE cc_start: 0.9221 (tt) cc_final: 0.8989 (mt) REVERT: A 481 MET cc_start: 0.8058 (tpp) cc_final: 0.7730 (tpp) REVERT: A 537 PHE cc_start: 0.8950 (t80) cc_final: 0.8695 (t80) REVERT: A 592 LEU cc_start: 0.8850 (tp) cc_final: 0.8089 (tt) REVERT: B 54 LYS cc_start: 0.7857 (tttm) cc_final: 0.7595 (tmtt) REVERT: B 93 GLU cc_start: 0.8343 (pp20) cc_final: 0.8022 (pp20) REVERT: B 128 GLN cc_start: 0.7822 (tt0) cc_final: 0.7580 (tp40) REVERT: B 146 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.6245 (mmt90) REVERT: B 321 TRP cc_start: 0.8828 (t-100) cc_final: 0.8142 (t-100) REVERT: B 435 LEU cc_start: 0.8955 (tp) cc_final: 0.8623 (tp) REVERT: B 554 MET cc_start: 0.7745 (tpt) cc_final: 0.7529 (tpp) REVERT: B 570 MET cc_start: 0.7446 (tpp) cc_final: 0.6669 (tpp) REVERT: B 603 MET cc_start: 0.7199 (tpt) cc_final: 0.6629 (tpp) REVERT: B 635 ASN cc_start: 0.8272 (t0) cc_final: 0.7997 (t0) REVERT: C 128 GLN cc_start: 0.7921 (tt0) cc_final: 0.7540 (tp40) REVERT: C 219 LEU cc_start: 0.9312 (mm) cc_final: 0.8989 (mt) REVERT: C 315 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6903 (mm-30) REVERT: C 317 VAL cc_start: 0.8858 (m) cc_final: 0.8578 (p) REVERT: C 432 TYR cc_start: 0.8806 (t80) cc_final: 0.8428 (t80) REVERT: C 481 MET cc_start: 0.8433 (tpp) cc_final: 0.7714 (tpp) REVERT: C 489 ASP cc_start: 0.7461 (m-30) cc_final: 0.7257 (m-30) REVERT: C 592 LEU cc_start: 0.8778 (tp) cc_final: 0.8316 (tt) REVERT: D 146 ARG cc_start: 0.8064 (ttp-110) cc_final: 0.6640 (ttm170) REVERT: D 266 VAL cc_start: 0.8797 (t) cc_final: 0.8466 (p) REVERT: D 268 TRP cc_start: 0.7750 (p-90) cc_final: 0.7395 (p-90) REVERT: D 324 TYR cc_start: 0.7932 (m-80) cc_final: 0.7513 (m-10) REVERT: D 370 GLN cc_start: 0.7486 (tp40) cc_final: 0.6769 (tt0) REVERT: D 485 MET cc_start: 0.7598 (tpp) cc_final: 0.7363 (tpp) REVERT: D 554 MET cc_start: 0.8488 (tpt) cc_final: 0.8205 (tpp) REVERT: D 615 ARG cc_start: 0.8222 (tpt90) cc_final: 0.7278 (tpt-90) REVERT: D 629 TRP cc_start: 0.8297 (m-90) cc_final: 0.7804 (m-90) REVERT: D 635 ASN cc_start: 0.8379 (t0) cc_final: 0.8063 (t0) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.1150 time to fit residues: 90.7134 Evaluate side-chains 382 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A 483 GLN B 84 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134707 restraints weight = 36635.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137732 restraints weight = 20023.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139721 restraints weight = 12951.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140931 restraints weight = 9525.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141843 restraints weight = 7808.189| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18928 Z= 0.128 Angle : 0.625 10.546 25772 Z= 0.308 Chirality : 0.042 0.311 2964 Planarity : 0.004 0.046 3252 Dihedral : 7.031 80.072 2688 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.05 % Allowed : 1.36 % Favored : 98.58 % 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: -0.66 (0.18), residues: 2368 helix: 0.90 (0.14), residues: 1424 sheet: -1.14 (0.64), residues: 56 loop : -2.71 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.019 0.001 TYR D 161 PHE 0.023 0.002 PHE D 512 TRP 0.020 0.002 TRP B 286 HIS 0.005 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00293 (18928) covalent geometry : angle 0.62502 (25772) hydrogen bonds : bond 0.03515 ( 984) hydrogen bonds : angle 3.64732 ( 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 454 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 29 TRP cc_start: 0.6423 (p90) cc_final: 0.6179 (p90) REVERT: A 128 GLN cc_start: 0.8321 (tt0) cc_final: 0.7932 (tp40) REVERT: