Starting phenix.real_space_refine on Tue Jun 17 16:23:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tf2_41217/06_2025/8tf2_41217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tf2_41217/06_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_41217/06_2025/8tf2_41217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tf2_41217/06_2025/8tf2_41217.map" model { file = "/net/cci-nas-00/data/ceres_data/8tf2_41217/06_2025/8tf2_41217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tf2_41217/06_2025/8tf2_41217.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.056 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 5, 'CPL:plan-1': 5} 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-4': 3, 'CPL:plan-3': 3, 'CPL:plan-2': 2, 'CPL:plan-1': 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-4': 5, 'CPL:plan-3': 5, 'CPL:plan-2': 4, 'CPL:plan-1': 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-4': 2, 'CPL:plan-3': 2, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 13.31, per 1000 atoms: 0.67 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: 5.42 Conformation dependent library (CDL) restraints added in 2.9 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... 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: 2.34 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: 6.86 Time building geometry restraints manager: 6.37 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.090 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (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 TRP 0.140 0.021 TRP C 593 HIS 0.010 0.004 HIS C 582 PHE 0.066 0.015 PHE B 256 TYR 0.110 0.024 TYR C 336 ARG 0.006 0.001 ARG D 492 Details of bonding type rmsd hydrogen bonds : bond 0.16620 ( 1181) hydrogen bonds : angle 6.12139 ( 3363) covalent geometry : bond 0.01188 (20304) covalent geometry : angle 1.75443 (27520) *********************** 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 : 2.241 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: 2.0187 time to fit residues: 958.9305 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 : 2.530 ------------------------------------------------------------------------------- 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 202 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN 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 40 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 40 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 40 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097985 restraints weight = 22014.116| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.57 r_work: 0.2958 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20304 Z= 0.131 Angle : 0.533 5.690 27520 Z= 0.288 Chirality : 0.039 0.148 3124 Planarity : 0.004 0.042 3404 Dihedral : 13.201 176.655 3452 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.12 % Allowed : 6.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.17), residues: 2384 helix: 1.50 (0.13), residues: 1512 sheet: 0.61 (0.49), residues: 80 loop : 1.11 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 593 HIS 0.004 0.001 HIS B 201 PHE 0.016 0.002 PHE C 456 TYR 0.019 0.002 TYR D 555 ARG 0.005 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 1181) hydrogen bonds : angle 4.17965 ( 3363) covalent geometry : bond 0.00281 (20304) covalent geometry : angle 0.53310 (27520) *********************** 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 369 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 325 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7716 (tt0) cc_final: 0.7432 (mt0) REVERT: A 99 MET cc_start: 0.8031 (mtm) cc_final: 0.7648 (mtm) REVERT: A 100 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 104 GLU cc_start: 0.7776 (pm20) cc_final: 0.6547 (tm-30) REVERT: A 107 LYS cc_start: 0.7683 (mttt) cc_final: 0.7354 (mttp) REVERT: A 176 GLU cc_start: 0.7654 (tt0) cc_final: 0.7147 (mt-10) REVERT: A 190 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.6831 (mtm180) REVERT: A 194 SER cc_start: 0.8796 (m) cc_final: 0.8523 (p) REVERT: A 257 GLN cc_start: 0.8003 (pt0) cc_final: 0.7547 (tp-100) REVERT: A 262 LYS cc_start: 0.8646 (mttt) cc_final: 0.8403 (mptt) REVERT: A 302 ARG cc_start: 0.7781 (ptm160) cc_final: 0.7329 (tmt-80) REVERT: A 381 GLN cc_start: 0.7791 (mp10) cc_final: 0.6152 (mm-40) REVERT: A 408 PHE cc_start: 0.7698 (m-10) cc_final: 0.7471 (m-10) REVERT: A 414 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7627 (tpp80) REVERT: A 491 MET cc_start: 0.8725 (mmm) cc_final: 0.8393 (tpp) REVERT: B 35 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8276 (ttt90) REVERT: B 40 GLN cc_start: 0.7714 (tt0) cc_final: 0.7441 (mt0) REVERT: B 99 MET cc_start: 0.8052 (mtm) cc_final: 0.7663 (mtm) REVERT: B 100 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7285 (mt-10) REVERT: B 104 GLU cc_start: 0.7789 (pm20) cc_final: 0.6518 (tm-30) REVERT: B 107 LYS cc_start: 0.7671 (mttt) cc_final: 0.7351 (mttp) REVERT: B 176 GLU cc_start: 0.7645 (tt0) cc_final: 0.7131 (mt-10) REVERT: B 190 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.6845 (mtm180) REVERT: B 194 SER cc_start: 0.8797 (m) cc_final: 0.8567 (p) REVERT: B 257 GLN cc_start: 0.8011 (pt0) cc_final: 0.7555 (tp-100) REVERT: B 302 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7358 (tmt-80) REVERT: B 381 GLN cc_start: 0.7798 (mp10) cc_final: 0.6149 (mm-40) REVERT: B 408 PHE cc_start: 0.7685 (m-10) cc_final: 0.7456 (m-10) REVERT: B 414 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7609 (tpp80) REVERT: B 491 MET cc_start: 0.8733 (mmm) cc_final: 0.8400 (tpp) REVERT: C 40 GLN cc_start: 0.7722 (tt0) cc_final: 0.7453 (mt0) REVERT: C 93 GLU cc_start: 0.8018 (mp0) cc_final: 0.7806 (mp0) REVERT: C 99 MET cc_start: 0.8043 (mtm) cc_final: 0.7653 (mtm) REVERT: C 100 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7274 (mt-10) REVERT: C 104 GLU cc_start: 0.7787 (pm20) cc_final: 0.6516 (tm-30) REVERT: C 107 LYS cc_start: 0.7680 (mttt) cc_final: 0.7310 (mttp) REVERT: C 176 GLU cc_start: 0.7651 (tt0) cc_final: 0.7135 (mt-10) REVERT: C 190 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.6834 (mtm180) REVERT: C 194 SER cc_start: 0.8805 (m) cc_final: 0.8572 (p) REVERT: C 257 GLN cc_start: 0.8016 (pt0) cc_final: 0.7553 (tp-100) REVERT: C 302 ARG cc_start: 0.7778 (ptm160) cc_final: 0.7323 (tmt-80) REVERT: C 379 THR cc_start: 0.8007 (m) cc_final: 0.7805 (m) REVERT: C 381 GLN cc_start: 0.7779 (mp10) cc_final: 0.6134 (mm-40) REVERT: C 408 PHE cc_start: 0.7691 (m-10) cc_final: 0.7371 (m-10) REVERT: C 414 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7612 (tpp80) REVERT: C 491 MET cc_start: 0.8742 (mmm) cc_final: 0.8414 (tpp) REVERT: D 35 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8267 (ttt90) REVERT: D 40 GLN cc_start: 0.7715 (tt0) cc_final: 0.7433 (mt0) REVERT: D 99 MET cc_start: 0.8058 (mtm) cc_final: 0.7800 (mtm) REVERT: D 100 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7263 (mt-10) REVERT: D 104 GLU cc_start: 0.7793 (pm20) cc_final: 0.6527 (tm-30) REVERT: D 107 LYS cc_start: 0.7666 (mttt) cc_final: 0.7355 (mttp) REVERT: D 176 GLU cc_start: 0.7662 (tt0) cc_final: 