Starting phenix.real_space_refine on Thu Sep 18 22:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0a_39700/09_2025/8z0a_39700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0a_39700/09_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_39700/09_2025/8z0a_39700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0a_39700/09_2025/8z0a_39700.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0a_39700/09_2025/8z0a_39700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0a_39700/09_2025/8z0a_39700.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.089 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.96, per 1000 atoms: 0.24 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: 1.88 Conformation dependent library (CDL) restraints added in 962.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.72 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: 4.12 Time building geometry restraints manager: 2.47 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: 0.02 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: 3.770 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (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 ARG 0.004 0.000 ARG B 558 TYR 0.008 0.001 TYR B 144 PHE 0.011 0.001 PHE C 496 TRP 0.015 0.002 TRP A 160 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00408 (21212) covalent geometry : angle 0.53291 (28724) hydrogen bonds : bond 0.13080 ( 1036) hydrogen bonds : angle 5.72177 ( 3060) *********************** 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 : 0.831 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.7335 time to fit residues: 273.1425 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 : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.0870 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 overall best weight: 1.1560 ------------------------------------------------------------------------------- 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 356 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.196217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155533 restraints weight = 20323.292| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.25 r_work: 0.3417 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0953 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= 0.152 Angle : 0.504 5.873 28724 Z= 0.263 Chirality : 0.041 0.125 3048 Planarity : 0.004 0.039 3704 Dihedral : 3.907 13.989 2808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.87 % Allowed : 7.95 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2520 helix: 1.59 (0.14), residues: 1368 sheet: -1.43 (0.25), residues: 352 loop : -0.03 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 354 TYR 0.009 0.001 TYR C 144 PHE 0.011 0.001 PHE A 165 TRP 0.015 0.001 TRP A 160 HIS 0.010 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00352 (21212) covalent geometry : angle 0.50438 (28724) hydrogen bonds : bond 0.04189 ( 1036) hydrogen bonds : angle 4.41247 ( 3060) *********************** 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 320 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 0.833 Fit side-chains REVERT: A 102 TYR cc_start: 0.7690 (m-80) cc_final: 0.7439 (m-80) REVERT: A 394 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8102 (m110) REVERT: A 437 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7103 (tmm-80) REVERT: B 128 ARG cc_start: 0.6886 (ttp80) cc_final: 0.6661 (ptt90) REVERT: B 394 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8067 (m110) REVERT: B 402 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7605 (ttp-110) REVERT: B 420 LEU cc_start: 0.7562 (mt) cc_final: 0.7252 (mt) REVERT: B 437 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7135 (tmm-80) REVERT: C 394 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8118 (m110) REVERT: C 437 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7160 (tmm-80) REVERT: D 128 ARG cc_start: 0.6876 (ttp80) cc_final: 0.6643 (ptt90) REVERT: D 394 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8130 (m110) REVERT: D 437 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7133 (tmm-80) outliers start: 19 outliers final: 2 residues processed: 311 average time/residue: 0.7389 time to fit residues: 255.8713 Evaluate side-chains 279 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 222 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN B 585 GLN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.192897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152614 restraints weight = 20423.673| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.52 r_work: 0.3370 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21212 Z= 0.250 Angle : 0.577 6.093 28724 Z= 0.298 Chirality : 0.044 0.129 3048 Planarity : 0.004 0.046 3704 Dihedral : 4.187 15.258 2808 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.01 % Allowed : 11.29 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.17), residues: 2520 helix: 1.53 (0.14), residues: 1340 sheet: -1.57 (0.25), residues: 372 loop : -0.12 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 354 TYR 0.010 0.002 TYR C 68 PHE 0.012 0.002 PHE B 327 TRP 0.017 0.002 TRP C 160 HIS 0.006 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00602 (21212) covalent geometry : angle 0.57669 (28724) hydrogen bonds : bond 0.04877 ( 1036) hydrogen bonds : angle 4.46484 ( 3060) *********************** 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 322 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 0.659 Fit side-chains REVERT: A 100 LYS cc_start: 0.7547 (tptt) cc_final: 0.7290 (tptp) REVERT: A 394 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8139 (m110) REVERT: A 437 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7292 (tmm-80) REVERT: B 394 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (m110) REVERT: B 437 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7332 (tmm-80) REVERT: C 394 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8122 (m110) REVERT: C 437 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7302 (tmm-80) REVERT: D 80 LEU cc_start: 0.8189 (mp) cc_final: 0.7952 (mt) REVERT: D 394 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (m110) REVERT: D 437 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7371 (tmm-80) outliers start: 22 outliers final: 2 residues processed: 317 average time/residue: 0.7481 time to fit residues: 264.0502 Evaluate side-chains 280 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 270 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 187 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.193774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153570 restraints weight = 