A 202 ILE cc_start: 0.8793 (mm) cc_final: 0.8396 (mm) REVERT: A 245 LYS cc_start: 0.8433 (mttp) cc_final: 0.8186 (mtpt) REVERT: A 266 VAL cc_start: 0.9184 (t) cc_final: 0.8922 (p) REVERT: A 315 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 317 VAL cc_start: 0.8574 (t) cc_final: 0.8339 (p) REVERT: A 481 MET cc_start: 0.8167 (tpp) cc_final: 0.7690 (tpp) REVERT: A 570 MET cc_start: 0.7492 (tpp) cc_final: 0.7242 (tpp) REVERT: A 592 LEU cc_start: 0.8841 (tp) cc_final: 0.8157 (tt) REVERT: B 54 LYS cc_start: 0.7871 (tttm) cc_final: 0.7577 (tmtt) REVERT: B 88 LEU cc_start: 0.9135 (tp) cc_final: 0.8754 (tp) REVERT: B 93 GLU cc_start: 0.8482 (pp20) cc_final: 0.8197 (pp20) REVERT: B 146 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.6234 (mmt90) REVERT: B 435 LEU cc_start: 0.9001 (tp) cc_final: 0.8702 (tp) REVERT: B 466 MET cc_start: 0.8631 (mtm) cc_final: 0.8384 (mtt) REVERT: B 481 MET cc_start: 0.8269 (tpp) cc_final: 0.7674 (tpp) REVERT: B 501 ILE cc_start: 0.9130 (tt) cc_final: 0.8863 (tp) REVERT: B 554 MET cc_start: 0.7814 (tpt) cc_final: 0.7602 (tpp) REVERT: B 568 LEU cc_start: 0.9171 (tp) cc_final: 0.8952 (tt) REVERT: B 578 MET cc_start: 0.8216 (ttm) cc_final: 0.7958 (ttm) REVERT: B 603 MET cc_start: 0.7371 (tpt) cc_final: 0.6508 (tpp) REVERT: C 128 GLN cc_start: 0.8001 (tt0) cc_final: 0.7638 (tp40) REVERT: C 178 ILE cc_start: 0.8697 (mm) cc_final: 0.8410 (mm) REVERT: C 315 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 317 VAL cc_start: 0.8930 (m) cc_final: 0.8605 (p) REVERT: C 318 SER cc_start: 0.8672 (m) cc_final: 0.8315 (t) REVERT: C 501 ILE cc_start: 0.8817 (tt) cc_final: 0.8402 (tp) REVERT: C 592 LEU cc_start: 0.8906 (tp) cc_final: 0.8397 (tt) REVERT: D 146 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.6634 (mmt90) REVERT: D 324 TYR cc_start: 0.7926 (m-80) cc_final: 0.7558 (m-10) REVERT: D 489 ASP cc_start: 0.7539 (m-30) cc_final: 0.7157 (m-30) REVERT: D 635 ASN cc_start: 0.8310 (t0) cc_final: 0.8068 (t0) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.1148 time to fit residues: 85.5796 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 : 0.713 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 153 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 37 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132194 restraints weight = 37227.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135291 restraints weight = 20712.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137334 restraints weight = 13537.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138683 restraints weight = 10011.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139459 restraints weight = 8128.791| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18928 Z= 0.109 Angle : 0.609 12.146 25772 Z= 0.294 Chirality : 0.041 0.313 2964 Planarity : 0.004 0.036 3252 Dihedral : 6.898 81.558 2688 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -0.46 (0.18), residues: 2368 helix: 1.00 (0.14), residues: 1432 sheet: -1.12 (0.64), residues: 56 loop : -2.55 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.010 0.001 TYR D 467 PHE 0.022 0.001 PHE A 456 TRP 0.017 0.001 TRP B 286 HIS 0.005 0.001 HIS D 582 Details of bonding type rmsd covalent geometry : bond 0.00244 (18928) covalent geometry : angle 0.60904 (25772) hydrogen bonds : bond 0.03101 ( 984) hydrogen bonds : angle 3.57731 ( 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 454 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8357 (tt0) cc_final: 0.7925 (tp40) REVERT: A 202 ILE cc_start: 0.8819 (mm) cc_final: 0.8421 (mm) REVERT: A 245 LYS cc_start: 0.8418 (mttp) cc_final: 0.8147 (mtpt) REVERT: A 266 VAL cc_start: 0.9176 (t) cc_final: 0.8972 (p) REVERT: A 315 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6895 (tp30) REVERT: A 317 VAL cc_start: 0.8675 (t) cc_final: 0.8469 (p) REVERT: A 435 LEU cc_start: 0.8894 (tp) cc_final: 0.8595 (tt) REVERT: A 481 MET cc_start: 0.8146 (tpp) cc_final: 0.7709 (tpp) REVERT: A 491 MET cc_start: 0.8584 (mmm) cc_final: 0.8153 (tpp) REVERT: A 570 MET cc_start: 0.7412 (tpp) cc_final: 0.6947 (mmm) REVERT: A 592 LEU cc_start: 0.8899 (tp) cc_final: 0.8697 (tp) REVERT: B 54 LYS cc_start: 0.7920 (tttm) cc_final: 0.7621 (tmtt) REVERT: B 93 GLU cc_start: 0.8456 (pp20) cc_final: 0.8217 (pp20) REVERT: B 146 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.6225 (mmt90) REVERT: B 321 TRP cc_start: 0.8974 (t-100) cc_final: 0.7994 (t-100) REVERT: B 435 LEU cc_start: 0.9004 (tp) cc_final: 0.8677 (tp) REVERT: B 466 MET cc_start: 0.8630 (mtm) cc_final: 0.8384 (mtt) REVERT: B 481 MET cc_start: 0.8062 (tpp) cc_final: 0.7557 (tpp) REVERT: B 501 ILE cc_start: 0.9103 (tt) cc_final: 0.8819 (tp) REVERT: B 603 MET cc_start: 0.7278 (tpt) cc_final: 0.6760 (tpp) REVERT: C 128 GLN cc_start: 0.7965 (tt0) cc_final: 0.7628 (tp40) REVERT: C 219 LEU cc_start: 0.9211 (mm) cc_final: 0.8996 (mt) REVERT: C 315 GLU cc_start: 0.7768 (mm-30) cc_final: 0.6784 (mm-30) REVERT: C 317 VAL cc_start: 0.8895 (m) cc_final: 0.8589 (p) REVERT: C 481 MET cc_start: 0.8453 (tpp) cc_final: 0.7826 (tpp) REVERT: C 501 ILE cc_start: 0.8758 (tt) cc_final: 0.8422 (tp) REVERT: C 592 LEU cc_start: 0.8893 (tp) cc_final: 0.8374 (tt) REVERT: D 146 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.6713 (mmt90) REVERT: D 324 TYR cc_start: 0.7780 (m-80) cc_final: 0.7487 (m-10) REVERT: D 370 GLN cc_start: 0.7562 (tp40) cc_final: 0.6776 (tt0) REVERT: D 481 MET cc_start: 0.8126 (tpp) cc_final: 0.7921 (ttm) REVERT: D 489 ASP cc_start: 0.7573 (m-30) cc_final: 0.7097 (m-30) REVERT: D 495 TRP cc_start: 0.8184 (m100) cc_final: 0.7890 (m100) REVERT: D 635 ASN cc_start: 0.8343 (t0) cc_final: 0.8100 (t0) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1102 time to fit residues: 82.7646 Evaluate side-chains 369 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 8.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 370 GLN C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123488 restraints weight = 38299.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126539 restraints weight = 20965.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128566 restraints weight = 13629.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129893 restraints weight = 10048.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130671 restraints weight = 8145.481| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18928 Z= 0.217 Angle : 0.738 8.700 25772 Z= 0.369 Chirality : 0.046 0.308 2964 Planarity : 0.005 0.058 3252 Dihedral : 7.299 77.787 2688 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -0.86 (0.17), residues: 2368 helix: 0.67 (0.14), residues: 1436 sheet: -1.04 (0.69), residues: 56 loop : -2.71 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.016 0.002 TYR B 555 PHE 0.029 0.002 PHE C 456 TRP 0.036 0.003 TRP D 286 HIS 0.006 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00494 (18928) covalent geometry : angle 0.73797 (25772) hydrogen bonds : bond 0.04563 ( 984) hydrogen bonds : angle 4.09323 ( 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 431 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7964 (tttm) cc_final: 0.7449 (tmtt) REVERT: A 105 LEU cc_start: 0.9436 (tp) cc_final: 0.9038 (tp) REVERT: A 128 GLN cc_start: 0.8488 (tt0) cc_final: 0.7678 (tm-30) REVERT: A 130 LEU cc_start: 0.7722 (tp) cc_final: 0.7346 (mp) REVERT: A 198 THR cc_start: 0.6964 (t) cc_final: 0.6427 (t) REVERT: A 202 ILE cc_start: 0.8844 (mm) cc_final: 0.8446 (mm) REVERT: A 315 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 317 VAL cc_start: 0.8845 (t) cc_final: 0.8624 (p) REVERT: A 435 LEU cc_start: 0.8998 (tp) cc_final: 0.8709 (tt) REVERT: A 491 MET cc_start: 0.8744 (mmm) cc_final: 0.8414 (tpp) REVERT: A 570 MET cc_start: 0.7636 (tpp) cc_final: 0.7331 (tpp) REVERT: B 54 LYS cc_start: 0.7941 (tttm) cc_final: 0.7623 (tmtt) REVERT: B 146 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.6369 (mmt90) REVERT: B 435 LEU cc_start: 0.9034 (tp) cc_final: 0.8743 (tp) REVERT: B 466 MET cc_start: 0.8938 (mtm) cc_final: 0.8684 (mtt) REVERT: B 491 MET cc_start: 0.8805 (mmm) cc_final: 0.8477 (tpp) REVERT: B 501 ILE cc_start: 0.9112 (tt) cc_final: 0.8814 (tp) REVERT: B 596 GLN cc_start: 0.8180 (pt0) cc_final: 0.7877 (pt0) REVERT: C 128 GLN cc_start: 0.8037 (tt0) cc_final: 0.7796 (tp40) REVERT: C 315 GLU cc_start: 0.7808 (mm-30) cc_final: 0.6862 (mm-30) REVERT: C 317 VAL cc_start: 0.8979 (m) cc_final: 0.8713 (p) REVERT: D 146 ARG cc_start: 0.8117 (ttp-110) cc_final: 0.6623 (ttm110) REVERT: D 324 TYR cc_start: 0.8049 (m-80) cc_final: 0.7574 (m-10) REVERT: D 415 TYR cc_start: 0.7944 (t80) cc_final: 0.7383 (t80) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1111 time to fit residues: 78.7194 Evaluate side-chains 351 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 chunk 217 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.151344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130182 restraints weight = 37110.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133254 restraints weight = 20574.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135283 restraints weight = 13463.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136489 restraints weight = 9954.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137468 restraints weight = 8174.942| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6848 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= 0.118 Angle : 0.647 10.368 25772 Z= 0.312 Chirality : 0.043 0.316 2964 Planarity : 0.004 0.038 3252 Dihedral : 6.981 82.782 2688 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.52 (0.18), residues: 2368 helix: 0.97 (0.14), residues: 1412 sheet: -1.26 (0.64), residues: 56 loop : -2.53 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.022 0.001 TYR B 432 PHE 0.020 0.001 PHE D 512 TRP 0.016 0.001 TRP A 286 HIS 0.005 0.001 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00266 (18928) covalent geometry : angle 0.64667 (25772) hydrogen bonds : bond 0.03375 ( 984) hydrogen bonds : angle 3.79132 ( 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 444 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7996 (tttm) cc_final: 0.7493 (tmtt) REVERT: A 105 LEU cc_start: 0.9427 (tp) cc_final: 0.9108 (tp) REVERT: A 128 GLN cc_start: 0.8364 (tt0) cc_final: 0.7969 (tp40) REVERT: A 130 LEU cc_start: 0.7924 (tp) cc_final: 0.7636 (mt) REVERT: A 198 THR cc_start: 0.6925 (t) cc_final: 0.6380 (t) REVERT: A 202 ILE cc_start: 0.8766 (mm) cc_final: 0.8343 (mm) REVERT: A 245 LYS cc_start: 0.8403 (mttp) cc_final: 0.8115 (mtpt) REVERT: A 315 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 317 VAL cc_start: 0.8676 (t) cc_final: 0.8434 (p) REVERT: A 432 TYR cc_start: 0.8657 (t80) cc_final: 0.8391 (t80) REVERT: A 435 LEU cc_start: 0.8923 (tp) cc_final: 0.8668 (tt) REVERT: A 463 CYS cc_start: 0.8719 (m) cc_final: 0.8510 (m) REVERT: B 54 LYS cc_start: 0.8000 (tttm) cc_final: 0.7703 (tmtt) REVERT: B 98 LEU cc_start: 0.8786 (mt) cc_final: 0.8550 (mt) REVERT: B 146 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.6442 (mmt90) REVERT: B 294 