0.7112 (mt-10) REVERT: D 190 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6835 (mtm180) REVERT: D 194 SER cc_start: 0.8805 (m) cc_final: 0.8554 (p) REVERT: D 257 GLN cc_start: 0.8000 (pt0) cc_final: 0.7550 (tp-100) REVERT: D 262 LYS cc_start: 0.8648 (mttt) cc_final: 0.8413 (mptt) REVERT: D 302 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7348 (tmt-80) REVERT: D 379 THR cc_start: 0.8018 (m) cc_final: 0.7817 (m) REVERT: D 381 GLN cc_start: 0.7796 (mp10) cc_final: 0.6147 (mm-40) REVERT: D 408 PHE cc_start: 0.7689 (m-10) cc_final: 0.7372 (m-10) REVERT: D 414 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7614 (tpp80) REVERT: D 491 MET cc_start: 0.8736 (mmm) cc_final: 0.8401 (tpp) outliers start: 44 outliers final: 11 residues processed: 339 average time/residue: 2.2069 time to fit residues: 828.9846 Evaluate side-chains 297 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 3.213 ------------------------------------------------------------------------------- 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 35 ARG 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 35 ARG 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.0070 chunk 16 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.127409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099710 restraints weight = 21941.059| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.56 r_work: 0.2983 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2349 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= 0.111 Angle : 0.489 9.032 27520 Z= 0.253 Chirality : 0.038 0.148 3124 Planarity : 0.004 0.042 3404 Dihedral : 12.229 171.553 3444 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.07 % Allowed : 8.65 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.17), residues: 2384 helix: 1.92 (0.13), residues: 1500 sheet: 1.18 (0.50), residues: 68 loop : 0.95 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 593 HIS 0.004 0.001 HIS B 201 PHE 0.010 0.001 PHE A 152 TYR 0.015 0.001 TYR A 555 ARG 0.004 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1181) hydrogen bonds : angle 3.99179 ( 3363) covalent geometry : bond 0.00233 (20304) covalent geometry : angle 0.48867 (27520) *********************** 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 333 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 40 GLN cc_start: 0.7631 (tt0) cc_final: 0.7381 (mt0) REVERT: A 64 LEU cc_start: 0.8178 (mt) cc_final: 0.7901 (mt) REVERT: A 99 MET cc_start: 0.8009 (mtm) cc_final: 0.7653 (mtm) REVERT: A 100 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 104 GLU cc_start: 0.7800 (pm20) cc_final: 0.6573 (tm-30) REVERT: A 107 LYS cc_start: 0.7665 (mttt) cc_final: 0.7316 (mttp) REVERT: A 176 GLU cc_start: 0.7739 (tt0) cc_final: 0.7262 (mt-10) REVERT: A 190 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6854 (mtm180) REVERT: A 194 SER cc_start: 0.8720 (m) cc_final: 0.8497 (p) REVERT: A 257 GLN cc_start: 0.7986 (pt0) cc_final: 0.7558 (tp-100) REVERT: A 302 ARG cc_start: 0.7762 (ptm160) cc_final: 0.7385 (tmt-80) REVERT: A 381 GLN cc_start: 0.7581 (mp10) cc_final: 0.5981 (mm-40) REVERT: A 414 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7554 (tpp80) REVERT: A 570 MET cc_start: 0.8728 (mmm) cc_final: 0.8228 (mmm) REVERT: B 30 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7289 (mp0) REVERT: B 35 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8248 (ttt90) REVERT: B 40 GLN cc_start: 0.7635 (tt0) cc_final: 0.7376 (mt0) REVERT: B 64 LEU cc_start: 0.8182 (mt) cc_final: 0.7907 (mt) REVERT: B 99 MET cc_start: 0.8019 (mtm) cc_final: 0.7664 (mtm) REVERT: B 100 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7220 (mt-10) REVERT: B 104 GLU cc_start: 0.7814 (pm20) cc_final: 0.6578 (tm-30) REVERT: B 107 LYS cc_start: 0.7662 (mttt) cc_final: 0.7316 (mttp) REVERT: B 176 GLU cc_start: 0.7743 (tt0) cc_final: 0.7252 (mt-10) REVERT: B 190 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6848 (mtm180) REVERT: B 194 SER cc_start: 0.8742 (m) cc_final: 0.8515 (p) REVERT: B 257 GLN cc_start: 0.7994 (pt0) cc_final: 0.7565 (tp-100) REVERT: B 302 ARG cc_start: 0.7753 (ptm160) cc_final: 0.7383 (tmt-80) REVERT: B 381 GLN cc_start: 0.7582 (mp10) cc_final: 0.5979 (mm-40) REVERT: B 414 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7550 (tpp80) REVERT: B 570 MET cc_start: 0.8726 (mmm) cc_final: 0.8229 (mmm) REVERT: C 30 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7293 (mp0) REVERT: C 40 GLN cc_start: 0.7640 (tt0) cc_final: 0.7420 (mt0) REVERT: C 64 LEU cc_start: 0.8175 (mt) cc_final: 0.7901 (mt) REVERT: C 99 MET cc_start: 0.8018 (mtm) cc_final: 0.7662 (mtm) REVERT: C 100 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7222 (mt-10) REVERT: C 104 GLU cc_start: 0.7813 (pm20) cc_final: 0.6570 (tm-30) REVERT: C 107 LYS cc_start: 0.7662 (mttt) cc_final: 0.7315 (mttp) REVERT: C 176 GLU cc_start: 0.7751 (tt0) cc_final: 0.7256 (mt-10) REVERT: C 190 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6856 (mtm180) REVERT: C 194 SER cc_start: 0.8739 (m) cc_final: 0.8510 (p) REVERT: C 257 GLN cc_start: 0.7992 (pt0) cc_final: 0.7562 (tp-100) REVERT: C 302 ARG cc_start: 0.7754 (ptm160) cc_final: 0.7380 (tmt-80) REVERT: C 381 GLN cc_start: 0.7747 (mp10) cc_final: 0.6107 (mm-40) REVERT: C 414 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7544 (tpp80) REVERT: C 570 MET cc_start: 0.8727 (mmm) cc_final: 0.8227 (mmm) REVERT: D 30 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7305 (mp0) REVERT: D 35 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8236 (ttt90) REVERT: D 40 GLN cc_start: 0.7641 (tt0) cc_final: 0.7375 (mt0) REVERT: D 64 LEU cc_start: 0.8186 (mt) cc_final: 0.7953 (mt) REVERT: D 99 MET cc_start: 0.8005 (mtm) cc_final: 0.7784 (mtm) REVERT: D 100 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 104 GLU cc_start: 0.7808 (pm20) cc_final: 0.6546 (tm-30) REVERT: D 107 LYS cc_start: 0.7667 (mttt) cc_final: 0.7327 (mttp) REVERT: D 176 GLU cc_start: 0.7796 (tt0) cc_final: 0.7278 (mt-10) REVERT: D 190 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6862 (mtm180) REVERT: D 194 SER cc_start: 0.8728 (m) cc_final: 0.8512 (p) REVERT: D 257 GLN cc_start: 0.7981 (pt0) cc_final: 0.7574 (tp-100) REVERT: D 302 ARG cc_start: 0.7755 (ptm160) cc_final: 0.7379 (tmt-80) REVERT: D 381 GLN cc_start: 0.7751 (mp10) cc_final: 0.6086 (mm-40) REVERT: D 414 ARG cc_start: 0.7750 (tpp80) cc_final: 0.7545 (tpp80) REVERT: D 570 MET cc_start: 0.8713 (mmm) cc_final: 0.8218 (mmm) outliers start: 43 outliers final: 16 residues processed: 308 average time/residue: 2.6805 time to fit residues: 924.2218 Evaluate side-chains 293 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 4.889 ------------------------------------------------------------------------------- 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 A residue 354 LEU Chi-restraints excluded: chain B residue 35 ARG 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 C residue 354 LEU Chi-restraints excluded: chain D residue 35 ARG 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 28 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 152 optimal weight: 