Starting phenix.real_space_refine on Sun Aug 24 13:21:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf2_41217/08_2025/8tf2_41217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf2_41217/08_2025/8tf2_41217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tf2_41217/08_2025/8tf2_41217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf2_41217/08_2025/8tf2_41217.map" model { file = "/net/cci-nas-00/data/ceres_data/8tf2_41217/08_2025/8tf2_41217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf2_41217/08_2025/8tf2_41217.cif" } resolution = 2.57 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= 0.003 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 C 13000 2.51 5 N 3260 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "D" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4822 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Unusual residues: {'CPL': 6, 'ERG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-1': 5, 'CPL:plan-2': 5, 'CPL:plan-3': 6, 'CPL:plan-4': 6} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {'CPL': 3, 'ERG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CPL:plan-3': 3, 'CPL:plan-4': 3, 'CPL:plan-1': 2, 'CPL:plan-2': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {'CPL': 5, 'ERG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-3': 5, 'CPL:plan-4': 5, 'CPL:plan-1': 4, 'CPL:plan-2': 4} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CPL': 2, 'ERG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 2, 'CPL:plan-4': 2, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.29, per 1000 atoms: 0.22 Number of scatterers: 19856 At special positions: 0 Unit cell: (138.61, 138.61, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 4 15.00 O 3456 8.00 N 3260 7.00 C 13000 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: 1.80 Conformation dependent library (CDL) restraints added in 648.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 72.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.620A pdb=" N ARG A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.575A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.516A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY A 624 " --> pdb=" O TYR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'B' and resid 29 through 46 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.620A pdb=" N ARG B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.575A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.516A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY B 624 " --> pdb=" O TYR B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.621A pdb=" N ARG C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.576A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.516A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY C 624 " --> pdb=" O TYR C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'D' and resid 29 through 46 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.822A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.714A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.619A pdb=" N ARG D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.575A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.032A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.983A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.516A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.631A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 488 through 513 removed outlier: 3.503A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.855A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 608 removed outlier: 3.740A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.677A pdb=" N GLY D 624 " --> pdb=" O TYR D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.616A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.616A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.616A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.617A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1181 hydrogen bonds defined for protein. 3363 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: 3.36 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3691 1.32 - 1.45: 4765 1.45 - 1.57: 11608 1.57 - 1.70: 16 1.70 - 1.82: 224 Bond restraints: 20304 Sorted by residual: bond pdb=" N ARG D 263 " pdb=" CA ARG D 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG B 263 " pdb=" CA ARG B 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG C 263 " pdb=" CA ARG C 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" N ARG A 263 " pdb=" CA ARG A 263 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" C ARG D 326 " pdb=" O ARG D 326 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.08e+01 ... (remaining 20299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21177 2.07 - 4.15: 5835 4.15 - 6.22: 474 6.22 - 8.29: 30 8.29 - 10.36: 4 Bond angle restraints: 27520 Sorted by residual: angle pdb=" CB HIS B 84 " pdb=" CG HIS B 84 " pdb=" CD2 HIS B 84 " ideal model delta sigma weight residual 131.20 124.46 6.74 1.30e+00 5.92e-01 2.69e+01 angle pdb=" CB HIS C 84 " pdb=" CG HIS C 84 " pdb=" CD2 HIS C 84 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS A 84 " pdb=" CG HIS A 84 " pdb=" CD2 HIS A 84 " ideal model delta sigma weight residual 131.20 124.49 6.71 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS D 84 " pdb=" CG HIS D 84 " pdb=" CD2 HIS D 84 " ideal model delta sigma weight residual 131.20 124.56 6.64 1.30e+00 5.92e-01 2.61e+01 angle pdb=" CA ASP C 57 " pdb=" CB ASP C 57 " pdb=" CG ASP C 57 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 27515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 12282 35.18 - 70.36: 217 70.36 - 105.54: 25 105.54 - 140.71: 4 140.71 - 175.89: 12 Dihedral angle restraints: 12540 sinusoidal: 5512 harmonic: 7028 Sorted by residual: dihedral pdb=" CA CYS D 112 " pdb=" C CYS D 112 " pdb=" N GLU D 113 " pdb=" CA GLU D 113 " ideal model delta harmonic sigma weight residual -180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS C 112 " pdb=" C CYS C 112 " pdb=" N GLU C 113 " pdb=" CA GLU C 113 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA CYS B 112 " pdb=" C CYS B 112 " pdb=" N GLU B 113 " pdb=" CA GLU B 113 " ideal model delta harmonic sigma weight residual 180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 12537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1639 0.058 - 0.115: 985 0.115 - 0.173: 355 0.173 - 0.230: 101 0.230 - 0.287: 44 Chirality restraints: 3124 Sorted by residual: chirality pdb=" CA THR B 567 " pdb=" N THR B 567 " pdb=" C THR B 567 " pdb=" CB THR B 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA THR C 567 " pdb=" N THR C 567 " pdb=" C THR C 567 " pdb=" CB THR C 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA THR A 567 " pdb=" N THR A 567 " pdb=" C THR A 567 " pdb=" CB THR A 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3121 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 593 " 0.140 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" CG TRP C 593 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 593 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 593 " -0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP C 593 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 593 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP C 593 " -0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 593 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 593 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 593 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 593 " -0.140 2.00e-02 2.50e+03 6.56e-02 1.08e+02 pdb=" CG TRP D 593 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 593 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 593 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP D 593 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 593 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP D 593 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 593 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 593 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 