Starting phenix.real_space_refine on Tue May 20 23:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0a_39700/05_2025/8z0a_39700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0a_39700/05_2025/8z0a_39700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0a_39700/05_2025/8z0a_39700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0a_39700/05_2025/8z0a_39700.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0a_39700/05_2025/8z0a_39700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0a_39700/05_2025/8z0a_39700.cif" } resolution = 2.84 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= -0.001 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 13268 2.51 5 N 3560 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20668 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4891 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Chain: "B" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4891 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Chain: "C" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4891 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Chain: "D" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4891 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 1 Chain: "E" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 276 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 276 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 276 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 276 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 12.12, per 1000 atoms: 0.59 Number of scatterers: 20668 At special positions: 0 Unit cell: (137.78, 110.39, 120.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3740 8.00 N 3560 7.00 C 13268 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: 4.98 Conformation dependent library (CDL) restraints added in 2.7 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4768 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 57.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.548A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.899A pdb=" N TRP A 124 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 145 through 169 Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.028A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.139A pdb=" N ARG A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.742A pdb=" N GLY A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.711A pdb=" N ALA A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 578 through 593 removed outlier: 3.820A pdb=" N SER A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.968A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.549A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 84 through 97 Processing helix chain 'B' and resid 119 through 124 removed outlier: 4.914A pdb=" N TRP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 145 through 169 Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.025A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.145A pdb=" N ARG B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.812A pdb=" N GLY B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 removed outlier: 3.721A pdb=" N ALA B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 559 through 577 Processing helix chain 'B' and resid 578 through 593 removed outlier: 3.829A pdb=" N SER B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 597 through 617 removed outlier: 4.968A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.560A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 119 through 124 removed outlier: 4.895A pdb=" N TRP C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.749A pdb=" N ASN C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 169 Processing helix chain 'C' and resid 181 through 193 removed outlier: 4.028A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.106A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 319 through 321 No H-bonds generated for 'chain 'C' and resid 319 through 321' Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 499 removed outlier: 3.719A pdb=" N GLY C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 522 removed outlier: 3.709A pdb=" N ALA C 517 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 559 through 577 Processing helix chain 'C' and resid 578 through 593 removed outlier: 3.825A pdb=" N SER C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 596 No H-bonds generated for 'chain 'C' and resid 594 through 596' Processing helix chain 'C' and resid 597 through 617 removed outlier: 4.969A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.559A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 119 through 124 removed outlier: 4.886A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.730A pdb=" N ASN D 138 " --> pdb=" O TRP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 169 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.592A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.145A pdb=" N ARG D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 293 through 312 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 376 through 411 Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 499 removed outlier: 3.698A pdb=" N GLY D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 522 removed outlier: 3.717A pdb=" N ALA D 517 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 559 through 577 Processing helix chain 'D' and resid 578 through 593 removed outlier: 3.783A