0.2980 chunk 168 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.125827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098414 restraints weight = 22026.392| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.47 r_work: 0.2968 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2422 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= 0.127 Angle : 0.495 7.953 27520 Z= 0.258 Chirality : 0.038 0.155 3124 Planarity : 0.004 0.041 3404 Dihedral : 12.044 167.552 3444 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.08 % Allowed : 8.80 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.17), residues: 2384 helix: 1.87 (0.13), residues: 1500 sheet: 0.72 (0.53), residues: 68 loop : 0.93 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 593 HIS 0.004 0.001 HIS A 201 PHE 0.009 0.001 PHE C 472 TYR 0.015 0.002 TYR D 555 ARG 0.004 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 1181) hydrogen bonds : angle 3.99454 ( 3363) covalent geometry : bond 0.00288 (20304) covalent geometry : angle 0.49538 (27520) *********************** 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 352 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 40 GLN cc_start: 0.7419 (tt0) cc_final: 0.7122 (mt0) REVERT: A 51 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7680 (mm-40) REVERT: A 64 LEU cc_start: 0.8044 (mt) cc_final: 0.7775 (mt) REVERT: A 93 GLU cc_start: 0.7864 (mp0) cc_final: 0.7601 (mp0) REVERT: A 99 MET cc_start: 0.7810 (mtm) cc_final: 0.7467 (mtm) REVERT: A 100 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 104 GLU cc_start: 0.7740 (pm20) cc_final: 0.6469 (tm-30) REVERT: A 107 LYS cc_start: 0.7664 (mttt) cc_final: 0.7281 (mttp) REVERT: A 176 GLU cc_start: 0.7621 (tt0) cc_final: 0.7130 (mt-10) REVERT: A 190 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.6747 (mtm180) REVERT: A 194 SER cc_start: 0.8650 (m) cc_final: 0.8373 (p) REVERT: A 257 GLN cc_start: 0.7768 (pt0) cc_final: 0.7271 (tp-100) REVERT: A 262 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8011 (mptt) REVERT: A 302 ARG cc_start: 0.7689 (ptm160) cc_final: 0.7230 (tmt-80) REVERT: A 381 GLN cc_start: 0.7452 (mp10) cc_final: 0.5934 (mm-40) REVERT: A 414 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7280 (tpp80) REVERT: A 570 MET cc_start: 0.8633 (mmm) cc_final: 0.8060 (mmm) REVERT: B 30 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: B 35 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8045 (ttt90) REVERT: B 40 GLN cc_start: 0.7393 (tt0) cc_final: 0.7110 (mt0) REVERT: B 64 LEU cc_start: 0.8038 (mt) cc_final: 0.7773 (mt) REVERT: B 93 GLU cc_start: 0.7862 (mp0) cc_final: 0.7626 (mp0) REVERT: B 99 MET cc_start: 0.7814 (mtm) cc_final: 0.7470 (mtm) REVERT: B 100 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7046 (mt-10) REVERT: B 104 GLU cc_start: 0.7745 (pm20) cc_final: 0.6473 (tm-30) REVERT: B 107 LYS cc_start: 0.7646 (mttt) cc_final: 0.7263 (mttp) REVERT: B 176 GLU cc_start: 0.7632 (tt0) cc_final: 0.7123 (mt-10) REVERT: B 190 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.6726 (mtm180) REVERT: B 194 SER cc_start: 0.8682 (m) cc_final: 0.8407 (p) REVERT: B 257 GLN cc_start: 0.7771 (pt0) cc_final: 0.7271 (tp-100) REVERT: B 262 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7981 (mptt) REVERT: B 302 ARG cc_start: 0.7695 (ptm160) cc_final: 0.7233 (tmt-80) REVERT: B 381 GLN cc_start: 0.7431 (mp10) cc_final: 0.5901 (mm-40) REVERT: B 414 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7299 (tpp80) REVERT: B 570 MET cc_start: 0.8621 (mmm) cc_final: 0.8051 (mmm) REVERT: C 30 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: C 40 GLN cc_start: 0.7426 (tt0) cc_final: 0.7136 (mt0) REVERT: C 64 LEU cc_start: 0.8033 (mt) cc_final: 0.7767 (mt) REVERT: C 93 GLU cc_start: 0.7871 (mp0) cc_final: 0.7631 (mp0) REVERT: C 99 MET cc_start: 0.7842 (mtm) cc_final: 0.7497 (mtm) REVERT: C 100 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7039 (mt-10) REVERT: C 104 GLU cc_start: 0.7739 (pm20) cc_final: 0.6458 (tm-30) REVERT: C 107 LYS cc_start: 0.7662 (mttt) cc_final: 0.7280 (mttp) REVERT: C 176 GLU cc_start: 0.7639 (tt0) cc_final: 0.7140 (mt-10) REVERT: C 190 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.6741 (mtm180) REVERT: C 194 SER cc_start: 0.8692 (m) cc_final: 0.8416 (p) REVERT: C 257 GLN cc_start: 0.7764 (pt0) cc_final: 0.7258 (tp-100) REVERT: C 262 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7975 (mptt) REVERT: C 302 ARG cc_start: 0.7684 (ptm160) cc_final: 0.7223 (tmt-80) REVERT: C 381 GLN cc_start: 0.7499 (mp10) cc_final: 0.5907 (mm-40) REVERT: C 414 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7282 (tpp80) REVERT: C 570 MET cc_start: 0.8629 (mmm) cc_final: 0.8056 (mmm) REVERT: D 30 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: D 35 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8040 (ttt90) REVERT: D 40 GLN cc_start: 0.7421 (tt0) cc_final: 0.7129 (mt0) REVERT: D 51 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7705 (mm-40) REVERT: D 64 LEU cc_start: 0.8054 (mt) cc_final: 0.7780 (mt) REVERT: D 93 GLU cc_start: 0.7867 (mp0) cc_final: 0.7640 (mp0) REVERT: D 99 MET cc_start: 0.7867 (mtm) cc_final: 0.7647 (mtm) REVERT: D 100 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7036 (mt-10) REVERT: D 104 GLU cc_start: 0.7762 (pm20) cc_final: 0.6488 (tm-30) REVERT: D 107 LYS cc_start: 0.7652 (mttt) cc_final: 0.7273 (mttp) REVERT: D 176 GLU cc_start: 0.7623 (tt0) cc_final: 0.7132 (mt-10) REVERT: D 190 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6742 (mtm180) REVERT: D 194 SER cc_start: 0.8660 (m) cc_final: 0.8384 (p) REVERT: D 257 GLN cc_start: 0.7771 (pt0) cc_final: 0.7274 (tp-100) REVERT: D 262 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8006 (mptt) REVERT: D 302 ARG cc_start: 0.7691 (ptm160) cc_final: 0.7219 (tmt-80) REVERT: D 381 GLN cc_start: 0.7471 (mp10) cc_final: 0.5870 (mm-40) REVERT: D 414 ARG cc_start: 0.7692 (tpp80) cc_final: 0.7299 (tpp80) REVERT: D 570 MET cc_start: 0.8624 (mmm) cc_final: 0.8051 (mmm) outliers start: 64 outliers final: 24 residues processed: 314 average time/residue: 2.1545 time to fit residues: 754.6206 Evaluate side-chains 311 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 3.841 ------------------------------------------------------------------------------- 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 35 ARG 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 30 GLU Chi-restraints excluded: chain D residue 35 ARG 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 102 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN A 509 HIS ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 509 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 509 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3434 r_free = 0.3434 target = 0.125558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.098572 restraints weight = 22947.542| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.45 r_work: 0.2971 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20304 Z= 0.133 Angle : 0.497 7.772 27520 Z= 0.258 Chirality : 0.038 0.152 3124 Planarity : 0.004 0.038 3404 Dihedral : 