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7694 (tt0) REVERT: B 321 TRP cc_start: 0.9041 (t-100) cc_final: 0.8042 (t-100) REVERT: B 432 TYR cc_start: 0.8802 (t80) cc_final: 0.8577 (t80) REVERT: B 435 LEU cc_start: 0.8982 (tp) cc_final: 0.8673 (tp) REVERT: B 466 MET cc_start: 0.8855 (mtm) cc_final: 0.8605 (mtt) REVERT: B 481 MET cc_start: 0.8204 (tpp) cc_final: 0.7686 (tpp) REVERT: B 491 MET cc_start: 0.8743 (mmm) cc_final: 0.8367 (tpp) REVERT: B 501 ILE cc_start: 0.9147 (tt) cc_final: 0.8914 (tp) REVERT: B 536 LEU cc_start: 0.8847 (mm) cc_final: 0.8638 (mm) REVERT: B 570 MET cc_start: 0.7715 (tpp) cc_final: 0.7239 (tpp) REVERT: B 603 MET cc_start: 0.7191 (tpt) cc_final: 0.6623 (tpp) REVERT: B 608 MET cc_start: 0.7946 (tpp) cc_final: 0.7744 (tpp) REVERT: C 99 MET cc_start: 0.7437 (mtm) cc_final: 0.7183 (mtp) REVERT: C 128 GLN cc_start: 0.7917 (tt0) cc_final: 0.7665 (tp40) REVERT: C 315 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7232 (mm-30) REVERT: C 317 VAL cc_start: 0.8882 (m) cc_final: 0.8581 (p) REVERT: C 318 SER cc_start: 0.8588 (m) cc_final: 0.8267 (t) REVERT: C 481 MET cc_start: 0.8494 (tpp) cc_final: 0.7949 (tpp) REVERT: C 501 ILE cc_start: 0.8803 (tt) cc_final: 0.8461 (tp) REVERT: C 592 LEU cc_start: 0.8838 (tp) cc_final: 0.8557 (tt) REVERT: D 42 GLU cc_start: 0.8751 (tp30) cc_final: 0.8475 (tp30) REVERT: D 146 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.6682 (mmt90) REVERT: D 324 TYR cc_start: 0.7879 (m-80) cc_final: 0.7521 (m-10) REVERT: D 415 TYR cc_start: 0.7959 (t80) cc_final: 0.7328 (t80) REVERT: D 489 ASP cc_start: 0.7484 (m-30) cc_final: 0.7029 (m-30) REVERT: D 569 LEU cc_start: 0.8459 (mp) cc_final: 0.8172 (mp) REVERT: D 588 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1121 time to fit residues: 81.7427 Evaluate side-chains 362 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 0.0020 chunk 215 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 146 optimal weight: 0.0050 chunk 7 optimal weight: 20.0000 overall best weight: 0.9806 ------------------------------------------------------------------------------- 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 165 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN D 238 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132549 restraints weight = 37514.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135706 restraints weight = 20532.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137763 restraints weight = 13259.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139003 restraints weight = 9721.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140004 restraints weight = 7913.953| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18928 Z= 0.113 Angle : 0.641 8.895 25772 Z= 0.309 Chirality : 0.042 0.317 2964 Planarity : 0.004 0.036 3252 Dihedral : 6.856 81.986 2688 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.38 (0.18), residues: 2368 helix: 1.08 (0.14), residues: 1408 sheet: -1.22 (0.62), residues: 56 loop : -2.43 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.017 0.001 TYR B 324 PHE 0.021 0.001 PHE C 456 TRP 0.021 0.002 TRP C 462 HIS 0.006 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00249 (18928) covalent geometry : angle 0.64149 (25772) hydrogen bonds : bond 0.03255 ( 984) hydrogen bonds : angle 3.69284 ( 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 449 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8014 (tttm) cc_final: 0.7505 (tmtt) REVERT: A 128 GLN cc_start: 0.8337 (tt0) cc_final: 0.7945 (tp40) REVERT: A 130 LEU cc_start: 0.7823 (tp) cc_final: 0.7555 (mt) REVERT: A 245 LYS cc_start: 0.8344 (mttp) cc_final: 0.8103 (mtpt) REVERT: A 315 