pdb=" N SER D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 596 No H-bonds generated for 'chain 'D' and resid 594 through 596' Processing helix chain 'D' and resid 597 through 617 removed outlier: 4.968A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 477 Processing helix chain 'E' and resid 478 through 480 No H-bonds generated for 'chain 'E' and resid 478 through 480' Processing helix chain 'E' and resid 488 through 499 removed outlier: 3.604A pdb=" N ILE E 492 " --> pdb=" O ALA E 488 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE E 499 " --> pdb=" O LYS E 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 477 Processing helix chain 'F' and resid 478 through 480 No H-bonds generated for 'chain 'F' and resid 478 through 480' Processing helix chain 'F' and resid 488 through 499 removed outlier: 3.684A pdb=" N ILE F 492 " --> pdb=" O ALA F 488 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 499 " --> pdb=" O LYS F 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 477 Processing helix chain 'G' and resid 478 through 480 No H-bonds generated for 'chain 'G' and resid 478 through 480' Processing helix chain 'G' and resid 488 through 499 removed outlier: 3.675A pdb=" N ILE G 492 " --> pdb=" O ALA G 488 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE G 499 " --> pdb=" O LYS G 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 477 removed outlier: 3.567A pdb=" N ARG H 474 " --> pdb=" O GLU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 480 No H-bonds generated for 'chain 'H' and resid 478 through 480' Processing helix chain 'H' and resid 488 through 499 removed outlier: 3.708A pdb=" N ILE H 492 " --> pdb=" O ALA H 488 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE H 499 " --> pdb=" O LYS H 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.795A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 28 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS A 178 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 180 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 32 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 175 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE A 201 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 203 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 179 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL A 254 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 478 removed outlier: 8.907A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER A 526 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.512A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.825A pdb=" N TYR B 62 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL B 115 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 28 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS B 178 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS B 180 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 32 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 175 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 201 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 177 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR B 203 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 179 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL B 254 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 478 removed outlier: 8.909A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER B 526 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 6.506A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.808A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 28 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS C 178 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N HIS C 180 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL C 32 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 175 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE C 201 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA C 177 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR C 203 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE C 179 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL C 254 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 478 removed outlier: 8.912A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER C 526 " --> pdb=" O TYR C 551 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 375 removed outlier: 6.504A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.817A pdb=" N TYR D 62 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL D 115 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU D 64 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU D 117 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY D 66 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 65 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 28 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N HIS D 178 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N HIS D 180 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 32 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 175 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE D 201 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE D 179 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL D 254 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 473 through 478 removed outlier: 8.914A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER D 526 " --> pdb=" O TYR D 551 