11.897 164.459 3444 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.74 % Allowed : 10.14 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.17), residues: 2384 helix: 1.81 (0.12), residues: 1512 sheet: 0.48 (0.55), residues: 68 loop : 0.81 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 593 HIS 0.004 0.001 HIS A 201 PHE 0.009 0.001 PHE D 472 TYR 0.014 0.002 TYR A 555 ARG 0.003 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 1181) hydrogen bonds : angle 4.01483 ( 3363) covalent geometry : bond 0.00306 (20304) covalent geometry : angle 0.49700 (27520) *********************** 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 343 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: A 40 GLN cc_start: 0.7668 (tt0) cc_final: 0.7429 (mt0) REVERT: A 51 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7817 (mm-40) REVERT: A 93 GLU cc_start: 0.8013 (mp0) cc_final: 0.7772 (mp0) REVERT: A 99 MET cc_start: 0.8010 (mtm) cc_final: 0.7664 (mtm) REVERT: A 100 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 104 GLU cc_start: 0.7739 (pm20) cc_final: 0.6464 (tm-30) REVERT: A 107 LYS cc_start: 0.7745 (mttt) cc_final: 0.7372 (mttp) REVERT: A 176 GLU cc_start: 0.7715 (tt0) cc_final: 0.7271 (mt-10) REVERT: A 190 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6884 (mtm180) REVERT: A 194 SER cc_start: 0.8730 (m) cc_final: 0.8469 (p) REVERT: A 257 GLN cc_start: 0.7952 (pt0) cc_final: 0.7609 (tp-100) REVERT: A 262 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8116 (mptt) REVERT: A 302 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7438 (tmt-80) REVERT: A 381 GLN cc_start: 0.7637 (mp10) cc_final: 0.6168 (mm-40) REVERT: A 414 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7503 (tpp80) REVERT: B 30 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 35 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (ttt90) REVERT: B 40 GLN cc_start: 0.7684 (tt0) cc_final: 0.7436 (mt0) REVERT: B 51 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7809 (mm-40) REVERT: B 93 GLU cc_start: 0.8010 (mp0) cc_final: 0.7772 (mp0) REVERT: B 99 MET cc_start: 0.8006 (mtm) cc_final: 0.7659 (mtm) REVERT: B 100 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7084 (mt-10) REVERT: B 104 GLU cc_start: 0.7757 (pm20) cc_final: 0.6481 (tm-30) REVERT: B 107 LYS cc_start: 0.7744 (mttt) cc_final: 0.7372 (mttp) REVERT: B 176 GLU cc_start: 0.7703 (tt0) cc_final: 0.7268 (mt-10) REVERT: B 190 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6872 (mtm180) REVERT: B 194 SER cc_start: 0.8733 (m) cc_final: 0.8467 (p) REVERT: B 257 GLN cc_start: 0.7955 (pt0) cc_final: 0.7617 (tp-100) REVERT: B 262 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8122 (mptt) REVERT: B 302 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7438 (tmt-80) REVERT: B 381 GLN cc_start: 0.7633 (mp10) cc_final: 0.6162 (mm-40) REVERT: B 414 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7519 (tpp80) REVERT: C 30 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: C 40 GLN cc_start: 0.7668 (tt0) cc_final: 0.7407 (mt0) REVERT: C 51 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7809 (mm-40) REVERT: C 93 GLU cc_start: 0.8002 (mp0) cc_final: 0.7759 (mp0) REVERT: C 99 MET cc_start: 0.7997 (mtm) cc_final: 0.7655 (mtm) REVERT: C 100 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7082 (mt-10) REVERT: C 104 GLU cc_start: 0.7756 (pm20) cc_final: 0.6478 (tm-30) REVERT: C 107 LYS cc_start: 0.7748 (mttt) cc_final: 0.7375 (mttp) REVERT: C 176 GLU cc_start: 0.7710 (tt0) cc_final: 0.7276 (mt-10) REVERT: C 190 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.6900 (mtm180) REVERT: C 194 SER cc_start: 0.8736 (m) cc_final: 0.8472 (p) REVERT: C 257 GLN cc_start: 0.7954 (pt0) cc_final: 0.7603 (tp-100) REVERT: C 262 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8112 (mptt) REVERT: C 302 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7439 (tmt-80) REVERT: C 381 GLN cc_start: 0.7645 (mp10) cc_final: 0.6088 (mm-40) REVERT: C 414 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7506 (tpp80) REVERT: D 30 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7258 (mp0) REVERT: D 35 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8257 (ttt90) REVERT: D 51 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7851 (mm-40) REVERT: D 93 GLU cc_start: 0.8011 (mp0) cc_final: 0.7772 (mp0) REVERT: D 99 MET cc_start: 0.8047 (mtm) cc_final: 0.7813 (mtm) REVERT: D 100 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7099 (mt-10) REVERT: D 104 GLU cc_start: 0.7753 (pm20) cc_final: 0.6482 (tm-30) REVERT: D 107 LYS cc_start: 0.7755 (mttt) cc_final: 0.7387 (mttp) REVERT: D 176 GLU cc_start: 0.7724 (tt0) cc_final: 0.7284 (mt-10) REVERT: D 190 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.6904 (mtm180) REVERT: D 194 SER cc_start: 0.8740 (m) cc_final: 0.8480 (p) REVERT: D 257 GLN cc_start: 0.7960 (pt0) cc_final: 0.7610 (tp-100) REVERT: D 262 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8125 (mptt) REVERT: D 302 ARG cc_start: 0.7824 (ptm160) cc_final: 0.7436 (tmt-80) REVERT: D 381 GLN cc_start: 0.7629 (mp10) cc_final: 0.6109 (mm-40) REVERT: D 414 ARG cc_start: 0.7819 (tpp80) cc_final: 0.7479 (tpp80) outliers start: 57 outliers final: 24 residues processed: 320 average time/residue: 1.5742 time to fit residues: 559.0879 Evaluate side-chains 317 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 2.407 ------------------------------------------------------------------------------- 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 35 ARG 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 35 ARG 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 206 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 34 optimal weight: 0.0010 chunk 233 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 418 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101635 restraints weight = 22842.718| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.43 r_work: 0.3021 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20304 Z= 0.100 Angle : 0.468 8.058 27520 Z= 0.242 Chirality : 0.037 0.159 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.626 161.033 3444 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.31 % Allowed : 10.62 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.17), residues: 2384 helix: 1.99 (0.13), residues: 1508 sheet: 0.50 (0.57), residues: 68 loop : 0.78 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 593 HIS 0.002 0.001 HIS B 201 PHE 0.008 0.001 PHE A 456 TYR 0.013 0.001 TYR A 555 ARG 0.004 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 1181) hydrogen bonds : angle 3.92850 ( 3363) covalent geometry : bond 0.00208 (20304) covalent geometry : angle 0.46831 (27520) *********************** 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 340 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7420 (mp0) REVERT: A 35 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8284 (ttt90) REVERT: A 51 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7942 (mm-40) REVERT: A 93 GLU cc_start: 0.8084 (mp0) cc_final: 0.7785 (mp0) REVERT: A 99 MET cc_start: 0.8058 (mtm) cc_final: 