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7081 (tp30) REVERT: A 317 VAL cc_start: 0.8613 (t) cc_final: 0.8339 (p) REVERT: A 435 LEU cc_start: 0.8870 (tp) cc_final: 0.8589 (tt) REVERT: A 481 MET cc_start: 0.8214 (tpp) cc_final: 0.7737 (tpp) REVERT: A 497 MET cc_start: 0.8567 (ttp) cc_final: 0.8193 (ttp) REVERT: A 501 ILE cc_start: 0.8859 (tt) cc_final: 0.8499 (tp) REVERT: A 570 MET cc_start: 0.7671 (tpp) cc_final: 0.6795 (mmm) REVERT: B 54 LYS cc_start: 0.8094 (tttm) cc_final: 0.7676 (tmtt) REVERT: B 146 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.6394 (mmt90) REVERT: B 245 LYS cc_start: 0.8455 (mttm) cc_final: 0.7979 (mtpp) REVERT: B 321 TRP cc_start: 0.8993 (t-100) cc_final: 0.7958 (t-100) REVERT: B 403 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6752 (tp30) REVERT: B 415 TYR cc_start: 0.7560 (t80) cc_final: 0.7180 (t80) REVERT: B 466 MET cc_start: 0.8671 (mtm) cc_final: 0.8409 (mtt) REVERT: B 481 MET cc_start: 0.8208 (tpp) cc_final: 0.7629 (tpp) REVERT: B 491 MET cc_start: 0.8691 (mmm) cc_final: 0.8154 (tpp) REVERT: B 501 ILE cc_start: 0.9132 (tt) cc_final: 0.8907 (tp) REVERT: B 603 MET cc_start: 0.7026 (tpt) cc_final: 0.6508 (tpp) REVERT: C 99 MET cc_start: 0.7463 (mtm) cc_final: 0.7234 (mtp) REVERT: C 128 GLN cc_start: 0.7880 (tt0) cc_final: 0.7608 (tp40) REVERT: C 260 MET cc_start: 0.8995 (mmt) cc_final: 0.8703 (tpp) REVERT: C 315 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6773 (mm-30) REVERT: C 317 VAL cc_start: 0.8831 (m) cc_final: 0.8518 (p) REVERT: C 318 SER cc_start: 0.8583 (m) cc_final: 0.8225 (t) REVERT: C 481 MET cc_start: 0.8381 (tpp) cc_final: 0.8029 (tpp) REVERT: C 501 ILE cc_start: 0.8764 (tt) cc_final: 0.8389 (tp) REVERT: C 511 THR cc_start: 0.8874 (m) cc_final: 0.8595 (p) REVERT: C 554 MET cc_start: 0.8857 (tpp) cc_final: 0.8591 (tpp) REVERT: C 592 LEU cc_start: 0.8812 (tp) cc_final: 0.8526 (tt) REVERT: D 42 GLU cc_start: 0.8684 (tp30) cc_final: 0.8403 (tp30) REVERT: D 146 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.6663 (mmt90) REVERT: D 324 TYR cc_start: 0.7814 (m-80) cc_final: 0.7483 (m-80) REVERT: D 415 TYR cc_start: 0.7968 (t80) cc_final: 0.7732 (t80) REVERT: D 588 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7629 (mm-30) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.1099 time to fit residues: 81.3298 Evaluate side-chains 375 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 0.8980 chunk 183 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 0.0470 chunk 133 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135427 restraints weight = 35532.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138665 restraints weight = 19514.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140798 restraints weight = 12541.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142207 restraints weight = 9121.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142907 restraints weight = 7288.529| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18928 Z= 0.109 Angle : 0.633 8.741 25772 Z= 0.303 Chirality : 0.041 0.314 2964 Planarity : 0.004 0.041 3252 Dihedral : 6.875 83.102 2688 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.26 (0.18), residues: 2368 helix: 1.17 (0.14), residues: 1412 sheet: -1.27 (0.62), residues: 56 loop : -2.38 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.015 0.001 TYR B 324 PHE 0.023 0.001 PHE A 256 TRP 0.019 0.001 TRP B 629 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00238 (18928) covalent geometry : angle 0.63267 (25772) hydrogen bonds : bond 0.03021 ( 984) hydrogen bonds : angle 3.66194 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.86 seconds wall clock time: 52 minutes 21.15 seconds (3141.15 seconds total)