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 372 through 375 removed outlier: 6.508A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3060 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: 6.97 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6725 1.34 - 1.46: 4053 1.46 - 1.57: 10286 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 21212 Sorted by residual: bond pdb=" C TYR D 509 " pdb=" N GLU D 510 " ideal model delta sigma weight residual 1.332 1.322 0.009 7.50e-03 1.78e+04 1.53e+00 bond pdb=" C TYR B 509 " pdb=" N GLU B 510 " ideal model delta sigma weight residual 1.332 1.323 0.009 7.50e-03 1.78e+04 1.44e+00 bond pdb=" C TYR C 509 " pdb=" N GLU C 510 " ideal model delta sigma weight residual 1.332 1.323 0.009 7.50e-03 1.78e+04 1.37e+00 bond pdb=" CD GLU D 590 " pdb=" OE1 GLU D 590 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.33e+00 bond pdb=" C TYR A 509 " pdb=" N GLU A 510 " ideal model delta sigma weight residual 1.332 1.323 0.008 7.50e-03 1.78e+04 1.27e+00 ... (remaining 21207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 27706 1.20 - 2.41: 764 2.41 - 3.61: 197 3.61 - 4.81: 43 4.81 - 6.02: 14 Bond angle restraints: 28724 Sorted by residual: angle pdb=" N GLU D 590 " pdb=" CA GLU D 590 " pdb=" CB GLU D 590 " ideal model delta sigma weight residual 110.28 116.30 -6.02 1.55e+00 4.16e-01 1.51e+01 angle pdb=" C LYS B 286 " pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta sigma weight residual 121.70 127.06 -5.36 1.80e+00 3.09e-01 8.86e+00 angle pdb=" C LYS C 286 " pdb=" N PHE C 287 " pdb=" CA PHE C 287 " ideal model delta sigma weight residual 121.70 126.91 -5.21 1.80e+00 3.09e-01 8.37e+00 angle pdb=" CA GLU D 590 " pdb=" CB GLU D 590 " pdb=" CG GLU D 590 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.56e+00 angle pdb=" C GLU C 398 " pdb=" N LYS C 399 " pdb=" CA LYS C 399 " ideal model delta sigma weight residual 120.31 116.55 3.76 1.52e+00 4.33e-01 6.12e+00 ... (remaining 28719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 11210 17.26 - 34.52: 1032 34.52 - 51.78: 185 51.78 - 69.04: 33 69.04 - 86.30: 8 Dihedral angle restraints: 12468 sinusoidal: 5064 harmonic: 7404 Sorted by residual: dihedral pdb=" CA ASP C 317 " pdb=" CB ASP C 317 " pdb=" CG ASP C 317 " pdb=" OD1 ASP C 317 " ideal model delta sinusoidal sigma weight residual -30.00 -89.93 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA GLN C 294 " pdb=" C GLN C 294 " pdb=" N ASN C 295 " pdb=" CA ASN C 295 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 235 " pdb=" CG GLU A 235 " pdb=" CD GLU A 235 " pdb=" OE1 GLU A 235 " ideal model delta sinusoidal sigma weight residual 0.00 86.30 -86.30 1 3.00e+01 1.11e-03 9.98e+00 ... (remaining 12465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1690 0.028 - 0.056: 884 0.056 - 0.084: 286 0.084 - 0.111: 136 0.111 - 0.139: 52 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CA ILE A 201 " pdb=" N ILE A 201 " pdb=" C ILE A 201 " pdb=" CB ILE A 201 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3045 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 141 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 142 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 141 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO C 142 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 141 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO B 142 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.017 5.00e-02 4.00e+02 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3835 2.77 - 3.30: 19267 3.30 - 3.83: 35325 3.83 - 4.37: 43961 4.37 - 4.90: 75213 Nonbonded interactions: 177601 Sorted by model distance: nonbonded pdb=" OG SER B 300 " pdb=" OE2 GLU B 495 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP A 145 " pdb=" NE2 HIS A 240 " model vdw 2.248 3.120 nonbonded pdb=" OD2 ASP D 145 " pdb=" NE2 HIS D 240 " model vdw 2.251 3.120 nonbonded pdb=" OD2 ASP B 145 " pdb=" NE2 HIS B 240 " model vdw 2.253 3.120 nonbonded pdb=" OD2 ASP C 145 " pdb=" NE2 HIS C 240 " model vdw 2.257 3.120 ... (remaining 177596 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 44.850 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.033 21212 Z= 0.174 Angle : 0.533 6.016 28724 Z= 0.283 Chirality : 0.041 0.139 3048 Planarity : 0.004 0.039 3704 Dihedral : 13.587 86.297 7700 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2520 helix: 1.21 (0.14), residues: 1376 sheet: -1.43 (0.26), residues: 352 loop : -0.04 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 160 HIS 0.004 0.001 HIS D 250 PHE 0.011 0.001 PHE C 496 TYR 0.008 0.001 TYR B 144 ARG 0.004 0.000 ARG B 558 Details of bonding type rmsd hydrogen bonds : bond 0.13080 ( 1036) hydrogen bonds : angle 5.72177 ( 3060) covalent geometry : bond 0.00408 (21212) covalent geometry : angle 0.53291 (28724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 2.