Starting phenix.real_space_refine on Sun Sep 13 21:18:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n3y_48860/09_2026/9n3y_48860.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n3y_48860/09_2026/9n3y_48860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n3y_48860/09_2026/9n3y_48860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n3y_48860/09_2026/9n3y_48860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n3y_48860/09_2026/9n3y_48860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n3y_48860/09_2026/9n3y_48860.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 156 5.49 5 S 104 5.16 5 C 15380 2.51 5 N 4501 2.21 5 O 5064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25206 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1710 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1737 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1314 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 22, 'rna3p_pyr': 10} Link IDs: {'rna2p': 29, 'rna3p': 31} Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 996 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "K" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 972 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1889 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 224} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2482 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2499 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2465 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2460 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain breaks: 1 Chain: "G" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2090 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4591 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 32, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6955 SG CYS A 30 47.160 30.189 20.244 1.00111.89 S ATOM 6977 SG CYS A 33 50.842 29.269 20.289 1.00 94.68 S ATOM 7224 SG CYS A 66 48.059 27.024 18.731 1.00108.90 S ATOM 7255 SG CYS A 69 48.897 27.098 22.296 1.00122.11 S Time building chain proxies: 4.89, per 1000 atoms: 0.19 Number of scatterers: 25206 At special positions: 0 Unit cell: (114.148, 149.976, 175.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 104 16.00 P 156 15.00 O 5064 8.00 N 4501 7.00 C 15380 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 66 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 30 " Number of angles added : 6 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5234 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 39 sheets defined 39.2% alpha, 17.6% beta 38 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'B' and resid 22 through 40 Processing helix chain 'B' and resid 89 through 100 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.523A pdb=" N TRP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 180 " --> pdb=" O TRP B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'H' and resid 15 through 27 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 31 through 39 Processing helix chain 'H' and resid 69 through 95 removed outlier: 3.618A pdb=" N GLY H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 140 through 164 removed outlier: 3.747A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 10 removed outlier: 4.219A pdb=" N ASP A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.526A pdb=" N TYR A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 82 through 91 Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 127 through 133 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.614A pdb=" N ARG C 138 " --> pdb=" O GLY C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'C' and resid 200 through 223 Processing helix chain 'C' and resid 268 through 282 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.303A pdb=" N PHE C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 82 Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 95 through 105 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 127 through 133 removed outlier: 3.999A pdb=" N LEU D 132 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 removed outlier: 4.397A pdb=" N ARG D 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 223 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'E' and resid 66 through 82 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.563A pdb=" N GLU E 157 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.852A pdb=" N MET E 168 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.687A pdb=" N VAL E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 217 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 319 through 330 Processing helix chain 'E' and resid 334 through 343 removed outlier: 4.432A pdb=" N PHE E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 82 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 183 through 189 removed outlier: 4.279A pdb=" N GLY F 189 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 200 through 219 removed outlier: 3.557A pdb=" N ALA F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 280 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 319 through 331 removed outlier: 3.642A pdb=" N ALA F 325 " --> pdb=" O GLN F 321 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 326 " --> pdb=" O TYR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 343 Processing helix chain 'G' and resid 66 through 82 Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 117 through 126 Processing helix chain 'G' and resid 153 through 157 removed outlier: 3.872A pdb=" N GLU G 157 " --> pdb=" O THR G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 281 removed outlier: 3.653A pdb=" N LYS G 