593 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 593 " -0.140 2.00e-02 2.50e+03 6.55e-02 1.07e+02 pdb=" CG TRP A 593 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 593 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 593 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP A 593 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 593 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 593 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 593 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 593 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 593 " -0.065 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 8464 2.97 - 3.45: 21137 3.45 - 3.93: 35760 3.93 - 4.42: 39821 4.42 - 4.90: 65999 Nonbonded interactions: 171181 Sorted by model distance: nonbonded pdb=" OD1 ASP C 489 " pdb=" NH1 ARG C 492 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP B 489 " pdb=" NH1 ARG B 492 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP A 489 " pdb=" NH1 ARG A 492 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP D 489 " pdb=" NH1 ARG D 492 " model vdw 2.484 3.120 nonbonded pdb=" O THR D 311 " pdb=" OE1 GLU D 315 " model vdw 2.513 3.040 ... (remaining 171176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'B' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'C' and (resid 28 through 637 or resid 802 or resid 804)) selection = (chain 'D' and (resid 28 through 637 or resid 802 or resid 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.380 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.059 20304 Z= 0.726 Angle : 1.754 10.363 27520 Z= 1.197 Chirality : 0.086 0.287 3124 Planarity : 0.013 0.066 3404 Dihedral : 15.410 175.892 7996 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.38 % Allowed : 0.82 % Favored : 98.80 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: 0.29 (0.16), residues: 2384 helix: -0.12 (0.12), residues: 1480 sheet: 1.03 (0.54), residues: 76 loop : 1.13 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 492 TYR 0.110 0.024 TYR C 336 PHE 0.066 0.015 PHE B 256 TRP 0.140 0.021 TRP C 593 HIS 0.010 0.004 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.01188 (20304) covalent geometry : angle 1.75443 (27520) hydrogen bonds : bond 0.16620 ( 1181) hydrogen bonds : angle 6.12139 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 419 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6434 (mm-30) REVERT: A 74 GLN cc_start: 0.7343 (mt0) cc_final: 0.7083 (mt0) REVERT: A 99 MET cc_start: 0.7200 (mtm) cc_final: 0.6779 (mtm) REVERT: A 104 GLU cc_start: 0.7429 (pm20) cc_final: 0.6315 (tm-30) REVERT: A 107 LYS cc_start: 0.7095 (mttt) cc_final: 0.6510 (mttp) REVERT: A 155 SER cc_start: 0.7753 (m) cc_final: 0.7490 (p) REVERT: A 176 GLU cc_start: 0.6993 (tt0) cc_final: 0.6463 (mt-10) REVERT: A 194 SER cc_start: 0.8516 (m) cc_final: 0.8209 (p) REVERT: A 257 GLN cc_start: 0.7456 (pt0) cc_final: 0.6604 (tp-100) REVERT: A 262 LYS cc_start: 0.8328 (mttt) cc_final: 0.7990 (mptt) REVERT: A 300 LYS cc_start: 0.8437 (mttt) cc_final: 0.8163 (mmtt) REVERT: A 302 ARG cc_start: 0.7283 (ptm160) cc_final: 0.7057 (mtp-110) REVERT: A 322 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7390 (mppt) REVERT: A 473 GLN cc_start: 0.8664 (tt0) cc_final: 0.8238 (tp40) REVERT: A 491 MET cc_start: 0.8466 (mmm) cc_final: 0.7920 (tpp) REVERT: A 570 MET cc_start: 0.8466 (mtp) cc_final: 0.8241 (mmm) REVERT: A 605 GLU cc_start: 0.8474 (tt0) cc_final: 0.8145 (tt0) REVERT: A 621 TYR cc_start: 0.7848 (t80) cc_final: 0.7640 (t80) REVERT: B 55 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6413 (mm-30) REVERT: B 74 GLN cc_start: 0.7365 (mt0) cc_final: 0.7104 (mt0) REVERT: B 99 MET cc_start: 0.7206 (mtm) cc_final: 0.6793 (mtm) REVERT: B 104 GLU cc_start: 0.7432 (pm20) cc_final: 0.6308 (tm-30) REVERT: B 107 LYS cc_start: 0.7090 (mttt) cc_final: 0.6519 (mttp) REVERT: B 155 SER cc_start: 0.7751 (m) cc_final: 0.7491 (p) REVERT: B 176 GLU cc_start: 0.6983 (tt0) cc_final: 0.6430 (mt-10) REVERT: B 194 SER cc_start: 0.8530 (m) cc_final: 0.8224 (p) REVERT: B 257 GLN cc_start: 0.7447 (pt0) cc_final: 0.6574 (tp-100) REVERT: B 262 LYS cc_start: 0.8338 (mttt) cc_final: 0.8030 (mptt) REVERT: B 300 LYS cc_start: 0.8437 (mttt) cc_final: 0.8163 (mmtt) REVERT: B 302 ARG cc_start: 0.7270 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: B 322 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7450 (mppt) REVERT: B 473 GLN cc_start: 0.8661 (tt0) cc_final: 0.8226 (tp40) REVERT: B 491 MET cc_start: 0.8463 (mmm) cc_final: 0.7920 (tpp) REVERT: B 570 MET cc_start: 0.8467 (mtp) cc_final: 0.8247 (mmm) REVERT: B 605 GLU cc_start: 0.8465 (tt0) cc_final: 0.8132 (tt0) REVERT: C 55 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6413 (mm-30) REVERT: C 74 GLN cc_start: 0.7365 (mt0) cc_final: 0.7103 (mt0) REVERT: C 99 MET cc_start: 0.7203 (mtm) cc_final: 0.6791 (mtm) REVERT: C 104 GLU cc_start: 0.7431 (pm20) cc_final: 0.6306 (tm-30) REVERT: C 107 LYS cc_start: 0.7098 (mttt) cc_final: 0.6520 (mttp) REVERT: C 155 SER cc_start: 0.7764 (m) cc_final: 0.7508 (p) REVERT: C 176 GLU cc_start: 0.6989 (tt0) cc_final: 0.6431 (mt-10) REVERT: C 194 SER cc_start: 0.8525 (m) cc_final: 0.8206 (p) REVERT: C 257 GLN cc_start: 0.7449 (pt0) cc_final: 0.6572 (tp-100) REVERT: C 262 LYS cc_start: 0.8335 (mttt) cc_final: 0.8026 (mptt) REVERT: C 300 LYS cc_start: 0.8436 (mttt) cc_final: 0.8160 (mmtt) REVERT: C 302 ARG cc_start: 0.7271 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: C 322 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7446 (mppt) REVERT: C 473 GLN cc_start: 0.8670 (tt0) cc_final: 0.8239 (tp40) REVERT: C 491 MET cc_start: 0.8462 (mmm) cc_final: 0.7917 (tpp) REVERT: C 570 MET cc_start: 0.8468 (mtp) cc_final: 0.8240 (mmm) REVERT: D 43 ARG cc_start: 0.7209 (mmm-85) cc_final: 0.6972 (mmm160) REVERT: D 55 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6376 (mm-30) REVERT: D 74 GLN cc_start: 0.7409 (mt0) cc_final: 0.7157 (mt0) REVERT: D 99 MET cc_start: 0.7209 (mtm) cc_final: 0.6802 (mtm) REVERT: D 104 GLU cc_start: 0.7442 (pm20) cc_final: 0.6317 (tm-30) REVERT: D 107 LYS cc_start: 0.7097 (mttt) cc_final: 0.6532 (mttp) REVERT: D 155 SER cc_start: 0.7766 (m) cc_final: 0.7515 (p) REVERT: D 176 GLU cc_start: 0.6991 (tt0) cc_final: 0.6440 (mt-10) REVERT: D 194 SER cc_start: 0.8520 (m) cc_final: 0.8191 (p) REVERT: D 257 GLN cc_start: 0.7425 (pt0) cc_final: 0.6596 (tp-100) REVERT: D 262 LYS cc_start: 0.8332 (mttt) cc_final: 0.7994 (mptt) REVERT: D 300 LYS cc_start: 0.8436 (mttt) cc_final: 0.8161 (mmtt) REVERT: D 302 ARG cc_start: 0.7275 (ptm160) cc_final: 0.7053 (mtp-110) REVERT: D 322 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7456 (mppt) REVERT: D 473 GLN cc_start: 0.8664 (tt0) cc_final: 0.8231 (tp40) REVERT: D 491 MET cc_start: 0.8471 (mmm) cc_final: 0.7927 (tpp) REVERT: D 570 MET cc_start: 0.8460 (mtp) cc_final: 0.8250 (mmm) REVERT: D 621 TYR cc_start: 0.7842 (t80) cc_final: 0.7642 (t80) outliers start: 8 outliers final: 10 residues processed: 427 average time/residue: 0.7860 time to fit residues: 369.4339 Evaluate side-chains 312 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 302 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 627 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 217 ASN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 483 GLN A 518 ASN A 596 GLN B 51 GLN B 217 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 483 GLN B 596 GLN C 51 GLN C 217 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 483 GLN C 596 GLN D 51 GLN D 217 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN D 483 GLN D 596 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.098508 restraints weight = 22144.826| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.58 r_work: 0.2967 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20304 Z= 0.132 Angle : 0.528 5.688 27520 Z= 0.285 Chirality : 0.039 0.151 3124 Planarity : 0.004 0.042 3404 Dihedral : 13.197 176.518 3452 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.26 % Allowed : 6.20 % Favored : 91.54 % 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 aren not related in a simple way. whole: 1.92 (0.17), residues: 2384 helix: 1.51 (0.13), residues: 1516 sheet: 0.59 (0.49), residues: 80 loop : 1.15 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.019 0.002 TYR D 555 PHE 0.016 0.002 PHE C 456 TRP 0.025 0.002 TRP A 593 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00277 (20304) covalent geometry : angle 0.52773 (27520) hydrogen bonds : bond 0.04933 ( 1181) hydrogen bonds : angle 4.17360 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7732 (tt0) cc_final: 0.7429 (mt0) REVERT: A 99 MET cc_start: 0.8016 (mtm) cc_final: 0.7638 (mtm) REVERT: A 100 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 104 GLU cc_start: 0.7782 (pm20) cc_final: 0.6560 (tm-30) REVERT: A 107 LYS cc_start: 0.7670 (mttt) cc_final: 0.7294 (mttp) REVERT: A 176 GLU cc_start: 0.7671 (tt0) cc_final: 0.7152 (mt-10) REVERT: A 190 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6841 (mtm180) REVERT: A 194 SER cc_start: 0.8799 (m) cc_final: 0.8484 (p) REVERT: A 257 GLN cc_start: 0.8011 (pt0) cc_final: 0.7560 (tp-100) REVERT: A 302 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7337 (tmt-80) REVERT: A 381 GLN cc_start: 0.7766 (mp10) cc_final: 0.6122 (mm-40) REVERT: A 408 PHE cc_start: 0.7703 (m-10) cc_final: 0.7469 (m-10) REVERT: A 491 MET cc_start: 0.8751 (mmm) cc_final: 0.8428 (tpp) REVERT: B 40 GLN cc_start: 0.7724 (tt0) cc_final: 0.7421 (mt0) REVERT: B 99 MET cc_start: 0.8026 (mtm) cc_final: 0.7639 (mtm) REVERT: B 100 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 104 GLU cc_start: 0.7788 (pm20) cc_final: 0.6527 (tm-30) REVERT: B 107 LYS cc_start: 0.7659 (mttt) cc_final: 0.7289 (mttp) REVERT: B 176 GLU cc_start: 0.7664 (tt0) cc_final: 0.7143 (mt-10) REVERT: B 190 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6833 (mtm180) REVERT: B 194 SER cc_start: 0.8812 (m) cc_final: 0.8499 (p) REVERT: B 257 GLN cc_start: 0.8022 (pt0) cc_final: 0.7576 (tp-100) REVERT: B 302 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7363 (tmt-80) REVERT: B 381 GLN cc_start: 0.7785 (mp10) cc_final: 0.6139 (mm-40) REVERT: B 408 PHE cc_start: 0.7669 (m-10) cc_final: 0.7453 (m-10) REVERT: B 491 MET cc_start: 0.8756 (mmm) cc_final: 0.8434 (tpp) REVERT: C 40 GLN cc_start: 0.7730 (tt0) cc_final: 0.7429 (mt0) REVERT: C 99 MET cc_start: 0.8022 (mtm) cc_final: 0.7635 (mtm) REVERT: C 100 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7285 (mt-10) REVERT: C 104 GLU cc_start: 0.7788 (pm20) cc_final: 0.6530 (tm-30) REVERT: C 107 LYS cc_start: 0.7662 (mttt) cc_final: 0.7296 (mttp) REVERT: C 176 GLU cc_start: 0.7674 (tt0) cc_final: 0.7152 (mt-10) REVERT: C 190 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6836 (mtm180) REVERT: C 194 SER cc_start: 0.8810 (m) cc_final: 0.8585 (p) REVERT: C 257 GLN cc_start: 0.8019 (pt0) cc_final: 0.7569 (tp-100) REVERT: C 302 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7330 (tmt-80) REVERT: C 381 GLN cc_start: 0.7765 (mp10) cc_final: 0.6122 (mm-40) REVERT: C 408 PHE cc_start: 0.7667 (m-10) cc_final: 0.7442 (m-10) REVERT: C 414 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7617 (tpp80) REVERT: C 491 MET cc_start: 0.8758 (mmm) cc_final: 0.8435 (tpp) REVERT: D 40 GLN cc_start: 0.7720 (tt0) cc_final: 0.7421 (mt0) REVERT: D 99 MET cc_start: 0.8048 (mtm) cc_final: 0.7795 (mtm) REVERT: D 100 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7273 (mt-10) REVERT: D 104 GLU cc_start: 0.7793 (pm20) cc_final: 0.6551 (tm-30) REVERT: D 107 LYS cc_start: 0.7662 (mttt) cc_final: 0.7351 (mttp) REVERT: D 176 GLU cc_start: 0.7662 (tt0) cc_final: 0.7120 (mt-10) REVERT: D 194 SER cc_start: 0.8820 (m) cc_final: 0.8577 (p) REVERT: D 257 GLN cc_start: 0.8011 (pt0) cc_final: 0.7564 (tp-100) REVERT: D 302 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7348 (tmt-80) REVERT: D 381 GLN cc_start: 0.7783 (mp10) cc_final: 0.6137 (mm-40) REVERT: D 408 PHE cc_start: 0.7670 (m-10) cc_final: 0.7445 (m-10) REVERT: D 491 MET cc_start: 0.8755 (mmm) cc_final: 0.8430 (tpp) outliers start: 47 outliers final: 12 residues processed: 338 average time/residue: 0.6749 time to fit residues: 251.7779 Evaluate side-chains 290 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 275 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN B 74 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN C 74 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099794 restraints weight = 22147.255| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.57 r_work: 0.2987 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20304 Z= 0.110 Angle : 0.490 8.913 27520 Z= 0.254 Chirality : 0.038 0.149 3124 Planarity : 0.004 0.042 3404 Dihedral : 12.225 171.528 3444 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.88 % Allowed : 8.99 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.17), residues: 2384 helix: 1.91 (0.13), residues: 1500 sheet: 1.18 (0.50), residues: 68 loop : 0.94 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 180 TYR 0.015 0.001 TYR A 555 PHE 0.009 0.001 PHE C 152 TRP 0.020 0.001 TRP D 593 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00231 (20304) covalent geometry : angle 0.48980 (27520) hydrogen bonds : bond 0.04200 ( 1181) hydrogen bonds : angle 3.99625 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 40 GLN cc_start: 0.7648 (tt0) cc_final: 0.7360 (mt0) REVERT: A 64 LEU cc_start: 0.8201 (mt) cc_final: 0.7939 (mt) REVERT: A 99 MET cc_start: 0.7982 (mtm) cc_final: 0.7634 (mtm) REVERT: A 100 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 104 GLU cc_start: 0.7800 (pm20) cc_final: 0.6570 (tm-30) REVERT: A 107 LYS cc_start: 0.7666 (mttt) cc_final: 0.7318 (mttp) REVERT: A 176 GLU cc_start: 0.7758 (tt0) cc_final: 0.7277 (mt-10) REVERT: A 190 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6888 (mtm180) REVERT: A 194 SER cc_start: 0.8688 (m) cc_final: 0.8427 (p) REVERT: A 257 GLN cc_start: 0.7987 (pt0) cc_final: 0.7565 (tp-100) REVERT: A 302 ARG cc_start: 0.7762 (ptm160) cc_final: 0.7391 (tmt-80) REVERT: A 381 GLN cc_start: 0.7579 (mp10) cc_final: 0.5985 (mm-40) REVERT: B 30 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7286 (mp0) REVERT: B 40 GLN cc_start: 0.7651 (tt0) cc_final: 0.7385 (mt0) REVERT: B 64 LEU cc_start: 0.8197 (mt) cc_final: 0.7936 (mt) REVERT: B 99 MET cc_start: 0.8017 (mtm) cc_final: 0.7665 (mtm) REVERT: B 100 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 104 GLU cc_start: 0.7825 (pm20) cc_final: 0.6541 (tm-30) REVERT: B 107 LYS cc_start: 0.7663 (mttt) cc_final: 0.7319 (mttp) REVERT: B 176 GLU cc_start: 0.7768 (tt0) cc_final: 0.7273 (mt-10) REVERT: B 190 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6889 (mtm180) REVERT: B 194 SER cc_start: 0.8691 (m) cc_final: 0.8428 (p) REVERT: B 257 GLN cc_start: 0.7997 (pt0) cc_final: 0.7575 (tp-100) REVERT: B 302 ARG cc_start: 0.7754 (ptm160) cc_final: 0.7390 (tmt-80) REVERT: B 381 GLN cc_start: 0.7578 (mp10) cc_final: 0.5967 (mm-40) REVERT: C 30 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7283 (mp0) REVERT: C 40 GLN cc_start: 0.7674 (tt0) cc_final: 0.7409 (mt0) REVERT: C 64 LEU cc_start: 0.8195 (mt) cc_final: 0.7935 (mt) REVERT: C 99 MET cc_start: 0.8017 (mtm) cc_final: 0.7735 (mtm) REVERT: C 100 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7261 (mt-10) REVERT: C 104 GLU cc_start: 0.7822 (pm20) cc_final: 0.6541 (tm-30) REVERT: C 107 LYS cc_start: 0.7664 (mttt) cc_final: 0.7322 (mttp) REVERT: C 176 GLU cc_start: 0.7777 (tt0) cc_final: 0.7277 (mt-10) REVERT: C 190 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6822 (mtm180) REVERT: C 194 SER cc_start: 0.8740 (m) cc_final: 0.8511 (p) REVERT: C 257 GLN cc_start: 0.7992 (pt0) cc_final: 0.7568 (tp-100) REVERT: C 302 ARG cc_start: 0.7755 (ptm160) cc_final: 0.7383 (tmt-80) REVERT: C 381 GLN cc_start: 0.7575 (mp10) cc_final: 0.5979 (mm-40) REVERT: D 30 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7275 (mp0) REVERT: D 40 GLN cc_start: 0.7658 (tt0) cc_final: 0.7387 (mt0) REVERT: D 64 LEU cc_start: 0.8200 (mt) cc_final: 0.7981 (mt) REVERT: D 99 MET cc_start: 0.8003 (mtm) cc_final: 0.7768 (mtm) REVERT: D 100 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7249 (mt-10) REVERT: D 104 GLU cc_start: 0.7812 (pm20) cc_final: 0.6548 (tm-30) REVERT: D 107 LYS cc_start: 0.7671 (mttt) cc_final: 0.7333 (mttp) REVERT: D 176 GLU cc_start: 0.7810 (tt0) cc_final: 0.7285 (mt-10) REVERT: D 190 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.6875 (mtm180) REVERT: D 194 SER cc_start: 0.8765 (m) cc_final: 0.8534 (p) REVERT: D 257 GLN cc_start: 0.7984 (pt0) cc_final: 0.7570 (tp-100) REVERT: D 302 ARG cc_start: 0.7756 (ptm160) cc_final: 0.7386 (tmt-80) REVERT: D 381 GLN cc_start: 0.7555 (mp10) cc_final: 0.5975 (mm-40) outliers start: 39 outliers final: 14 residues processed: 302 average time/residue: 0.7249 time to fit residues: 242.1418 Evaluate side-chains 288 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 269 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 26 optimal weight: 0.0040 chunk 19 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.096739 restraints weight = 22027.296| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.47 r_work: 0.2945 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20304 Z= 0.156 Angle : 0.525 8.115 27520 Z= 0.273 Chirality : 0.040 0.159 3124 Planarity : 0.004 0.042 3404 Dihedral : 12.216 168.488 3444 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.32 % Allowed : 8.75 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.17), residues: 2384 helix: 1.76 (0.13), residues: 1500 sheet: 0.66 (0.53), residues: 68 loop : 0.90 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 180 TYR 0.016 0.002 TYR A 89 PHE 0.012 0.002 PHE D 472 TRP 0.017 0.002 TRP A 593 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00369 (20304) covalent geometry : angle 0.52450 (27520) hydrogen bonds : bond 0.04773 ( 1181) hydrogen bonds : angle 4.05273 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: A 40 GLN cc_start: 0.7492 (tt0) cc_final: 0.7153 (mt0) REVERT: A 64 LEU cc_start: 0.8060 (mt) cc_final: 0.7820 (mt) REVERT: A 93 GLU cc_start: 0.7884 (mp0) cc_final: 0.7617 (mp0) REVERT: A 99 MET cc_start: 0.7938 (mtm) cc_final: 0.7611 (mtm) REVERT: A 100 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 104 GLU cc_start: 0.7755 (pm20) cc_final: 0.6463 (tm-30) REVERT: A 107 LYS cc_start: 0.7629 (mttt) cc_final: 0.7249 (mttp) REVERT: A 176 GLU cc_start: 0.7579 (tt0) cc_final: 0.7072 (mt-10) REVERT: A 190 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6788 (mtm180) REVERT: A 194 SER cc_start: 0.8665 (m) cc_final: 0.8339 (p) REVERT: A 257 GLN cc_start: 0.7796 (pt0) cc_final: 0.7265 (tp-100) REVERT: A 262 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7930 (mptt) REVERT: A 302 ARG cc_start: 0.7736 (ptm160) cc_final: 0.7209 (tmt-80) REVERT: A 381 GLN cc_start: 0.7474 (mp10) cc_final: 0.5942 (mm-40) REVERT: A 414 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7214 (tpp80) REVERT: B 30 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 40 GLN cc_start: 0.7466 (tt0) cc_final: 0.7142 (mt0) REVERT: B 93 GLU cc_start: 0.7880 (mp0) cc_final: 0.7640 (mp0) REVERT: B 99 MET cc_start: 0.7907 (mtm) cc_final: 0.7574 (mtm) REVERT: B 100 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 104 GLU cc_start: 0.7759 (pm20) cc_final: 0.6428 (tm-30) REVERT: B 107 LYS cc_start: 0.7640 (mttt) cc_final: 0.7268 (mttp) REVERT: B 176 GLU cc_start: 0.7568 (tt0) cc_final: 0.7052 (mt-10) REVERT: B 190 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6789 (mtm180) REVERT: B 194 SER cc_start: 0.8660 (m) cc_final: 0.8330 (p) REVERT: B 257 GLN cc_start: 0.7801 (pt0) cc_final: 0.7275 (tp-100) REVERT: B 262 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7942 (mptt) REVERT: B 302 ARG cc_start: 0.7719 (ptm160) cc_final: 0.7203 (tmt-80) REVERT: B 381 GLN cc_start: 0.7454 (mp10) cc_final: 0.5963 (mm-40) REVERT: B 414 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7230 (tpp80) REVERT: C 30 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 40 GLN cc_start: 0.7467 (tt0) cc_final: 0.7141 (mt0) REVERT: C 99 MET cc_start: 0.7934 (mtm) cc_final: 0.7603 (mtm) REVERT: C 100 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7060 (mt-10) REVERT: C 104 GLU cc_start: 0.7760 (pm20) cc_final: 0.6430 (tm-30) REVERT: C 107 LYS cc_start: 0.7661 (mttt) cc_final: 0.7290 (mttp) REVERT: C 176 GLU cc_start: 0.7575 (tt0) cc_final: 0.7065 (mt-10) REVERT: C 190 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.6786 (mtm180) REVERT: C 257 GLN cc_start: 0.7798 (pt0) cc_final: 0.7267 (tp-100) REVERT: C 262 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7958 (mptt) REVERT: C 302 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7209 (tmt-80) REVERT: C 381 GLN cc_start: 0.7492 (mp10) cc_final: 0.5940 (mm-40) REVERT: C 414 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7123 (tpp80) REVERT: D 30 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: D 40 GLN cc_start: 0.7478 (tt0) cc_final: 0.7149 (mt0) REVERT: D 99 MET cc_start: 0.7883 (mtm) cc_final: 0.7652 (mtm) REVERT: D 100 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7047 (mt-10) REVERT: D 104 GLU cc_start: 0.7771 (pm20) cc_final: 0.6440 (tm-30) REVERT: D 107 LYS cc_start: 0.7655 (mttt) cc_final: 0.7286 (mttp) REVERT: D 176 GLU cc_start: 0.7599 (tt0) cc_final: 0.7092 (mt-10) REVERT: D 190 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6789 (mtm180) REVERT: D 194 SER cc_start: 0.8651 (m) cc_final: 0.8360 (p) REVERT: D 257 GLN cc_start: 0.7800 (pt0) cc_final: 0.7274 (tp-100) REVERT: D 262 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7947 (mptt) REVERT: D 302 ARG cc_start: 0.7727 (ptm160) cc_final: 0.7201 (tmt-80) REVERT: D 381 GLN cc_start: 0.7466 (mp10) cc_final: 0.5944 (mm-40) REVERT: D 414 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7228 (tpp80) REVERT: D 497 MET cc_start: 0.8677 (ttt) cc_final: 0.8449 (ttt) outliers start: 69 outliers final: 25 residues processed: 310 average time/residue: 0.6897 time to fit residues: 236.1696 Evaluate side-chains 313 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 418 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098537 restraints weight = 22728.577| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.44 r_work: 0.2976 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20304 Z= 0.129 Angle : 0.496 7.918 27520 Z= 0.258 Chirality : 0.038 0.154 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.998 166.144 3444 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.64 % Allowed : 10.10 % Favored : 87.26 % 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 aren not related in a simple way. whole: 1.96 (0.17), residues: 2384 helix: 1.77 (0.12), residues: 1508 sheet: -1.51 (0.43), residues: 108 loop : 0.99 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 180 TYR 0.014 0.001 TYR C 555 PHE 0.009 0.001 PHE D 537 TRP 0.018 0.001 TRP D 593 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00295 (20304) covalent geometry : angle 0.49608 (27520) hydrogen bonds : bond 0.04404 ( 1181) hydrogen bonds : angle 4.02702 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: A 40 GLN cc_start: 0.7673 (tt0) cc_final: 0.7432 (mt0) REVERT: A 51 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7813 (mm-40) REVERT: A 93 GLU cc_start: 0.8013 (mp0) cc_final: 0.7771 (mp0) REVERT: A 99 MET cc_start: 0.8020 (mtm) cc_final: 0.7686 (mtm) REVERT: A 100 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 104 GLU cc_start: 0.7753 (pm20) cc_final: 0.6499 (tm-30) REVERT: A 107 LYS cc_start: 0.7754 (mttt) cc_final: 0.7389 (mttp) REVERT: A 176 GLU cc_start: 0.7716 (tt0) cc_final: 0.7280 (mt-10) REVERT: A 190 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.6965 (mtm180) REVERT: A 194 SER cc_start: 0.8695 (m) cc_final: 0.8397 (p) REVERT: A 257 GLN cc_start: 0.7960 (pt0) cc_final: 0.7571 (tp-100) REVERT: A 262 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8106 (mptt) REVERT: A 302 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7499 (tmt-80) REVERT: A 381 GLN cc_start: 0.7646 (mp10) cc_final: 0.6171 (mm-40) REVERT: A 414 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7274 (tpp80) REVERT: B 30 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 40 GLN cc_start: 0.7668 (tt0) cc_final: 0.7413 (mt0) REVERT: B 51 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7814 (mm-40) REVERT: B 93 GLU cc_start: 0.8011 (mp0) cc_final: 0.7774 (mp0) REVERT: B 99 MET cc_start: 0.8083 (mtm) cc_final: 0.7750 (mtm) REVERT: B 100 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7113 (mt-10) REVERT: B 104 GLU cc_start: 0.7763 (pm20) cc_final: 0.6489 (tm-30) REVERT: B 107 LYS cc_start: 0.7749 (mttt) cc_final: 0.7386 (mttp) REVERT: B 176 GLU cc_start: 0.7703 (tt0) cc_final: 0.7274 (mt-10) REVERT: B 190 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6957 (mtm180) REVERT: B 194 SER cc_start: 0.8700 (m) cc_final: 0.8397 (p) REVERT: B 257 GLN cc_start: 0.7958 (pt0) cc_final: 0.7571 (tp-100) REVERT: B 262 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8102 (mptt) REVERT: B 302 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7472 (tmt-80) REVERT: B 381 GLN cc_start: 0.7643 (mp10) cc_final: 0.6179 (mm-40) REVERT: B 414 ARG cc_start: 0.7663 (tpp80) cc_final: 0.7279 (tpp80) REVERT: C 30 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: C 40 GLN cc_start: 0.7658 (tt0) cc_final: 0.7399 (mt0) REVERT: C 51 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7802 (mm-40) REVERT: C 99 MET cc_start: 0.8091 (mtm) cc_final: 0.7763 (mtm) REVERT: C 100 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7114 (mt-10) REVERT: C 104 GLU cc_start: 0.7764 (pm20) cc_final: 0.6489 (tm-30) REVERT: C 107 LYS cc_start: 0.7758 (mttt) cc_final: 0.7392 (mttp) REVERT: C 176 GLU cc_start: 0.7709 (tt0) cc_final: 0.7275 (mt-10) REVERT: C 190 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6870 (mtm180) REVERT: C 257 GLN cc_start: 0.7965 (pt0) cc_final: 0.7571 (tp-100) REVERT: C 262 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8103 (mptt) REVERT: C 302 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7436 (tmt-80) REVERT: C 381 GLN cc_start: 0.7649 (mp10) cc_final: 0.6157 (mm-40) REVERT: C 414 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7286 (tpp80) REVERT: D 30 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7319 (mp0) REVERT: D 40 GLN cc_start: 0.7682 (tt0) cc_final: 0.7448 (mt0) REVERT: D 51 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7813 (mm-40) REVERT: D 93 GLU cc_start: 0.8002 (mp0) cc_final: 0.7761 (mp0) REVERT: D 99 MET cc_start: 0.8051 (mtm) cc_final: 0.7816 (mtm) REVERT: D 100 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7107 (mt-10) REVERT: D 104 GLU cc_start: 0.7767 (pm20) cc_final: 0.6494 (tm-30) REVERT: D 107 LYS cc_start: 0.7757 (mttt) cc_final: 0.7397 (mttp) REVERT: D 176 GLU cc_start: 0.7719 (tt0) cc_final: 0.7287 (mt-10) REVERT: D 190 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6931 (mtm180) REVERT: D 194 SER cc_start: 0.8735 (m) cc_final: 0.8473 (p) REVERT: D 257 GLN cc_start: 0.7958 (pt0) cc_final: 0.7569 (tp-100) REVERT: D 262 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8113 (mptt) REVERT: D 302 ARG cc_start: 0.7809 (ptm160) cc_final: 0.7462 (tmt-80) REVERT: D 381 GLN cc_start: 0.7630 (mp10) cc_final: 0.6163 (mm-40) REVERT: D 414 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7283 (tpp80) outliers start: 55 outliers final: 23 residues processed: 325 average time/residue: 0.7341 time to fit residues: 264.8795 Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 44 optimal weight: 0.0770 chunk 161 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 261 GLN A 418 GLN B 261 GLN B 418 GLN C 261 GLN C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101034 restraints weight = 22720.750| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.44 r_work: 0.3013 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20304 Z= 0.104 Angle : 0.472 7.983 27520 Z= 0.245 Chirality : 0.037 0.158 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.665 161.576 3444 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.40 % Allowed : 10.87 % Favored : 86.73 % 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 aren not related in a simple way. whole: 2.18 (0.17), residues: 2384 helix: 1.96 (0.13), residues: 1500 sheet: 0.48 (0.56), residues: 68 loop : 0.72 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 180 TYR 0.013 0.001 TYR A 555 PHE 0.008 0.001 PHE D 456 TRP 0.018 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00220 (20304) covalent geometry : angle 0.47242 (27520) hydrogen bonds : bond 0.03887 ( 1181) hydrogen bonds : angle 3.94438 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7351 (mp0) REVERT: A 35 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (ttt90) REVERT: A 51 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7873 (mm-40) REVERT: A 93 GLU cc_start: 0.8064 (mp0) cc_final: 0.7779 (mp0) REVERT: A 99 MET cc_start: 0.8036 (mtm) cc_final: 0.7783 (mtm) REVERT: A 100 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 104 GLU cc_start: 0.7787 (pm20) cc_final: 0.6519 (tm-30) REVERT: A 107 LYS cc_start: 0.7766 (mttt) cc_final: 0.7399 (mttp) REVERT: A 176 GLU cc_start: 0.7747 (tt0) cc_final: 0.7346 (mt-10) REVERT: A 190 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6923 (mtm180) REVERT: A 194 SER cc_start: 0.8704 (m) cc_final: 0.8433 (p) REVERT: A 257 GLN cc_start: 0.7930 (pt0) cc_final: 0.7663 (tp-100) REVERT: A 262 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8171 (mptt) REVERT: A 298 SER cc_start: 0.8820 (p) cc_final: 0.8575 (m) REVERT: A 302 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7487 (tmt-80) REVERT: A 381 GLN cc_start: 0.7644 (mp10) cc_final: 0.6171 (mm-40) REVERT: A 414 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7390 (tpp80) REVERT: B 30 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7327 (mp0) REVERT: B 51 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7869 (mm-40) REVERT: B 93 GLU cc_start: 0.8058 (mp0) cc_final: 0.7802 (mp0) REVERT: B 99 MET cc_start: 0.8062 (mtm) cc_final: 0.7813 (mtm) REVERT: B 100 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 104 GLU cc_start: 0.7783 (pm20) cc_final: 0.6514 (tm-30) REVERT: B 107 LYS cc_start: 0.7780 (mttt) cc_final: 0.7411 (mttp) REVERT: B 176 GLU cc_start: 0.7736 (tt0) cc_final: 0.7348 (mt-10) REVERT: B 190 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6907 (mtm180) REVERT: B 194 SER cc_start: 0.8711 (m) cc_final: 0.8434 (p) REVERT: B 257 GLN cc_start: 0.7935 (pt0) cc_final: 0.7660 (tp-100) REVERT: B 262 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8166 (mptt) REVERT: B 298 SER cc_start: 0.8814 (p) cc_final: 0.8568 (m) REVERT: B 302 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7487 (tmt-80) REVERT: B 381 GLN cc_start: 0.7649 (mp10) cc_final: 0.6175 (mm-40) REVERT: B 414 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7389 (tpp80) REVERT: C 30 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7321 (mp0) REVERT: C 51 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7874 (mm-40) REVERT: C 99 MET cc_start: 0.8057 (mtm) cc_final: 0.7812 (mtm) REVERT: C 100 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7116 (mt-10) REVERT: C 104 GLU cc_start: 0.7785 (pm20) cc_final: 0.6515 (tm-30) REVERT: C 107 LYS cc_start: 0.7787 (mttt) cc_final: 0.7418 (mttp) REVERT: C 176 GLU cc_start: 0.7744 (tt0) cc_final: 0.7354 (mt-10) REVERT: C 190 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6852 (mtm180) REVERT: C 257 GLN cc_start: 0.7925 (pt0) cc_final: 0.7659 (tp-100) REVERT: C 262 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8170 (mptt) REVERT: C 298 SER cc_start: 0.8847 (p) cc_final: 0.8588 (m) REVERT: C 302 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7512 (tmt-80) REVERT: C 381 GLN cc_start: 0.7635 (mp10) cc_final: 0.6163 (mm-40) REVERT: C 414 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7388 (tpp80) REVERT: D 30 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7309 (mp0) REVERT: D 51 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7888 (mm-40) REVERT: D 93 GLU