0.7801 (mtm) REVERT: A 100 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 104 GLU cc_start: 0.7818 (pm20) cc_final: 0.6592 (tm-30) REVERT: A 107 LYS cc_start: 0.7799 (mttt) cc_final: 0.7448 (mttp) REVERT: A 176 GLU cc_start: 0.7776 (tt0) cc_final: 0.7391 (mt-10) REVERT: A 190 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.6901 (mtm180) REVERT: A 194 SER cc_start: 0.8725 (m) cc_final: 0.8508 (p) REVERT: A 257 GLN cc_start: 0.7974 (pt0) cc_final: 0.7714 (tp-100) REVERT: A 298 SER cc_start: 0.8860 (p) cc_final: 0.8654 (m) REVERT: A 302 ARG cc_start: 0.7808 (ptm160) cc_final: 0.7548 (tmt-80) REVERT: A 381 GLN cc_start: 0.7655 (mp10) cc_final: 0.6203 (mm-40) REVERT: A 414 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7515 (tpp80) REVERT: B 30 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7363 (mp0) REVERT: B 51 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7928 (mm-40) REVERT: B 93 GLU cc_start: 0.8074 (mp0) cc_final: 0.7835 (mp0) REVERT: B 99 MET cc_start: 0.8064 (mtm) cc_final: 0.7806 (mtm) REVERT: B 100 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7152 (mt-10) REVERT: B 104 GLU cc_start: 0.7828 (pm20) cc_final: 0.6602 (tm-30) REVERT: B 107 LYS cc_start: 0.7800 (mttt) cc_final: 0.7455 (mttp) REVERT: B 176 GLU cc_start: 0.7761 (tt0) cc_final: 0.7384 (mt-10) REVERT: B 190 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6860 (mtm180) REVERT: B 194 SER cc_start: 0.8739 (m) cc_final: 0.8505 (p) REVERT: B 257 GLN cc_start: 0.8005 (pt0) cc_final: 0.7768 (tp-100) REVERT: B 302 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7549 (tmt-80) REVERT: B 381 GLN cc_start: 0.7665 (mp10) cc_final: 0.6217 (mm-40) REVERT: B 414 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7519 (tpp80) REVERT: C 30 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7370 (mp0) REVERT: C 51 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7935 (mm-40) REVERT: C 93 GLU cc_start: 0.8076 (mp0) cc_final: 0.7833 (mp0) REVERT: C 99 MET cc_start: 0.8068 (mtm) cc_final: 0.7813 (mtm) REVERT: C 100 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7142 (mt-10) REVERT: C 104 GLU cc_start: 0.7812 (pm20) cc_final: 0.6568 (tm-30) REVERT: C 107 LYS cc_start: 0.7814 (mttt) cc_final: 0.7467 (mttp) REVERT: C 176 GLU cc_start: 0.7767 (tt0) cc_final: 0.7386 (mt-10) REVERT: C 190 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.6885 (mtm180) REVERT: C 194 SER cc_start: 0.8741 (m) cc_final: 0.8507 (p) REVERT: C 257 GLN cc_start: 0.7996 (pt0) cc_final: 0.7766 (tp-100) REVERT: C 302 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7552 (tmt-80) REVERT: C 381 GLN cc_start: 0.7688 (mp10) cc_final: 0.6205 (mm-40) REVERT: C 414 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7512 (tpp80) REVERT: D 30 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: D 51 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7945 (mm-40) REVERT: D 93 GLU cc_start: 0.8076 (mp0) cc_final: 0.7835 (mp0) REVERT: D 100 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7148 (mt-10) REVERT: D 104 GLU cc_start: 0.7832 (pm20) cc_final: 0.6605 (tm-30) REVERT: D 107 LYS cc_start: 0.7804 (mttt) cc_final: 0.7459 (mttp) REVERT: D 176 GLU cc_start: 0.7807 (tt0) cc_final: 0.7421 (mt-10) REVERT: D 190 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.6905 (mtm180) REVERT: D 194 SER cc_start: 0.8741 (m) cc_final: 0.8523 (p) REVERT: D 257 GLN cc_start: 0.7977 (pt0) cc_final: 0.7717 (tp-100) REVERT: D 302 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7548 (tmt-80) REVERT: D 381 GLN cc_start: 0.7680 (mp10) cc_final: 0.6197 (mm-40) REVERT: D 414 ARG cc_start: 0.7806 (tpp80) cc_final: 0.7503 (tpp80) outliers start: 48 outliers final: 20 residues processed: 328 average time/residue: 1.6017 time to fit residues: 581.8906 Evaluate side-chains 307 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 281 time to evaluate : 2.401 ------------------------------------------------------------------------------- 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 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 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 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 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 222 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN D 261 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099731 restraints weight = 22737.849| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.44 r_work: 0.2995 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20304 Z= 0.118 Angle : 0.492 9.215 27520 Z= 0.253 Chirality : 0.038 0.162 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.606 158.382 3444 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.64 % Allowed : 11.06 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2384 helix: 1.96 (0.13), residues: 1512 sheet: 0.39 (0.58), residues: 68 loop : 0.83 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 593 HIS 0.004 0.001 HIS C 201 PHE 0.008 0.001 PHE D 537 TYR 0.013 0.001 TYR A 555 ARG 0.007 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1181) hydrogen bonds : angle 3.94966 ( 3363) covalent geometry : bond 0.00264 (20304) covalent geometry : angle 0.49182 (27520) *********************** 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 335 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7286 (mp0) REVERT: A 35 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8217 (ttt90) REVERT: A 51 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7859 (mm-40) REVERT: A 93 GLU cc_start: 0.8060 (mp0) cc_final: 0.7770 (mp0) REVERT: A 99 MET cc_start: 0.7941 (mtm) cc_final: 0.7640 (mtm) REVERT: A 100 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 104 GLU cc_start: 0.7782 (pm20) cc_final: 0.6528 (tm-30) REVERT: A 107 LYS cc_start: 0.7730 (mttt) cc_final: 0.7352 (mttp) REVERT: A 176 GLU cc_start: 0.7633 (tt0) cc_final: 0.7304 (mt-10) REVERT: A 190 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6871 (mtm180) REVERT: A 194 SER cc_start: 0.8709 (m) cc_final: 0.8462 (p) REVERT: A 257 GLN cc_start: 0.7868 (pt0) cc_final: 0.7616 (tp-100) REVERT: A 262 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8164 (mptt) REVERT: A 298 SER cc_start: 0.8826 (p) cc_final: 0.8576 (m) REVERT: A 302 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7515 (tmt-80) REVERT: A 381 GLN cc_start: 0.7593 (mp10) cc_final: 0.7218 (mp10) REVERT: A 414 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7399 (tpp80) REVERT: A 491 MET cc_start: 0.8805 (mtp) cc_final: 0.8533 (mtt) REVERT: B 30 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: B 51 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7843 (mm-40) REVERT: B 93 GLU cc_start: 0.8049 (mp0) cc_final: 0.7786 (mp0) REVERT: B 99 MET cc_start: 0.7946 (mtm) cc_final: 0.7645 (mtm) REVERT: B 100 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7093 (mt-10) REVERT: B 104 GLU cc_start: 0.7768 (pm20) cc_final: 0.6504 (tm-30) REVERT: B 107 LYS cc_start: 0.7736 (mttt) cc_final: 0.7360 (mttp) REVERT: B 176 GLU cc_start: 0.7632 (tt0) cc_final: 0.7304 (mt-10) REVERT: B 190 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.6861 (mtm180) REVERT: B 194 SER cc_start: 0.8708 (m) cc_final: 0.8450 (p) REVERT: B 257 GLN cc_start: 0.7927 (pt0) cc_final: 0.7558 (tp-100) REVERT: B 262 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8150 (mptt) REVERT: B 302 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7485 (tmt-80) REVERT: B 381 GLN cc_start: 0.7625 (mp10) cc_final: 0.7248 (mp10) REVERT: B 414 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7396 (tpp80) REVERT: B 491 MET cc_start: 0.8796 (mtp) cc_final: 0.8522 (mtt) REVERT: C 30 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: C 51 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7854 (mm-40) REVERT: C 93 GLU cc_start: 0.8045 (mp0) cc_final: 0.7778 (mp0) REVERT: C 99 MET cc_start: 0.7934 (mtm) cc_final: 0.7637 (mtm) REVERT: C 100 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7099 (mt-10) REVERT: C 104 GLU cc_start: 0.7778 (pm20) cc_final: 0.6515 (tm-30) REVERT: C 107 LYS cc_start: 0.7744 (mttt) cc_final: 0.7368 (mttp) REVERT: C 176 GLU cc_start: 0.7634 (tt0) cc_final: 0.7302 (mt-10) REVERT: C 190 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6856 (mtm180) REVERT: C 194 SER cc_start: 0.8710 (m) cc_final: 0.8451 (p) REVERT: C 257 GLN cc_start: 0.7917 (pt0) cc_final: 0.7517 (tp-100) REVERT: C 262 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8127 (mptt) REVERT: C 302 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7470 (tmt-80) REVERT: C 381 GLN cc_start: 0.7645 (mp10) cc_final: 0.6151 (mm-40) REVERT: C 414 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7387 (tpp80) REVERT: C 491 MET cc_start: 0.8798 (mtp) cc_final: 0.8529 (mtt) REVERT: D 30 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: D 51 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7867 (mm-40) REVERT: D 93 GLU cc_start: 0.8090 (mp0) cc_final: 0.7770 (mp0) REVERT: D 100 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7107 (mt-10) REVERT: D 104 GLU cc_start: 0.7784 (pm20) cc_final: 0.6528 (tm-30) REVERT: D 107 LYS cc_start: 0.7738 (mttt) cc_final: 0.7363 (mttp) REVERT: D 176 GLU cc_start: 0.7653 (tt0) cc_final: 0.7314 (mt-10) REVERT: D 190 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.6884 (mtm180) REVERT: D 194 SER cc_start: 0.8718 (m) cc_final: 0.8463 (p) REVERT: D 257 GLN cc_start: 0.7876 (pt0) cc_final: 0.7618 (tp-100) REVERT: D 262 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8155 (mptt) REVERT: D 302 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7511 (tmt-80) REVERT: D 381 GLN cc_start: 0.7636 (mp10) cc_final: 0.6140 (mm-40) REVERT: D 414 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7397 (tpp80) REVERT: D 491 MET cc_start: 0.8794 (mtp) cc_final: 0.8521 (mtt) outliers start: 55 outliers final: 23 residues processed: 314 average time/residue: 1.5798 time to fit residues: 552.3727 Evaluate side-chains 308 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 2.346 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 261 GLN B 418 GLN C 261 GLN C 418 GLN D 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097112 restraints weight = 22723.269| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.44 r_work: 0.2952 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20304 Z= 0.153 Angle : 0.531 8.774 27520 Z= 0.274 Chirality : 0.040 0.204 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.754 157.531 3444 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.21 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2384 helix: 1.83 (0.13), residues: 1508 sheet: -1.65 (0.44), residues: 108 loop : 0.85 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS A 201 PHE 0.010 0.002 PHE B 472 TYR 0.014 0.002 TYR B 555 ARG 0.006 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 1181) hydrogen bonds : angle 4.05637 ( 3363) covalent geometry : bond 0.00361 (20304) covalent geometry : angle 0.53092 (27520) *********************** 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 323 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7274 (mp0) REVERT: A 35 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8280 (ttt90) REVERT: A 51 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7913 (mm-40) REVERT: A 93 GLU cc_start: 0.8118 (mp0) cc_final: 0.7866 (mp0) REVERT: A 99 MET cc_start: 0.8063 (mtm) cc_final: 0.7752 (mtm) REVERT: A 100 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7134 (mt-10) REVERT: A 104 GLU cc_start: 0.7766 (pm20) cc_final: 0.6504 (tm-30) REVERT: A 107 LYS cc_start: 0.7722 (mttt) cc_final: 0.7335 (mttp) REVERT: A 176 GLU cc_start: 0.7663 (tt0) cc_final: 0.7283 (mt-10) REVERT: A 190 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6972 (mtm180) REVERT: A 194 SER cc_start: 0.8733 (m) cc_final: 0.8473 (p) REVERT: A 257 GLN cc_start: 0.7970 (pt0) cc_final: 0.7647 (tp-100) REVERT: A 262 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8141 (mptt) REVERT: A 302 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7542 (tmt-80) REVERT: A 414 ARG cc_start: 0.7857 (ttp80) cc_final: 0.7471 (tpp80) REVERT: A 491 MET cc_start: 0.8829 (mtp) cc_final: 0.8557 (mtt) REVERT: B 30 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: B 51 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7904 (mm-40) REVERT: B 93 GLU cc_start: 0.8103 (mp0) cc_final: 0.7853 (mp0) REVERT: B 99 MET cc_start: 0.8066 (mtm) cc_final: 0.7757 (mtm) REVERT: B 100 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 104 GLU cc_start: 0.7786 (pm20) cc_final: 0.6529 (tm-30) REVERT: B 107 LYS cc_start: 0.7752 (mttt) cc_final: 0.7376 (mttp) REVERT: B 176 GLU cc_start: 0.7653 (tt0) cc_final: 0.7274 (mt-10) REVERT: B 190 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.6954 (mtm180) REVERT: B 194 SER cc_start: 0.8736 (m) cc_final: 0.8461 (p) REVERT: B 257 GLN cc_start: 0.7948 (pt0) cc_final: 0.7689 (tp-100) REVERT: B 262 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8151 (mptt) REVERT: B 302 ARG cc_start: 0.7906 (ptm160) cc_final: 0.7545 (tmt-80) REVERT: B 414 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7476 (tpp80) REVERT: B 491 MET cc_start: 0.8841 (mtp) cc_final: 0.8578 (mtt) REVERT: C 30 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: C 51 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7897 (mm-40) REVERT: C 93 GLU cc_start: 0.8096 (mp0) cc_final: 0.7841 (mp0) REVERT: C 99 MET cc_start: 0.8056 (mtm) cc_final: 0.7753 (mtm) REVERT: C 100 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7134 (mt-10) REVERT: C 104 GLU cc_start: 0.7776 (pm20) cc_final: 0.6508 (tm-30) REVERT: C 107 LYS cc_start: 0.7751 (mttt) cc_final: 0.7374 (mttp) REVERT: C 176 GLU cc_start: 0.7657 (tt0) cc_final: 0.7279 (mt-10) REVERT: C 190 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.6949 (mtm180) REVERT: C 194 SER cc_start: 0.8733 (m) cc_final: 0.8457 (p) REVERT: C 257 GLN cc_start: 0.7948 (pt0) cc_final: 0.7659 (tp-100) REVERT: C 262 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8146 (mptt) REVERT: C 302 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7541 (tmt-80) REVERT: C 414 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7450 (tpp80) REVERT: C 491 MET cc_start: 0.8843 (mtp) cc_final: 0.8583 (mtt) REVERT: D 30 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: D 51 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7916 (mm-40) REVERT: D 93 GLU cc_start: 0.8183 (mp0) cc_final: 0.7942 (mp0) REVERT: D 104 GLU cc_start: 0.7812 (pm20) cc_final: 0.6562 (tm-30) REVERT: D 107 LYS cc_start: 0.7750 (mttt) cc_final: 0.7374 (mttp) REVERT: D 176 GLU cc_start: 0.7676 (tt0) cc_final: 0.7293 (mt-10) REVERT: D 190 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6948 (mtm180) REVERT: D 194 SER cc_start: 0.8737 (m) cc_final: 0.8457 (p) REVERT: D 257 GLN cc_start: 0.7973 (pt0) cc_final: 0.7647 (tp-100) REVERT: D 262 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8145 (mptt) REVERT: D 302 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7545 (tmt-80) REVERT: D 414 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7517 (tpp80) REVERT: D 491 MET cc_start: 0.8837 (mtp) cc_final: 0.8574 (mtt) outliers start: 46 outliers final: 25 residues processed: 311 average time/residue: 1.5316 time to fit residues: 528.8301 Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 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 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 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 356 ASP 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 129 optimal weight: 1.9990 chunk 21 optimal weight: 0.0470 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 418 GLN C 261 GLN C 418 GLN 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 = 0.3443 r_free = 0.3443 target = 0.126274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.099537 restraints weight = 22684.833| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.43 r_work: 0.2996 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20304 Z= 0.114 Angle : 0.493 8.751 27520 Z= 0.254 Chirality : 0.038 0.178 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.447 156.614 3444 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.02 % Allowed : 11.78 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.17), residues: 2384 helix: 1.80 (0.13), residues: 1532 sheet: -1.66 (0.46), residues: 100 loop : 0.98 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.008 0.001 PHE D 537 TYR 0.013 0.001 TYR B 555 ARG 0.006 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 1181) hydrogen bonds : angle 3.99601 ( 3363) covalent geometry : bond 0.00251 (20304) covalent geometry : angle 0.49255 (27520) *********************** 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 319 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 35 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8197 (ttt90) REVERT: A 51 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7866 (mm-40) REVERT: A 93 GLU cc_start: 0.8078 (mp0) cc_final: 0.7792 (mp0) REVERT: A 99 MET cc_start: 0.7933 (mtm) cc_final: 0.7648 (mtm) REVERT: A 100 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7093 (mt-10) REVERT: A 104 GLU cc_start: 0.7836 (pm20) cc_final: 0.6599 (tm-30) REVERT: A 107 LYS cc_start: 0.7710 (mttt) cc_final: 0.7320 (mttp) REVERT: A 176 GLU cc_start: 0.7617 (tt0) cc_final: 0.7238 (mt-10) REVERT: A 190 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6890 (mtm180) REVERT: A 194 SER cc_start: 0.8713 (m) cc_final: 0.8460 (p) REVERT: A 257 GLN cc_start: 0.7853 (pt0) cc_final: 0.7583 (tp-100) REVERT: A 262 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8164 (mptt) REVERT: A 298 SER cc_start: 0.8780 (p) cc_final: 0.8543 (m) REVERT: A 302 ARG cc_start: 0.7851 (ptm160) cc_final: 0.7518 (tmt-80) REVERT: A 381 GLN cc_start: 0.7798 (mp10) cc_final: 0.6078 (mm-40) REVERT: A 414 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7399 (tpp80) REVERT: A 491 MET cc_start: 0.8782 (mtp) cc_final: 0.8499 (mtt) REVERT: B 30 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 51 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7851 (mm-40) REVERT: B 93 GLU cc_start: 0.8071 (mp0) cc_final: 0.7787 (mp0) REVERT: B 99 MET cc_start: 0.7943 (mtm) cc_final: 0.7656 (mtm) REVERT: B 100 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 104 GLU cc_start: 0.7843 (pm20) cc_final: 0.6599 (tm-30) REVERT: B 107 LYS cc_start: 0.7713 (mttt) cc_final: 0.7324 (mttp) REVERT: B 176 GLU cc_start: 0.7609 (tt0) cc_final: 0.7237 (mt-10) REVERT: B 190 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.6885 (mtm180) REVERT: B 194 SER cc_start: 0.8713 (m) cc_final: 0.8441 (p) REVERT: B 257 GLN cc_start: 0.7903 (pt0) cc_final: 0.7613 (tp-100) REVERT: B 262 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8146 (mptt) REVERT: B 302 ARG cc_start: 0.7878 (ptm160) cc_final: 0.7525 (tmt-80) REVERT: B 381 GLN cc_start: 0.7789 (mp10) cc_final: 0.6074 (mm-40) REVERT: B 414 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7408 (tpp80) REVERT: B 491 MET cc_start: 0.8782 (mtp) cc_final: 0.8507 (mtt) REVERT: C 30 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: C 51 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7847 (mm-40) REVERT: C 93 GLU cc_start: 0.8068 (mp0) cc_final: 0.7777 (mp0) REVERT: C 99 MET cc_start: 0.7931 (mtm) cc_final: 0.7647 (mtm) REVERT: C 100 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7095 (mt-10) REVERT: C 104 GLU cc_start: 0.7852 (pm20) cc_final: 0.6612 (tm-30) REVERT: C 107 LYS cc_start: 0.7724 (mttt) cc_final: 0.7335 (mttp) REVERT: C 176 GLU cc_start: 0.7608 (tt0) cc_final: 0.7236 (mt-10) REVERT: C 190 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6880 (mtm180) REVERT: C 194 SER cc_start: 0.8711 (m) cc_final: 0.8438 (p) REVERT: C 257 GLN cc_start: 0.7880 (pt0) cc_final: 0.7604 (tp-100) REVERT: C 262 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8152 (mptt) REVERT: C 302 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7518 (tmt-80) REVERT: C 381 GLN cc_start: 0.7789 (mp10) cc_final: 0.6092 (mm-40) REVERT: C 414 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7382 (tpp80) REVERT: C 491 MET cc_start: 0.8787 (mtp) cc_final: 0.8517 (mtt) REVERT: D 30 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: D 51 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7862 (mm-40) REVERT: D 93 GLU cc_start: 0.8178 (mp0) cc_final: 0.7867 (mp0) REVERT: D 104 GLU cc_start: 0.7862 (pm20) cc_final: 0.6633 (tm-30) REVERT: D 107 LYS cc_start: 0.7718 (mttt) cc_final: 0.7330 (mttp) REVERT: D 176 GLU cc_start: 0.7627 (tt0) cc_final: 0.7246 (mt-10) REVERT: D 190 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6884 (mtm180) REVERT: D 194 SER cc_start: 0.8710 (m) cc_final: 0.8433 (p) REVERT: D 257 GLN cc_start: 0.7852 (pt0) cc_final: 0.7583 (tp-100) REVERT: D 262 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8162 (mptt) REVERT: D 302 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7523 (tmt-80) REVERT: D 381 GLN cc_start: 0.7783 (mp10) cc_final: 0.6087 (mm-40) REVERT: D 414 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7394 (tpp80) REVERT: D 491 MET cc_start: 0.8780 (mtp) cc_final: 0.8508 (mtt) outliers start: 42 outliers final: 21 residues processed: 311 average time/residue: 1.5364 time to fit residues: 530.3242 Evaluate side-chains 306 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 