281 " --> pdb=" O LEU G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 332 Processing helix chain 'G' and resid 334 through 343 removed outlier: 4.122A pdb=" N PHE G 338 " --> pdb=" O SER G 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 154 removed outlier: 3.557A pdb=" N LYS L 145 " --> pdb=" O ARG L 141 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN L 146 " --> pdb=" O PRO L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 181 Processing helix chain 'L' and resid 190 through 204 removed outlier: 3.721A pdb=" N TRP L 195 " --> pdb=" O LEU L 191 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN L 196 " --> pdb=" O ALA L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 210 removed outlier: 3.559A pdb=" N VAL L 210 " --> pdb=" O GLU L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 234 Processing helix chain 'L' and resid 236 through 246 removed outlier: 3.555A pdb=" N ALA L 240 " --> pdb=" O ARG L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 276 removed outlier: 4.613A pdb=" N LEU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 306 Processing helix chain 'L' and resid 317 through 327 Processing helix chain 'L' and resid 360 through 362 No H-bonds generated for 'chain 'L' and resid 360 through 362' Processing helix chain 'L' and resid 363 through 371 Processing helix chain 'L' and resid 377 through 384 Processing helix chain 'L' and resid 388 through 413 Proline residue: L 394 - end of helix removed outlier: 4.105A pdb=" N ASP L 397 " --> pdb=" O LYS L 393 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS L 400 " --> pdb=" O LEU L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 441 Processing helix chain 'L' and resid 448 through 468 Processing helix chain 'L' and resid 492 through 502 Processing helix chain 'L' and resid 520 through 528 Processing helix chain 'L' and resid 530 through 532 No H-bonds generated for 'chain 'L' and resid 530 through 532' Processing helix chain 'L' and resid 563 through 580 removed outlier: 3.747A pdb=" N GLU L 569 " --> pdb=" O GLU L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 603 removed outlier: 4.069A pdb=" N ARG L 601 " --> pdb=" O LEU L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 622 through 632 removed outlier: 3.547A pdb=" N ALA L 628 " --> pdb=" O ALA L 624 " (cutoff:3.500A) Processing helix chain 'L' and resid 641 through 645 Processing helix chain 'L' and resid 658 through 662 Processing helix chain 'L' and resid 680 through 690 removed outlier: 3.933A pdb=" N ILE L 689 " --> pdb=" O ARG L 685 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY L 690 " --> pdb=" O ARG L 686 " (cutoff:3.500A) Processing helix chain 'L' and resid 690 through 708 removed outlier: 4.145A pdb=" N ILE L 695 " --> pdb=" O GLY L 691 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER L 696 " --> pdb=" O PHE L 692 " (cutoff:3.500A) Processing helix chain 'L' and resid 725 through 730 removed outlier: 3.746A pdb=" N TYR L 729 " --> pdb=" O ASP L 725 " (cutoff:3.500A) Processing helix chain 'L' and resid 735 through 746 removed outlier: 3.733A pdb=" N TYR L 745 " --> pdb=" O ILE L 741 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 746 " --> pdb=" O LEU L 742 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 15 removed outlier: 7.186A pdb=" N SER B 119 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLN B 84 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR B 121 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TRP B 82 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG B 123 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLN B 80 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 125 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN B 127 " --> pdb=" O GLN B 76 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 129 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 74 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 15 removed outlier: 6.245A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA4, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.652A pdb=" N VAL B 213 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 55 through 60 removed outlier: 3.706A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN H 102 " --> pdb=" O ASP H 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 111 through 123 removed outlier: 10.885A pdb=" N ARG H 115 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N LEU H 208 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR H 117 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA H 206 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASN H 205 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N VAL H 173 " --> pdb=" O ASN H 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 126 through 127 Processing sheet with id=AA8, first strand: chain 'H' and resid 212 through 213 Processing sheet with id=AA9, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.527A pdb=" N VAL A 115 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 140 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 141 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 144 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.352A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 308 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 23 removed outlier: 8.020A pdb=" N GLU C 250 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C 41 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL C 252 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.506A pdb=" N ALA C 50 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AB7, first strand: chain 'D' and resid 144 through 