cc_start: 0.8056 (mp0) cc_final: 0.7806 (mp0) REVERT: D 100 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7108 (mt-10) REVERT: D 104 GLU cc_start: 0.7832 (pm20) cc_final: 0.6576 (tm-30) REVERT: D 107 LYS cc_start: 0.7790 (mttt) cc_final: 0.7427 (mttp) REVERT: D 176 GLU cc_start: 0.7762 (tt0) cc_final: 0.7363 (mt-10) REVERT: D 190 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6881 (mtm180) REVERT: D 194 SER cc_start: 0.8738 (m) cc_final: 0.8507 (p) REVERT: D 257 GLN cc_start: 0.7911 (pt0) cc_final: 0.7657 (tp-100) REVERT: D 298 SER cc_start: 0.8835 (p) cc_final: 0.8610 (m) REVERT: D 302 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7506 (tmt-80) REVERT: D 381 GLN cc_start: 0.7628 (mp10) cc_final: 0.6151 (mm-40) REVERT: D 414 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7384 (tpp80) outliers start: 50 outliers final: 20 residues processed: 326 average time/residue: 0.6116 time to fit residues: 220.8961 Evaluate side-chains 308 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 228 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 509 HIS B 418 GLN B 509 HIS C 418 GLN C 509 HIS D 418 GLN D 509 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101677 restraints weight = 22869.924| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.45 r_work: 0.3009 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20304 Z= 0.107 Angle : 0.480 8.998 27520 Z= 0.247 Chirality : 0.037 0.160 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.583 158.752 3444 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.40 % Allowed : 10.91 % Favored : 86.68 % 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 aren not related in a simple way. whole: 2.22 (0.17), residues: 2384 helix: 1.99 (0.13), residues: 1500 sheet: 0.40 (0.58), residues: 68 loop : 0.73 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.013 0.001 TYR C 555 PHE 0.008 0.001 PHE B 537 TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00230 (20304) covalent geometry : angle 0.47962 (27520) hydrogen bonds : bond 0.03936 ( 1181) hydrogen bonds : angle 3.92720 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 298 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7305 (mp0) REVERT: A 35 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8202 (ttt90) REVERT: A 51 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7838 (mm-40) REVERT: A 93 GLU cc_start: 0.8045 (mp0) cc_final: 0.7749 (mp0) REVERT: A 99 MET cc_start: 0.7943 (mtm) cc_final: 0.7648 (mtm) REVERT: A 100 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 104 GLU cc_start: 0.7760 (pm20) cc_final: 0.6498 (tm-30) REVERT: A 107 LYS cc_start: 0.7717 (mttt) cc_final: 0.7336 (mttp) REVERT: A 176 GLU cc_start: 0.7613 (tt0) cc_final: 0.7262 (mt-10) REVERT: A 190 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6868 (mtm180) REVERT: A 194 SER cc_start: 0.8676 (m) cc_final: 0.8391 (p) REVERT: A 257 GLN cc_start: 0.7897 (pt0) cc_final: 0.7537 (tp-100) REVERT: A 262 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8163 (mptt) REVERT: A 298 SER cc_start: 0.8776 (p) cc_final: 0.8535 (m) REVERT: A 302 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7431 (tmt-80) REVERT: A 381 GLN cc_start: 0.7593 (mp10) cc_final: 0.7214 (mp10) REVERT: A 414 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7262 (tpp80) REVERT: A 491 MET cc_start: 0.8783 (mtp) cc_final: 0.8510 (mtt) REVERT: B 30 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: B 51 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7825 (mm-40) REVERT: B 93 GLU cc_start: 0.8039 (mp0) cc_final: 0.7770 (mp0) REVERT: B 99 MET cc_start: 0.7944 (mtm) cc_final: 0.7713 (mtm) REVERT: B 100 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7079 (mt-10) REVERT: B 104 GLU cc_start: 0.7764 (pm20) cc_final: 0.6493 (tm-30) REVERT: B 107 LYS cc_start: 0.7716 (mttt) cc_final: 0.7336 (mttp) REVERT: B 176 GLU cc_start: 0.7607 (tt0) cc_final: 0.7262 (mt-10) REVERT: B 190 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6859 (mtm180) REVERT: B 194 SER cc_start: 0.8679 (m) cc_final: 0.8391 (p) REVERT: B 257 GLN cc_start: 0.7908 (pt0) cc_final: 0.7551 (tp-100) REVERT: B 262 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8164 (mptt) REVERT: B 298 SER cc_start: 0.8781 (p) cc_final: 0.8541 (m) REVERT: B 302 ARG cc_start: 0.7802 (ptm160) cc_final: 0.7435 (tmt-80) REVERT: B 381 GLN cc_start: 0.7577 (mp10) cc_final: 0.6094 (mm-40) REVERT: B 414 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7267 (tpp80) REVERT: B 491 MET cc_start: 0.8775 (mtp) cc_final: 0.8500 (mtt) REVERT: C 30 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 51 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7840 (mm-40) REVERT: C 99 MET cc_start: 0.7977 (mtm) cc_final: 0.7672 (mtm) REVERT: C 100 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7076 (mt-10) REVERT: C 104 GLU cc_start: 0.7765 (pm20) cc_final: 0.6497 (tm-30) REVERT: C 107 LYS cc_start: 0.7730 (mttt) cc_final: 0.7351 (mttp) REVERT: C 176 GLU cc_start: 0.7613 (tt0) cc_final: 0.7263 (mt-10) REVERT: C 190 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6802 (mtm180) REVERT: C 257 GLN cc_start: 0.7905 (pt0) cc_final: 0.7542 (tp-100) REVERT: C 262 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8169 (mptt) REVERT: C 298 SER cc_start: 0.8805 (p) cc_final: 0.8550 (m) REVERT: C 302 ARG cc_start: 0.7834 (ptm160) cc_final: 0.7453 (tmt-80) REVERT: C 381 GLN cc_start: 0.7576 (mp10) cc_final: 0.6096 (mm-40) REVERT: C 414 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7269 (tpp80) REVERT: C 491 MET cc_start: 0.8778 (mtp) cc_final: 0.8495 (mtt) REVERT: D 30 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: D 51 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7844 (mm-40) REVERT: D 93 GLU cc_start: 0.8067 (mp0) cc_final: 0.7780 (mp0) REVERT: D 100 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7086 (mt-10) REVERT: D 104 GLU cc_start: 0.7795 (pm20) cc_final: 0.6521 (tm-30) REVERT: D 107 LYS cc_start: 0.7723 (mttt) cc_final: 0.7347 (mttp) REVERT: D 176 GLU cc_start: 0.7617 (tt0) cc_final: 0.7263 (mt-10) REVERT: D 190 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.6847 (mtm180) REVERT: D 194 SER cc_start: 0.8702 (m) cc_final: 0.8456 (p) REVERT: D 257 GLN cc_start: 0.7904 (pt0) cc_final: 0.7534 (tp-100) REVERT: D 262 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8141 (mptt) REVERT: D 298 SER cc_start: 0.8786 (p) cc_final: 0.8559 (m) REVERT: D 302 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7435 (tmt-80) REVERT: D 381 GLN cc_start: 0.7581 (mp10) cc_final: 0.6098 (mm-40) REVERT: D 414 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7251 (tpp80) REVERT: D 491 MET cc_start: 0.8780 (mtp) cc_final: 0.8507 (mtt) outliers start: 50 outliers final: 24 residues processed: 330 average time/residue: 0.7104 time to fit residues: 261.0101 Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 125 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 226 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 418 GLN B 261 GLN B 418 GLN C 261 GLN C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100529 restraints weight = 22789.260| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.45 r_work: 0.3006 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20304 Z= 0.110 Angle : 0.491 8.813 27520 Z= 0.252 Chirality : 0.038 0.197 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.543 156.017 3444 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.02 % Allowed : 11.59 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.17), residues: 2384 helix: 2.02 (0.13), residues: 1500 sheet: -1.45 (0.45), residues: 108 loop : 0.86 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.013 0.001 TYR A 555 PHE 0.008 0.001 PHE D 456 TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00239 (20304) covalent geometry : angle 0.49068 (27520) hydrogen bonds : bond 0.03939 ( 1181) hydrogen bonds : angle 3.93652 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7257 (mp0) REVERT: A 35 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8203 (ttt90) REVERT: A 51 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7843 (mm-40) REVERT: A 93 GLU cc_start: 0.8063 (mp0) cc_final: 0.7773 (mp0) REVERT: A 99 MET cc_start: 0.7889 (mtm) cc_final: 0.7637 (mtm) REVERT: A 100 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 104 GLU cc_start: 0.7823 (pm20) cc_final: 0.6576 (tm-30) REVERT: A 107 LYS cc_start: 0.7685 (mttt) cc_final: 0.7305 (mttp) REVERT: A 176 GLU cc_start: 0.7634 (tt0) cc_final: 0.7259 (mt-10) REVERT: A 190 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6847 (mtm180) REVERT: A 194 SER cc_start: 0.8675 (m) cc_final: 0.8388 (p) REVERT: A 257 GLN cc_start: 0.7861 (pt0) cc_final: 0.7601 (tp-100) REVERT: A 262 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8173 (mptt) REVERT: A 298 SER cc_start: 0.8772 (p) cc_final: 0.8559 (m) REVERT: A 302 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7441 (tmt-80) REVERT: A 381 GLN cc_start: 0.7581 (mp10) cc_final: 0.7211 (mp10) REVERT: A 414 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7384 (tpp80) REVERT: A 491 MET cc_start: 0.8777 (mtp) cc_final: 0.8504 (mtt) REVERT: B 30 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 51 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7825 (mm-40) REVERT: B 93 GLU cc_start: 0.8069 (mp0) cc_final: 0.7810 (mp0) REVERT: B 100 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7072 (mt-10) REVERT: B 104 GLU cc_start: 0.7829 (pm20) cc_final: 0.6575 (tm-30) REVERT: B 107 LYS cc_start: 0.7690 (mttt) cc_final: 0.7310 (mttp) REVERT: B 176 GLU cc_start: 0.7634 (tt0) cc_final: 0.7265 (mt-10) REVERT: B 190 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6839 (mtm180) REVERT: B 194 SER cc_start: 0.8678 (m) cc_final: 0.8390 (p) REVERT: B 257 GLN cc_start: 0.7844 (pt0) cc_final: 0.7588 (tp-100) REVERT: B 298 SER cc_start: 0.8783 (p) cc_final: 0.8568 (m) REVERT: B 302 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7452 (tmt-80) REVERT: B 381 GLN cc_start: 0.7567 (mp10) cc_final: 0.7162 (mp10) REVERT: B 414 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7387 (tpp80) REVERT: B 491 MET cc_start: 0.8768 (mtp) cc_final: 0.8496 (mtt) REVERT: C 30 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: C 51 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7841 (mm-40) REVERT: C 99 MET cc_start: 0.7896 (mtm) cc_final: 0.7626 (mtm) REVERT: C 100 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7050 (mt-10) REVERT: C 104 GLU cc_start: 0.7832 (pm20) cc_final: 0.6577 (tm-30) REVERT: C 107 LYS cc_start: 0.7698 (mttt) cc_final: 0.7320 (mttp) REVERT: C 176 GLU cc_start: 0.7630 (tt0) cc_final: 0.7256 (mt-10) REVERT: C 190 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6813 (mtm180) REVERT: C 257 GLN cc_start: 0.7839 (pt0) cc_final: 0.7582 (tp-100) REVERT: C 298 SER cc_start: 0.8811 (p) cc_final: 0.8563 (m) REVERT: C 302 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7459 (tmt-80) REVERT: C 381 GLN cc_start: 0.7580 (mp10) cc_final: 0.7204 (mp10) REVERT: C 414 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7382 (tpp80) REVERT: C 491 MET cc_start: 0.8770 (mtp) cc_final: 0.8491 (mtt) REVERT: D 30 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: D 51 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7849 (mm-40) REVERT: D 93 GLU cc_start: 0.8106 (mp0) cc_final: 0.7848 (mp0) REVERT: D 100 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7048 (mt-10) REVERT: D 104 GLU cc_start: 0.7841 (pm20) cc_final: 0.6592 (tm-30) REVERT: D 107 LYS cc_start: 0.7685 (mttt) cc_final: 0.7308 (mttp) REVERT: D 176 GLU cc_start: 0.7632 (tt0) cc_final: 0.7252 (mt-10) REVERT: D 190 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6840 (mtm180) REVERT: D 194 SER cc_start: 0.8698 (m) cc_final: 0.8450 (p) REVERT: D 257 GLN cc_start: 0.7866 (pt0) cc_final: 0.7607 (tp-100) REVERT: D 262 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8164 (mptt) REVERT: D 298 SER cc_start: 0.8790 (p) cc_final: 0.8573 (m) REVERT: D 302 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7458 (tmt-80) REVERT: D 381 GLN cc_start: 0.7576 (mp10) cc_final: 0.7173 (mp10) REVERT: D 414 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7372 (tpp80) REVERT: D 491 MET cc_start: 0.8772 (mtp) cc_final: 0.8498 (mtt) outliers start: 42 outliers final: 23 residues processed: 316 average time/residue: 0.7662 time to fit residues: 268.9668 Evaluate side-chains 315 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 483 GLN B 418 GLN B 483 GLN C 418 GLN C 483 GLN D 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099376 restraints weight = 22732.505| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.44 r_work: 0.2987 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20304 Z= 0.121 Angle : 0.501 8.767 27520 Z= 0.257 Chirality : 0.038 0.181 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.413 154.758 3444 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.88 % Allowed : 12.36 % Favored : 85.77 % 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 aren not related in a simple way. whole: 2.12 (0.17), residues: 2384 helix: 1.98 (0.13), residues: 1504 sheet: -1.54 (0.44), residues: 108 loop : 0.87 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 180 TYR 0.013 0.001 TYR D 555 PHE 0.009 0.001 PHE A 537 TRP 0.015 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00275 (20304) covalent geometry : angle 0.50056 (27520) hydrogen bonds : bond 0.04161 ( 1181) hydrogen bonds : angle 3.98093 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 35 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8193 (ttt90) REVERT: A 51 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7853 (mm-40) REVERT: A 93 GLU cc_start: 0.8095 (mp0) cc_final: 0.7825 (mp0) REVERT: A 99 MET cc_start: 0.7903 (mtm) cc_final: 0.7650 (mtm) REVERT: A 100 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7055 (mt-10) REVERT: A 104 GLU cc_start: 0.7830 (pm20) cc_final: 0.6581 (tm-30) REVERT: A 107 LYS cc_start: 0.7692 (mttt) cc_final: 0.7304 (mttp) REVERT: A 176 GLU cc_start: 0.7616 (tt0) cc_final: 0.7220 (mt-10) REVERT: A 190 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.6861 (mtm180) REVERT: A 194 SER cc_start: 0.8684 (m) cc_final: 0.8387 (p) REVERT: A 257 GLN cc_start: 0.7890 (pt0) cc_final: 0.7565 (tp-100) REVERT: A 298 SER cc_start: 0.8813 (p) cc_final: 0.8557 (m) REVERT: A 302 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7447 (tmt-80) REVERT: A 381 GLN cc_start: 0.7601 (mp10) cc_final: 0.7213 (mp10) REVERT: A 414 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7363 (tpp80) REVERT: A 491 MET cc_start: 0.8790 (mtp) cc_final: 0.8522 (mtt) REVERT: B 30 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: B 51 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7843 (mm-40) REVERT: B 93 GLU cc_start: 0.8147 (mp0) cc_final: 0.7844 (mp0) REVERT: B 100 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7047 (mt-10) REVERT: B 104 GLU cc_start: 0.7842 (pm20) cc_final: 0.6594 (tm-30) REVERT: B 107 LYS cc_start: 0.7687 (mttt) cc_final: 0.7298 (mttp) REVERT: B 176 GLU cc_start: 0.7611 (tt0) cc_final: 0.7226 (mt-10) REVERT: B 190 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6854 (mtm180) REVERT: B 194 SER cc_start: 0.8684 (m) cc_final: 0.8386 (p) REVERT: B 257 GLN cc_start: 0.7887 (pt0) cc_final: 0.7574 (tp-100) REVERT: B 262 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8151 (mptt) REVERT: B 298 SER cc_start: 0.8823 (p) cc_final: 0.8565 (m) REVERT: B 302 ARG cc_start: 0.7857 (ptm160) cc_final: 0.7464 (tmt-80) REVERT: B 381 GLN cc_start: 0.7592 (mp10) cc_final: 0.7168 (mp10) REVERT: B 414 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7374 (tpp80) REVERT: B 491 MET cc_start: 0.8785 (mtp) cc_final: 0.8512 (mtt) REVERT: C 30 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: C 51 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7852 (mm-40) REVERT: C 99 MET cc_start: 0.7908 (mtm) cc_final: 0.7633 (mtm) REVERT: C 100 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7107 (mt-10) REVERT: C 104 GLU cc_start: 0.7831 (pm20) cc_final: 0.6581 (tm-30) REVERT: C 107 LYS cc_start: 0.7706 (mttt) cc_final: 0.7321 (mttp) REVERT: C 176 GLU cc_start: 0.7609 (tt0) cc_final: 0.7218 (mt-10) REVERT: C 190 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6807 (mtm180) REVERT: C 257 GLN cc_start: 0.7893 (pt0) cc_final: 0.7578 (tp-100) REVERT: C 262 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8163 (mptt) REVERT: C 302 ARG cc_start: 0.7853 (ptm160) cc_final: 0.7452 (tmt-80) REVERT: C 381 GLN cc_start: 0.7597 (mp10) cc_final: 0.7210 (mp10) REVERT: C 414 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7385 (tpp80) REVERT: C 491 MET cc_start: 0.8785 (mtp) cc_final: 0.8511 (mtt) REVERT: D 30 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: D 51 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7865 (mm-40) REVERT: D 93 GLU cc_start: 0.8148 (mp0) cc_final: 0.7854 (mp0) REVERT: D 104 GLU cc_start: 0.7845 (pm20) cc_final: 0.6599 (tm-30) REVERT: D 107 LYS cc_start: 0.7690 (mttt) cc_final: 0.7300 (mttp) REVERT: D 176 GLU cc_start: 0.7609 (tt0) cc_final: 0.7216 (mt-10) REVERT: D 190 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6872 (mtm180) REVERT: D 194 SER cc_start: 0.8693 (m) cc_final: 0.8424 (p) REVERT: D 257 GLN cc_start: 0.7902 (pt0) cc_final: 0.7560 (tp-100) REVERT: D 262 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8136 (mptt) REVERT: D 298 SER cc_start: 0.8817 (p) cc_final: 0.8584 (m) REVERT: D 302 ARG cc_start: 0.7842 (ptm160) cc_final: 0.7466 (tmt-80) REVERT: D 381 GLN cc_start: 0.7600 (mp10) cc_final: 0.7179 (mp10) REVERT: D 414 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7399 (tpp80) REVERT: D 491 MET cc_start: 0.8789 (mtp) cc_final: 0.8511 (mtt) outliers start: 39 outliers final: 22 residues processed: 309 average time/residue: 0.7874 time to fit residues: 269.3985 Evaluate side-chains 307 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 418 GLN B 261 GLN B 418 GLN C 261 GLN C 418 GLN D 261 GLN D 418 GLN D 483 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100374 restraints weight = 22822.590| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.44 r_work: 0.3005 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20304 Z= 0.112 Angle : 0.500 8.768 27520 Z= 0.256 Chirality : 0.038 0.213 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.297 155.374 3444 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.83 % Allowed : 12.55 % Favored : 85.62 % 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 aren not related in a simple way. whole: 2.15 (0.17), residues: 2384 helix: 2.01 (0.13), residues: 1504 sheet: -1.46 (0.45), residues: 108 loop : 0.87 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.013 0.001 TYR A 555 PHE 0.010 0.001 PHE A 456 TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00247 (20304) covalent geometry : angle 0.49981 (27520) hydrogen bonds : bond 0.03990 ( 1181) hydrogen bonds : angle 3.99284 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7195 (mp0) REVERT: A 35 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8198 (ttt90) REVERT: A 51 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7883 (mm-40) REVERT: A 93 GLU cc_start: 0.8109 (mp0) cc_final: 0.7807 (mp0) REVERT: A 99 MET cc_start: 0.7914 (mtm) cc_final: 0.7637 (mtm) REVERT: A 100 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 104 GLU cc_start: 0.7859 (pm20) cc_final: 0.6730 (tm-30) REVERT: A 107 LYS cc_start: 0.7689 (mttt) cc_final: 0.7347 (mttp) REVERT: A 176 GLU cc_start: 0.7619 (tt0) cc_final: 0.7235 (mt-10) REVERT: A 190 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.6851 (mtm180) REVERT: A 194 SER cc_start: 0.8675 (m) cc_final: 0.8381 (p) REVERT: A 257 GLN cc_start: 0.7825 (pt0) cc_final: 0.7614 (tp-100) REVERT: A 298 SER cc_start: 0.8786 (p) cc_final: 0.8584 (m) REVERT: A 302 ARG cc_start: 0.7805 (ptm160) cc_final: 0.7435 (tmt-80) REVERT: A 381 GLN cc_start: 0.7607 (mp10) cc_final: 0.7199 (mp10) REVERT: A 414 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7335 (tpp80) REVERT: A 491 MET cc_start: 0.8811 (mtp) cc_final: 0.8541 (mtt) REVERT: B 30 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 51 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7870 (mm-40) REVERT: B 93 GLU cc_start: 0.8157 (mp0) cc_final: 0.7858 (mp0) REVERT: B 104 GLU cc_start: 0.7868 (pm20) cc_final: 0.6743 (tm-30) REVERT: B 107 LYS cc_start: 0.7696 (mttt) cc_final: 0.7352 (mttp) REVERT: B 176 GLU cc_start: 0.7621 (tt0) cc_final: 0.7245 (mt-10) REVERT: B 190 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6841 (mtm180) REVERT: B 194 SER cc_start: 0.8678 (m) cc_final: 0.8383 (p) REVERT: B 302 ARG cc_start: 0.7808 (ptm160) cc_final: 0.7442 (tmt-80) REVERT: B 381 GLN cc_start: 0.7597 (mp10) cc_final: 0.7186 (mp10) REVERT: B 414 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7338 (tpp80) REVERT: B 491 MET cc_start: 0.8810 (mtp) cc_final: 0.8541 (mtt) REVERT: C 30 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 51 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7877 (mm-40) REVERT: C 99 MET cc_start: 0.7930 (mtm) cc_final: 0.7672 (mtm) REVERT: C 100 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 104 GLU cc_start: 0.7868 (pm20) cc_final: 0.6736 (tm-30) REVERT: C 107 LYS cc_start: 0.7706 (mttt) cc_final: 0.7358 (mttp) REVERT: C 176 GLU cc_start: 0.7618 (tt0) cc_final: 0.7234 (mt-10) REVERT: C 190 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.6786 (mtm180) REVERT: C 298 SER cc_start: 0.8826 (p) cc_final: 0.8595 (m) REVERT: C 302 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7459 (tmt-80) REVERT: C 381 GLN cc_start: 0.7594 (mp10) cc_final: 0.7187 (mp10) REVERT: C 414 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7332 (tpp80) REVERT: C 491 MET cc_start: 0.8785 (mtp) cc_final: 0.8517 (mtt) REVERT: D 30 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7141 (mp0) REVERT: D 51 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7896 (mm-40) REVERT: D 93 GLU cc_start: 0.8167 (mp0) cc_final: 0.7874 (mp0) REVERT: D 104 GLU cc_start: 0.7892 (pm20) cc_final: 0.6717 (tm-30) REVERT: D 107 LYS cc_start: 0.7713 (mttt) cc_final: 0.7339 (mttp) REVERT: D 176 GLU cc_start: 0.7612 (tt0) cc_final: 0.7224 (mt-10) REVERT: D 190 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.6859 (mtm180) REVERT: D 194 SER cc_start: 0.8684 (m) cc_final: 0.8420 (p) REVERT: D 257 GLN cc_start: 0.7864 (pt0) cc_final: 0.7641 (tp-100) REVERT: D 298 SER cc_start: 0.8798 (p) cc_final: 0.8589 (m) REVERT: D 302 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7451 (tmt-80) REVERT: D 381 GLN cc_start: 0.7596 (mp10) cc_final: 0.7188 (mp10) REVERT: D 414 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7365 (tpp80) REVERT: D 491 MET cc_start: 0.8772 (mtp) cc_final: 0.8496 (mtt) outliers start: 38 outliers final: 23 residues processed: 310 average time/residue: 0.7465 time to fit residues: 256.9411 Evaluate side-chains 307 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 261 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 418 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.099967 restraints weight = 22897.726| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.45 r_work: 0.2989 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20304 Z= 0.115 Angle : 0.498 8.613 27520 Z= 0.255 Chirality : 0.038 0.179 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.252 154.858 3444 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.68 % Allowed : 13.03 % Favored : 85.29 % 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 aren not related in a simple way. whole: 2.14 (0.17), residues: 2384 helix: 2.01 (0.13), residues: 1504 sheet: -1.50 (0.44), residues: 108 loop : 0.86 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.013 0.001 TYR A 555 PHE 0.008 0.001 PHE A 537 TRP 0.015 0.001 TRP A 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00256 (20304) covalent geometry : angle 0.49837 (27520) hydrogen bonds : bond 0.04043 ( 1181) hydrogen bonds : angle 3.98670 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7267.38 seconds wall clock time: 124 minutes 30.26 seconds (7470.26 seconds total)