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 1.3903 time to fit residues: 520.4967 Evaluate side-chains 263 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 120 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 294 GLN A 356 ASN B 222 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN C 222 ASN C 356 ASN D 222 ASN D 250 HIS D 356 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153567 restraints weight = 20249.324| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.11 r_work: 0.3401 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21212 Z= 0.210 Angle : 0.553 6.328 28724 Z= 0.287 Chirality : 0.043 0.125 3048 Planarity : 0.004 0.047 3704 Dihedral : 4.083 14.450 2808 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.05 % Allowed : 8.27 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.17), residues: 2520 helix: 1.43 (0.14), residues: 1368 sheet: -1.44 (0.25), residues: 352 loop : -0.04 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 160 HIS 0.010 0.001 HIS A 250 PHE 0.012 0.002 PHE D 165 TYR 0.010 0.002 TYR A 68 ARG 0.006 0.001 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 1036) hydrogen bonds : angle 4.53120 ( 3060) covalent geometry : bond 0.00499 (21212) covalent geometry : angle 0.55295 (28724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 2.200 Fit side-chains REVERT: A 102 TYR cc_start: 0.7702 (m-80) cc_final: 0.7417 (m-80) REVERT: A 394 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8148 (m110) REVERT: A 437 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7183 (tmm-80) REVERT: A 580 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7372 (mmm160) REVERT: B 128 ARG cc_start: 0.6924 (ttp80) cc_final: 0.6698 (ptt90) REVERT: B 394 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8119 (m110) REVERT: B 402 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7550 (ttp-110) REVERT: B 420 LEU cc_start: 0.7666 (mt) cc_final: 0.7361 (mt) REVERT: B 437 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7199 (tmm-80) REVERT: C 394 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8107 (m110) REVERT: C 437 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7235 (tmm-80) REVERT: D 128 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6697 (ptt90) REVERT: D 394 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8151 (m110) REVERT: D 437 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7176 (tmm-80) REVERT: D 580 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7355 (mmm160) outliers start: 23 outliers final: 2 residues processed: 309 average time/residue: 1.4550 time to fit residues: 502.7005 Evaluate side-chains 283 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 580 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 145 optimal weight: 0.3980 chunk 80 optimal weight: 0.0870 chunk 218 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 149 ASN A 222 ASN A 356 ASN B 76 GLN B 149 ASN B 222 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN C 76 GLN C 149 ASN C 222 ASN C 356 ASN D 76 GLN D 149 ASN D 222 ASN D 356 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.196185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155809 restraints weight = 20278.471| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.12 r_work: 0.3425 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21212 Z= 0.138 Angle : 0.481 5.587 28724 Z= 0.251 Chirality : 0.040 0.125 3048 Planarity : 0.003 0.034 3704 Dihedral : 3.871 14.713 2808 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.19 % Allowed : 10.97 % Favored : 87.84 % 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: 1.04 (0.17), residues: 2520 helix: 1.80 (0.14), residues: 1344 sheet: -1.46 (0.25), residues: 352 loop : -0.04 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 160 HIS 0.003 0.001 HIS D 250 PHE 0.010 0.001 PHE C 496 TYR 0.008 0.001 TYR D 572 ARG 0.008 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 1036) hydrogen bonds : angle 4.22283 ( 3060) covalent geometry : bond 0.00320 (21212) covalent geometry : angle 0.48076 (28724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 316 time to evaluate : 2.258 Fit side-chains REVERT: A 102 TYR cc_start: 0.7697 (m-80) cc_final: 0.7429 (m-80) REVERT: A 394 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.8091 (m110) REVERT: A 402 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7400 (ttp-110) REVERT: A 437 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6940 (tmm-80) REVERT: B 128 ARG cc_start: 0.6948 (ttp80) cc_final: 0.6731 (ptt90) REVERT: B 394 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8062 (m110) REVERT: B 437 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.6976 (tmm-80) REVERT: C 394 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8075 (m110) REVERT: C 437 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6999 (tmm-80) REVERT: D 394 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8075 (m110) REVERT: D 437 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6990 (tmm-80) REVERT: D 590 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8079 (mt-10) outliers start: 26 outliers final: 5 residues processed: 333 average time/residue: 1.4298 time to fit residues: 535.6337 Evaluate side-chains 286 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 272 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 83 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN B 294 GLN B 356 ASN B 585 GLN C 76 GLN C 222 ASN C 356 ASN D 76 GLN D 222 ASN D 356 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155746 restraints weight = 20468.551| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.13 r_work: 0.3425 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21212 Z= 0.147 Angle : 0.487 6.000 28724 Z= 0.253 Chirality : 0.040 0.123 3048 Planarity : 0.003 0.034 3704 Dihedral : 3.866 16.363 2808 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.42 % Allowed : 12.29 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.17), residues: 2520 helix: 1.77 (0.14), residues: 1352 sheet: -1.46 (0.25), residues: 