20385.743| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.28 r_work: 0.3381 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1288 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= 0.197 Angle : 0.530 5.792 28724 Z= 0.275 Chirality : 0.042 0.128 3048 Planarity : 0.004 0.064 3704 Dihedral : 4.105 16.604 2808 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.28 % Allowed : 13.12 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.17), residues: 2520 helix: 1.62 (0.14), residues: 1336 sheet: -1.60 (0.25), residues: 372 loop : -0.07 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 354 TYR 0.009 0.001 TYR D 68 PHE 0.011 0.002 PHE D 327 TRP 0.015 0.002 TRP A 160 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00469 (21212) covalent geometry : angle 0.52951 (28724) hydrogen bonds : bond 0.04346 ( 1036) hydrogen bonds : angle 4.31337 ( 3060) *********************** 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 323 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 0.818 Fit side-chains REVERT: A 294 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6760 (mm-40) REVERT: A 394 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8114 (m110) REVERT: A 437 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7161 (tmm-80) REVERT: A 580 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7180 (mmm160) REVERT: B 394 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8079 (m110) REVERT: B 437 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7152 (tmm-80) REVERT: C 394 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8085 (m110) REVERT: C 437 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7208 (tmm-80) REVERT: D 394 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8075 (m110) REVERT: D 437 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7106 (tmm-80) REVERT: D 590 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8068 (mp0) outliers start: 28 outliers final: 5 residues processed: 309 average time/residue: 0.7254 time to fit residues: 248.9170 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 : 0.790 ------------------------------------------------------------------------------- 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 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 172 optimal weight: 0.0980 chunk 144 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.195054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157049 restraints weight = 20249.407| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.76 r_work: 0.3458 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1429 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= 0.140 Angle : 0.481 5.441 28724 Z= 0.251 Chirality : 0.041 0.127 3048 Planarity : 0.004 0.042 3704 Dihedral : 3.921 16.849 2808 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.01 % Allowed : 12.61 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2520 helix: 1.78 (0.14), residues: 1340 sheet: -1.60 (0.24), residues: 372 loop : -0.07 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 354 TYR 0.009 0.001 TYR C 572 PHE 0.012 0.001 PHE B 375 TRP 0.013 0.001 TRP A 160 HIS 0.002 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00327 (21212) covalent geometry : angle 0.48115 (28724) hydrogen bonds : bond 0.03799 ( 1036) hydrogen bonds : angle 4.14924 ( 3060) *********************** 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 354 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.936 Fit side-chains REVERT: A 294 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6618 (mm-40) REVERT: A 394 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8226 (m110) REVERT: A 437 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7173 (tmm-80) REVERT: B 394 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8193 (m110) REVERT: B 437 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7152 (tmm-80) REVERT: C 294 GLN cc_start: 0.6728 (mt0) cc_final: 0.6339 (tm-30) REVERT: C 394 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8191 (m110) REVERT: C 437 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7256 (tmm-80) REVERT: D 394 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8217 (m110) REVERT: D 437 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7159 (tmm-80) REVERT: D 590 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: H 481 ILE cc_start: 0.3714 (OUTLIER) cc_final: 0.3489 (tp) outliers start: 44 outliers final: 8 residues processed: 339 average time/residue: 0.7121 time to fit residues: 270.1594 Evaluate side-chains 289 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 270 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 294 GLN 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 79 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU 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 229 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 78 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.195600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155691 restraints weight = 20171.564| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.22 r_work: 0.3429 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1530 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= 0.131 Angle : 0.474 5.403 28724 Z= 0.247 Chirality : 0.040 0.124 3048 Planarity : 0.004 0.046 3704 Dihedral : 3.862 18.816 2808 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.65 % Allowed : 13.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2520 helix: 1.80 (0.14), residues: 1344 sheet: -1.55 (0.25), residues: 372 loop : -0.13 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 354 TYR 0.009 0.001 TYR A 102 PHE 0.013 0.001 PHE D 375 TRP 0.014 0.001 TRP A 160 HIS 0.002 0.000 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00304 (21212) covalent geometry : angle 0.47438 (28724) hydrogen bonds : bond 0.03679 ( 1036) hydrogen bonds : angle 4.08808 ( 3060) *********************** 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 319 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.876 Fit side-chains REVERT: A 294 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6569 (mm-40) REVERT: A 394 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8223 (m110) REVERT: A 437 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7204 (tmm-80) REVERT: A 580 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7252 (mmm-85) REVERT: B 394 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8180 (m110) REVERT: B 437 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7195 (tmm-80) REVERT: C 294 GLN cc_start: 0.6644 (mt0) cc_final: 0.6217 (tm-30) REVERT: C 394 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8218 (m110) REVERT: C 437 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7244 (tmm-80) REVERT: D 394 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8197 (m110) REVERT: D 437 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7199 (tmm-80) REVERT: D 590 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: H 481 ILE cc_start: 0.3571 (OUTLIER) cc_final: 0.3354 (tp) outliers start: 36 outliers final: 6 residues processed: 310 average time/residue: 0.7695 time to fit residues: 265.6560 Evaluate side-chains 286 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 269 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 B residue 141 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain C residue 79 LEU 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 190 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain H residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 76 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 206 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.193555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153584 restraints weight = 20259.456| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.33 r_work: 0.3400 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21212 Z= 0.189 Angle : 0.524 6.230 28724 Z= 0.271 Chirality : 0.042 0.124 3048 Planarity : 0.004 0.052 3704 Dihedral : 4.050 20.021 2808 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.65 % Allowed : 14.17 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2520 helix: 1.74 (0.14), residues: 1336 sheet: -1.67 (0.25), residues: 376 loop : -0.10 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 354 TYR 0.010 0.002 TYR D 68 PHE 0.011 0.002 PHE D 307 TRP 0.019 0.002 TRP A 160 HIS 0.003 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00452 (21212) covalent geometry : angle 0.52363 (28724) hydrogen bonds : bond 0.04214 ( 1036) hydrogen bonds : angle 4.23468 ( 3060) *********************** 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 319 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.819 Fit side-chains REVERT: A 294 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6615 (mm-40) REVERT: A 394 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8244 (m110) REVERT: A 437 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7282 (tmm-80) REVERT: A 580 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7338 (mmm-85) REVERT: B 394 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8207 (m110) REVERT: B 437 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7273 (tmm-80) REVERT: C 294 GLN cc_start: 0.6818 (mt0) cc_final: 0.6362 (tm-30) REVERT: C 394 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8222 (m110) REVERT: C 437 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7334 (tmm-80) REVERT: D 394 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8254 (m110) REVERT: D 437 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7279 (tmm-80) REVERT: D 590 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: H 481 ILE cc_start: 0.3761 (OUTLIER) cc_final: 0.3510 (tp) outliers start: 36 outliers final: 7 residues processed: 308 average time/residue: 0.7568 time to fit residues: 259.8841 Evaluate side-chains 285 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 267 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 294 GLN 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 C residue 79 LEU 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 190 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain H residue 481 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.0070 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.195156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157971 restraints weight = 20193.926| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.89 r_work: 0.3424 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1582 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= 0.139 Angle : 0.487 6.365 28724 Z= 0.253 Chirality : 0.041 0.125 3048 Planarity : 0.004 0.053 3704 Dihedral : 3.917 20.715 2808 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.83 % Allowed : 14.31 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.17), residues: 2520 helix: 1.84 (0.14), residues: 1336 sheet: -1.58 (0.25), residues: 372 loop : -0.05 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 354 TYR 0.009 0.001 TYR D 68 PHE 0.017 0.001 PHE B 375 TRP 0.018 0.001 TRP A 160 HIS 0.002 0.000 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00326 (21212) covalent geometry : angle 0.48706 (28724) hydrogen bonds : bond 0.03771 ( 1036) hydrogen bonds : angle 4.14851 ( 3060) *********************** 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 322 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 0.861 Fit side-chains REVERT: A 294 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6586 (mm-40) REVERT: A 394 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8250 (m110) REVERT: A 437 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7241 (tmm-80) REVERT: A 580 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7307 (mmm-85) REVERT: B 394 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8207 (m110) REVERT: B 437 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7270 (tmm-80) REVERT: C 294 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: C 394 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8226 (m110) REVERT: C 437 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7267 (tmm-80) REVERT: D 394 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8227 (m110) REVERT: D 437 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7232 (tmm-80) REVERT: D 558 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7876 (mtp85) REVERT: D 590 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: H 481 ILE cc_start: 0.3753 (OUTLIER) cc_final: 0.3523 (tp) outliers start: 40 outliers final: 10 residues processed: 310 average time/residue: 0.7427 time to fit residues: 257.3845 Evaluate side-chains 289 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 294 GLN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 437 ARG 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 437 ARG 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 C residue 437 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain H residue 481 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 120 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.194056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152973 restraints weight = 20236.044| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.22 r_work: 0.3414 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1619 