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 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 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 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 171 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.099334 restraints weight = 22620.811| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.44 r_work: 0.2992 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20304 Z= 0.119 Angle : 0.504 8.851 27520 Z= 0.261 Chirality : 0.038 0.216 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.409 156.174 3444 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.07 % Allowed : 12.26 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2384 helix: 1.92 (0.13), residues: 1508 sheet: -1.58 (0.45), residues: 108 loop : 0.86 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE A 456 TYR 0.013 0.001 TYR D 555 ARG 0.006 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1181) hydrogen bonds : angle 4.02648 ( 3363) covalent geometry : bond 0.00266 (20304) covalent geometry : angle 0.50418 (27520) ********************** 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 324 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 35 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (ttt90) REVERT: A 51 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7883 (mm-40) REVERT: A 93 GLU cc_start: 0.8095 (mp0) cc_final: 0.7813 (mp0) REVERT: A 99 MET cc_start: 0.7942 (mtm) cc_final: 0.7678 (mtm) REVERT: A 100 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7098 (mt-10) REVERT: A 104 GLU cc_start: 0.7825 (pm20) cc_final: 0.6689 (tm-30) REVERT: A 107 LYS cc_start: 0.7692 (mttt) cc_final: 0.7344 (mttp) REVERT: A 176 GLU cc_start: 0.7606 (tt0) cc_final: 0.7225 (mt-10) REVERT: A 190 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.6886 (mtm180) REVERT: A 194 SER cc_start: 0.8706 (m) cc_final: 0.8450 (p) REVERT: A 257 GLN cc_start: 0.7859 (pt0) cc_final: 0.7649 (tp-100) REVERT: A 262 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8140 (mptt) REVERT: A 298 SER cc_start: 0.8797 (p) cc_final: 0.8532 (m) REVERT: A 302 ARG cc_start: 0.7855 (ptm160) cc_final: 0.7528 (tmt-80) REVERT: A 381 GLN cc_start: 0.7807 (mp10) cc_final: 0.6101 (mm-40) REVERT: A 414 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7278 (tpp80) REVERT: A 491 MET cc_start: 0.8792 (mtp) cc_final: 0.8508 (mtt) REVERT: B 30 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: B 51 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7870 (mm-40) REVERT: B 93 GLU cc_start: 0.8088 (mp0) cc_final: 0.7808 (mp0) REVERT: B 99 MET cc_start: 0.7945 (mtm) cc_final: 0.7668 (mtm) REVERT: B 100 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7116 (mt-10) REVERT: B 104 GLU cc_start: 0.7826 (pm20) cc_final: 0.6685 (tm-30) REVERT: B 107 LYS cc_start: 0.7691 (mttt) cc_final: 0.7340 (mttp) REVERT: B 176 GLU cc_start: 0.7605 (tt0) cc_final: 0.7224 (mt-10) REVERT: B 190 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6889 (mtm180) REVERT: B 194 SER cc_start: 0.8708 (m) cc_final: 0.8440 (p) REVERT: B 257 GLN cc_start: 0.7843 (pt0) cc_final: 0.7642 (tp-100) REVERT: B 262 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8143 (mptt) REVERT: B 302 ARG cc_start: 0.7880 (ptm160) cc_final: 0.7510 (tmt-80) REVERT: B 381 GLN cc_start: 0.7775 (mp10) cc_final: 0.6087 (mm-40) REVERT: B 414 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7273 (tpp80) REVERT: B 491 MET cc_start: 0.8781 (mtp) cc_final: 0.8501 (mtt) REVERT: C 30 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: C 51 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7866 (mm-40) REVERT: C 93 GLU cc_start: 0.8087 (mp0) cc_final: 0.7802 (mp0) REVERT: C 99 MET cc_start: 0.7953 (mtm) cc_final: 0.7680 (mtm) REVERT: C 100 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7095 (mt-10) REVERT: C 104 GLU cc_start: 0.7837 (pm20) cc_final: 0.6642 (tm-30) REVERT: C 107 LYS cc_start: 0.7713 (mttt) cc_final: 0.7345 (mttp) REVERT: C 176 GLU cc_start: 0.7600 (tt0) cc_final: 0.7223 (mt-10) REVERT: C 190 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6879 (mtm180) REVERT: C 194 SER cc_start: 0.8704 (m) cc_final: 0.8434 (p) REVERT: C 257 GLN cc_start: 0.7876 (pt0) cc_final: 0.7654 (tp-100) REVERT: C 262 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8138 (mptt) REVERT: C 302 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7503 (tmt-80) REVERT: C 381 GLN cc_start: 0.7797 (mp10) cc_final: 0.6101 (mm-40) REVERT: C 414 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7264 (tpp80) REVERT: C 491 MET cc_start: 0.8795 (mtp) cc_final: 0.8525 (mtt) REVERT: D 30 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: D 51 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7879 (mm-40) REVERT: D 93 GLU cc_start: 0.8162 (mp0) cc_final: 0.7858 (mp0) REVERT: D 104 GLU cc_start: 0.7903 (pm20) cc_final: 0.6699 (tm-30) REVERT: D 107 LYS cc_start: 0.7722 (mttt) cc_final: 0.7335 (mttp) REVERT: D 176 GLU cc_start: 0.7618 (tt0) cc_final: 0.7241 (mt-10) REVERT: D 190 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6878 (mtm180) REVERT: D 194 SER cc_start: 0.8709 (m) cc_final: 0.8432 (p) REVERT: D 257 GLN cc_start: 0.7856 (pt0) cc_final: 0.7646 (tp-100) REVERT: D 262 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8156 (mptt) REVERT: D 302 ARG cc_start: 0.7851 (ptm160) cc_final: 0.7508 (tmt-80) REVERT: D 381 GLN cc_start: 0.7792 (mp10) cc_final: 0.6094 (mm-40) REVERT: D 414 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7310 (tpp80) REVERT: D 491 MET cc_start: 0.8788 (mtp) cc_final: 0.8515 (mtt) outliers start: 43 outliers final: 22 residues processed: 311 average time/residue: 1.6189 time to fit residues: 559.3361 Evaluate side-chains 308 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 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 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 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 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 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 43 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.123936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.096907 restraints weight = 22736.062| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.44 r_work: 0.2956 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20304 Z= 0.154 Angle : 0.536 8.612 27520 Z= 0.276 Chirality : 0.040 0.190 3124 Planarity : 0.004 0.039 3404 Dihedral : 11.562 156.692 3444 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.78 % Allowed : 12.40 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.17), residues: 2384 helix: 1.78 (0.13), residues: 1508 sheet: -1.64 (0.44), residues: 108 loop : 0.81 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS D 201 PHE 0.010 0.002 PHE B 472 TYR 0.014 0.002 TYR C 555 ARG 0.006 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 1181) hydrogen bonds : angle 4.11116 ( 3363) covalent geometry : bond 0.00363 (20304) covalent geometry : angle 0.53597 (27520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17860.25 seconds wall clock time: 315 minutes 33.82 seconds (18933.82 seconds total)