352 loop : -0.07 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 160 HIS 0.002 0.001 HIS D 268 PHE 0.010 0.001 PHE A 496 TYR 0.008 0.001 TYR A 68 ARG 0.008 0.000 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1036) hydrogen bonds : angle 4.14525 ( 3060) covalent geometry : bond 0.00345 (21212) covalent geometry : angle 0.48669 (28724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 2.287 Fit side-chains REVERT: A 394 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8065 (m110) REVERT: A 437 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7157 (tmm-80) REVERT: B 394 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (m110) REVERT: B 437 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7146 (tmm-80) REVERT: C 294 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: C 394 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8045 (m110) REVERT: C 437 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7151 (tmm-80) REVERT: D 394 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8046 (m110) REVERT: D 437 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7208 (tmm-80) REVERT: D 590 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8131 (mt-10) outliers start: 31 outliers final: 5 residues processed: 324 average time/residue: 1.4479 time to fit residues: 524.8414 Evaluate side-chains 290 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 275 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 5 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN C 76 GLN C 222 ASN C 356 ASN C 585 GLN D 76 GLN D 222 ASN D 356 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.192695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155354 restraints weight = 20373.304| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.12 r_work: 0.3396 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21212 Z= 0.218 Angle : 0.547 6.442 28724 Z= 0.282 Chirality : 0.043 0.124 3048 Planarity : 0.004 0.050 3704 Dihedral : 4.099 17.836 2808 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.78 % Allowed : 12.93 % Favored : 85.28 % 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: 0.81 (0.17), residues: 2520 helix: 1.66 (0.14), residues: 1336 sheet: -1.62 (0.25), residues: 376 loop : -0.12 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 160 HIS 0.003 0.001 HIS D 268 PHE 0.015 0.002 PHE A 375 TYR 0.010 0.002 TYR C 68 ARG 0.010 0.001 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 1036) hydrogen bonds : angle 4.31844 ( 3060) covalent geometry : bond 0.00522 (21212) covalent geometry : angle 0.54696 (28724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 2.225 Fit side-chains REVERT: A 294 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6681 (mm-40) REVERT: A 394 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (m110) REVERT: A 437 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7361 (tmm-80) REVERT: A 580 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7365 (mmm160) REVERT: B 394 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8201 (m110) REVERT: B 437 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7354 (tmm-80) REVERT: C 294 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: C 394 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8212 (m110) REVERT: C 437 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7355 (tmm-80) REVERT: D 394 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8237 (m110) REVERT: D 437 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7362 (tmm-80) REVERT: D 580 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7316 (mmm160) REVERT: H 481 ILE cc_start: 0.3822 (OUTLIER) cc_final: 0.3596 (tp) outliers start: 39 outliers final: 5 residues processed: 325 average time/residue: 1.4273 time to fit residues: 520.1827 Evaluate side-chains 288 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 580 ARG Chi-restraints excluded: chain H residue 481 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 213 optimal weight: 0.8980 chunk 135 optimal weight: 0.0870 chunk 12 optimal weight: 0.0870 chunk 10 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN C 76 GLN C 222 ASN C 356 ASN D 76 GLN D 222 ASN D 356 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.197949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.159246 restraints weight = 20320.270| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.96 r_work: 0.3472 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21212 Z= 0.096 Angle : 0.445 5.507 28724 Z= 0.233 Chirality : 0.039 0.124 3048 Planarity : 0.003 0.040 3704 Dihedral : 3.735 17.954 2808 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.78 % Allowed : 13.53 % Favored : 84.69 % 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: 1.18 (0.17), residues: 2520 helix: 1.93 (0.14), residues: 1344 sheet: -1.35 (0.25), residues: 352 loop : -0.03 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 160 HIS 0.002 0.000 HIS A 446 PHE 0.014 0.001 PHE A 375 TYR 0.005 0.001 TYR C 493 ARG 0.010 0.001 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 1036) hydrogen bonds : angle 4.00530 ( 3060) covalent geometry : bond 0.00209 (21212) covalent geometry : angle 0.44490 (28724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 2.191 Fit side-chains REVERT: A 294 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6464 (mm-40) REVERT: A 394 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8199 (m110) REVERT: B 355 VAL cc_start: 0.8374 (t) cc_final: 0.8041 (m) REVERT: B 394 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8194 (m110) REVERT: C 294 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6073 (tm-30) REVERT: C 355 VAL cc_start: 0.8362 (t) cc_final: 0.8036 (m) REVERT: C 394 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8210 (m110) REVERT: D 355 VAL cc_start: 0.8358 (t) cc_final: 0.8022 (m) REVERT: D 394 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8184 (m110) outliers start: 39 outliers final: 4 residues processed: 326 average time/residue: 1.4179 time to fit residues: 519.7708 Evaluate side-chains 296 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 286 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 176 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 243 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN B 294 GLN C 76 GLN C 222 ASN D 76 GLN D 222 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.196552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.157688 restraints weight = 20149.746| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.04 r_work: 0.3439 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21212 Z= 0.130 Angle : 0.474 7.482 28724 Z= 0.246 Chirality : 0.040 0.122 3048 Planarity : 0.003 0.046 3704 Dihedral : 3.787 19.185 2808 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.42 % Allowed : 14.35 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.17), residues: 2520 helix: 1.91 (0.14), residues: 1348 sheet: -1.46 (0.25), residues: 376 loop : -0.16 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 160 HIS 0.009 0.001 HIS B 250 PHE 0.014 0.001 PHE D 375 TYR 0.010 0.001 TYR A 102 ARG 0.011 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1036) hydrogen bonds : angle 4.03262 ( 3060) covalent geometry : bond 0.00304 (21212) covalent geometry : angle 0.47412 (28724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 2.700 Fit side-chains REVERT: A 294 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6527 (mm-40) REVERT: A 394 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8213 (m110) REVERT: A 580 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7349 (mmp80) REVERT: B 394 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8186 (m110) REVERT: C 294 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6164 (tm-30) REVERT: C 394 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8215 (m110) REVERT: C 416 MET cc_start: 0.8155 (mmm) cc_final: 0.7870 (mmt) REVERT: D 394 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8214 (m110) REVERT: D 580 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7311 (mmp80) outliers start: 31 outliers final: 11 residues processed: 313 average time/residue: 1.4049 time to fit residues: 494.9813 Evaluate side-chains 281 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 432 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 85 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN B 294 GLN C 76 GLN C 222 ASN D 76 GLN D 222 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.192721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152066 restraints weight = 20228.619| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.41 r_work: 0.3374 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21212 Z= 0.231 Angle : 0.557 6.816 28724 Z= 0.288 Chirality : 0.044 0.130 3048 Planarity : 0.004 0.052 3704 Dihedral : 4.122 19.998 2808 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.51 % Allowed : 14.99 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2520 helix: 1.67 (0.14), residues: 1344 sheet: -1.52 (0.25), residues: 372 loop : -0.15 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 160 HIS 0.009 0.001 HIS B 250 PHE 0.018 0.002 PHE A 375 TYR 0.012 0.002 TYR D 68 ARG 0.012 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 1036) hydrogen bonds : angle 4.29934 ( 3060) covalent geometry : bond 0.00559 (21212) covalent geometry : angle 0.55697 (28724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 2.422 Fit side-chains REVERT: A 294 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6609 (mm-40) REVERT: A 394 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8271 (m110) REVERT: A 416 MET cc_start: 0.8146 (mmm) cc_final: 0.7786 (mmt) REVERT: A 580 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7325 (mmm-85) REVERT: B 394 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (m110) REVERT: C 294 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6224 (tm-30) REVERT: C 394 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8253 (m110) REVERT: C 416 MET cc_start: 0.8109 (mmm) cc_final: 0.7865 (mmt) REVERT: D 394 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8258 (m110) REVERT: D 580 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7316 (mmm-85) REVERT: D 594 ASP cc_start: 0.7900 (m-30) cc_final: 0.7535 (p0) outliers start: 33 outliers final: 6 residues processed: 308 average time/residue: 1.3788 time to fit residues: 477.3014 Evaluate side-chains 282 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 4 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 242 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN B 294 GLN C 76 GLN C 222 ASN C 223 ASN D 76 GLN D 222 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.194558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152816 restraints weight = 20242.934| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.63 r_work: 0.3375 