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= 0.178 Angle : 0.515 6.050 28724 Z= 0.267 Chirality : 0.042 0.124 3048 Planarity : 0.004 0.058 3704 Dihedral : 4.012 21.152 2808 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 14.53 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.17), residues: 2520 helix: 1.78 (0.14), residues: 1336 sheet: -1.58 (0.25), residues: 372 loop : -0.00 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 354 TYR 0.011 0.001 TYR D 68 PHE 0.012 0.001 PHE C 496 TRP 0.023 0.002 TRP A 160 HIS 0.003 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00424 (21212) covalent geometry : angle 0.51493 (28724) hydrogen bonds : bond 0.04094 ( 1036) hydrogen bonds : angle 4.23748 ( 3060) *********************** 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 322 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.831 Fit side-chains REVERT: A 294 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6592 (mm-40) REVERT: A 394 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8233 (m110) REVERT: A 416 MET cc_start: 0.8167 (mmm) cc_final: 0.7897 (mmt) REVERT: A 437 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7302 (tmm-80) REVERT: A 580 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7325 (mmm-85) REVERT: B 394 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8185 (m110) REVERT: B 437 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7290 (tmm-80) REVERT: C 294 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: C 394 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8194 (m110) REVERT: C 437 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7326 (tmm-80) REVERT: C 580 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7165 (mmm160) REVERT: D 394 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8248 (m110) REVERT: D 437 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7297 (tmm-80) REVERT: D 580 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7122 (mmm160) REVERT: D 590 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: F 481 ILE cc_start: 0.3739 (OUTLIER) cc_final: 0.3493 (tp) REVERT: H 481 ILE cc_start: 0.3816 (OUTLIER) cc_final: 0.3560 (tp) outliers start: 39 outliers final: 9 residues processed: 312 average time/residue: 0.7479 time to fit residues: 260.7634 Evaluate side-chains 293 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 294 GLN 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 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 C residue 437 ARG Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 190 LEU 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 D residue 590 GLU Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain H residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.196287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.157242 restraints weight = 20276.834| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.05 r_work: 0.3439 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1686 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= 0.124 Angle : 0.478 7.423 28724 Z= 0.249 Chirality : 0.040 0.124 3048 Planarity : 0.004 0.057 3704 Dihedral : 3.851 21.292 2808 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.55 % Allowed : 14.85 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2520 helix: 1.87 (0.14), residues: 1344 sheet: -1.47 (0.25), residues: 368 loop : -0.10 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 354 TYR 0.009 0.001 TYR B 68 PHE 0.018 0.001 PHE A 375 TRP 0.020 0.001 TRP A 160 HIS 0.002 0.000 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00286 (21212) covalent geometry : angle 0.47800 (28724) hydrogen bonds : bond 0.03576 ( 1036) hydrogen bonds : angle 4.12888 ( 3060) ********************** 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 319 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.946 Fit side-chains REVERT: A 294 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6486 (mm-40) REVERT: A 394 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8222 (m110) REVERT: A 416 MET cc_start: 0.8163 (mmm) cc_final: 0.7906 (mmt) REVERT: A 437 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7194 (tmm-80) REVERT: A 580 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7288 (mmp80) REVERT: B 394 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8176 (m110) REVERT: B 437 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7189 (tmm-80) REVERT: C 294 GLN cc_start: 0.6656 (mt0) cc_final: 0.6225 (tm-30) REVERT: C 394 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8198 (m110) REVERT: C 437 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7227 (tmm-80) REVERT: D 394 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8224 (m110) REVERT: D 425 PHE cc_start: 0.7860 (m-80) cc_final: 0.7518 (m-80) REVERT: D 437 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7198 (tmm-80) REVERT: D 590 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: F 481 ILE cc_start: 0.3530 (OUTLIER) cc_final: 0.3276 (tp) REVERT: H 481 ILE cc_start: 0.3681 (OUTLIER) cc_final: 0.3411 (tp) outliers start: 34 outliers final: 7 residues processed: 311 average time/residue: 0.7372 time to fit residues: 256.2385 Evaluate side-chains 296 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 277 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 79 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain D residue 590 GLU Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain H residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 21 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 159 optimal weight: 0.0060 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.194141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153531 restraints weight = 20252.955| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.41 r_work: 0.3390 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21212 Z= 0.186 Angle : 0.532 6.373 28724 Z= 0.277 Chirality : 0.042 0.127 3048 Planarity : 0.004 0.059 3704 Dihedral : 4.029 21.848 2808 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.51 % Allowed : 15.13 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.17), residues: 2520 helix: 1.75 (0.14), residues: 1344 sheet: -1.47 (0.25), residues: 368 loop : -0.04 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 354 TYR 0.012 0.002 TYR B 68 PHE 0.023 0.002 PHE C 375 TRP 0.024 0.002 TRP A 160 HIS 0.003 0.001 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00445 (21212) covalent geometry : angle 0.53202 (28724) hydrogen bonds : bond 0.04137 ( 1036) hydrogen bonds : angle 4.26836 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7552.11 seconds wall clock time: 129 minutes 34.06 seconds (7774.06 seconds total)