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21212 Z= 0.158 Angle : 0.511 6.458 28724 Z= 0.264 Chirality : 0.041 0.138 3048 Planarity : 0.004 0.056 3704 Dihedral : 4.004 20.728 2808 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 14.90 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2520 helix: 1.76 (0.14), residues: 1344 sheet: -1.46 (0.25), residues: 368 loop : -0.07 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 160 HIS 0.002 0.001 HIS D 250 PHE 0.022 0.001 PHE A 375 TYR 0.010 0.001 TYR C 572 ARG 0.012 0.001 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1036) hydrogen bonds : angle 4.19714 ( 3060) covalent geometry : bond 0.00374 (21212) covalent geometry : angle 0.51077 (28724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 2.441 Fit side-chains REVERT: A 294 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6607 (mm-40) REVERT: A 394 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8069 (m110) REVERT: A 580 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7207 (mmm-85) REVERT: B 394 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.8052 (m110) REVERT: C 294 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: C 394 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8055 (m110) REVERT: C 416 MET cc_start: 0.8173 (mmm) cc_final: 0.7862 (mmt) REVERT: C 580 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7262 (mmp80) REVERT: D 394 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8086 (m110) REVERT: D 580 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7185 (mmm-85) REVERT: F 481 ILE cc_start: 0.3609 (OUTLIER) cc_final: 0.3396 (tp) outliers start: 29 outliers final: 9 residues processed: 303 average time/residue: 1.4853 time to fit residues: 511.4061 Evaluate side-chains 282 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain F residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 213 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN B 294 GLN C 76 GLN D 76 GLN D 222 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.194724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155048 restraints weight = 20183.840| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.34 r_work: 0.3422 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21212 Z= 0.164 Angle : 0.518 6.744 28724 Z= 0.268 Chirality : 0.042 0.124 3048 Planarity : 0.004 0.055 3704 Dihedral : 4.013 21.369 2808 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.01 % Allowed : 15.68 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2520 helix: 1.75 (0.14), residues: 1344 sheet: -1.43 (0.25), residues: 368 loop : -0.08 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 160 HIS 0.002 0.001 HIS C 250 PHE 0.012 0.001 PHE C 496 TYR 0.011 0.001 TYR D 68 ARG 0.014 0.001 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 1036) hydrogen bonds : angle 4.22450 ( 3060) covalent geometry : bond 0.00390 (21212) covalent geometry : angle 0.51772 (28724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 2.508 Fit side-chains REVERT: A 294 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6552 (mm-40) REVERT: A 394 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8229 (m110) REVERT: A 416 MET cc_start: 0.8117 (mmm) cc_final: 0.7810 (mmt) REVERT: A 580 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7255 (mmm-85) REVERT: B 394 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8185 (m110) REVERT: C 294 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: C 394 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8188 (m110) REVERT: C 416 MET cc_start: 0.8118 (mmm) cc_final: 0.7859 (mmt) REVERT: C 580 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7309 (mmp80) REVERT: D 394 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8233 (m110) REVERT: D 425 PHE cc_start: 0.7909 (m-80) cc_final: 0.7529 (m-80) REVERT: D 580 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7244 (mmm-85) REVERT: F 481 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3360 (tp) outliers start: 22 outliers final: 8 residues processed: 298 average time/residue: 1.4234 time to fit residues: 476.3157 Evaluate side-chains 286 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain F residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 225 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 222 ASN A 356 ASN B 76 GLN B 222 ASN B 294 GLN C 76 GLN D 76 GLN D 222 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.197188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158135 restraints weight = 20257.903| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.99 r_work: 0.3449 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21212 Z= 0.115 Angle : 0.477 6.296 28724 Z= 0.248 Chirality : 0.040 0.124 3048 Planarity : 0.004 0.059 3704 Dihedral : 3.826 21.594 2808 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.19 % Allowed : 15.63 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2520 helix: 1.91 (0.14), residues: 1344 sheet: -1.28 (0.25), residues: 364 loop : -0.19 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 160 HIS 0.001 0.000 HIS B 268 PHE 0.011 0.001 PHE C 496 TYR 0.009 0.001 TYR C 572 ARG 0.014 0.001 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 1036) hydrogen bonds : angle 4.10361 ( 3060) covalent geometry : bond 0.00264 (21212) covalent geometry : angle 0.47740 (28724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14555.29 seconds wall clock time: 251 minutes 10.48 seconds (15070.48 seconds total)