146 Processing sheet with id=AB8, first strand: chain 'D' and resid 144 through 146 removed outlier: 7.035A pdb=" N GLN D 2 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 305 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU D 4 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL D 303 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR D 6 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 21 through 23 removed outlier: 4.133A pdb=" N ASN D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLU D 250 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 41 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL D 252 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 52 removed outlier: 3.853A pdb=" N VAL D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 144 through 151 removed outlier: 4.978A pdb=" N VAL E 146 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER E 263 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N SER E 148 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG E 261 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.908A pdb=" N ASN E 21 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU E 250 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 41 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N VAL E 252 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 53 removed outlier: 7.457A pdb=" N VAL E 56 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 134 through 135 Processing sheet with id=AC6, first strand: chain 'E' and resid 311 through 312 Processing sheet with id=AC7, first strand: chain 'F' and resid 144 through 146 Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 146 removed outlier: 3.646A pdb=" N GLY F 302 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.891A pdb=" N ASN F 21 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU F 250 " --> pdb=" O PRO F 39 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL F 41 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N VAL F 252 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 45 through 51 Processing sheet with id=AD2, first strand: chain 'F' and resid 134 through 135 Processing sheet with id=AD3, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.514A pdb=" N GLY F 315 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 144 through 146 Processing sheet with id=AD5, first strand: chain 'G' and resid 144 through 146 removed outlier: 6.208A pdb=" N ARG G 8 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE G 300 " --> pdb=" O ARG G 8 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.802A pdb=" N ASN G 21 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 53 removed outlier: 3.556A pdb=" N ALA G 50 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS G 58 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 52 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 174 through 176 Processing sheet with id=AD9, first strand: chain 'L' and resid 357 through 358 removed outlier: 5.905A pdb=" N VAL L 357 " --> pdb=" O VAL L 509 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 185 through 189 removed outlier: 6.606A pdb=" N VAL L 185 " --> pdb=" O ILE L 313 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS L 315 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL L 187 " --> pdb=" O CYS L 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 372 through 374 removed outlier: 3.592A pdb=" N ARG L 473 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 488 " --> pdb=" O ARG L 471 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 549 through 552 removed outlier: 4.510A pdb=" N VAL L 723 " --> pdb=" O HIS L 552 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 180 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 2.98 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: 7584 1.34 - 1.46: 5638 1.46 - 1.58: 12337 1.58 - 1.70: 310 1.70 - 1.82: 191 Bond restraints: 26060 Sorted by residual: bond pdb=" C1' DT J 40 " pdb=" N1 DT J 40 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" C3' DC K 4 " pdb=" O3' DC K 4 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" N VAL L 479 " pdb=" CA VAL L 479 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N VAL L 476 " pdb=" CA VAL L 476 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE L 474 " pdb=" CA ILE L 474 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.14e-02 7.69e+03 1.02e+01 ... (remaining 26055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 34868 2.65 - 5.31: 929 5.31 - 7.96: 276 7.96 - 10.62: 14 10.62 - 13.27: 2 Bond angle restraints: 36089 Sorted by residual: angle pdb=" N PRO L 483 " pdb=" CA PRO L 483 " pdb=" C PRO L 483 " ideal model delta sigma weight residual 114.92 105.09 9.83 1.19e+00 7.06e-01 6.82e+01 angle pdb=" N TYR L 300 " pdb=" CA TYR L 300 " pdb=" CB TYR L 300 " ideal model delta sigma weight residual 109.94 101.63 8.31 1.49e+00 4.50e-01 3.11e+01 angle pdb=" N TYR B 50 " pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 113.97 106.99 6.98 1.28e+00 6.10e-01 2.98e+01 angle pdb=" N SER L 481 " pdb=" CA SER L 481 " pdb=" C SER L 481 " ideal model delta sigma weight residual 108.17 99.30 8.87 1.85e+00 2.92e-01 2.30e+01 angle pdb=" C3' G I 30 " pdb=" C2' G I 30 " pdb=" C1' G I 30 " ideal model delta sigma weight residual 101.30 104.63 -3.33 7.00e-01 2.04e+00 2.27e+01 ... (remaining 36084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 14477 35.95 - 71.90: 873 71.90 - 107.85: 48 107.85 - 143.80: 4 143.80 - 179.75: 15 Dihedral angle restraints: 15417 sinusoidal: 7247 harmonic: 8170 Sorted by residual: dihedral pdb=" O4' C I 6 " pdb=" C1' C I 6 " pdb=" N1 C I 6 " pdb=" C2 C I 6 " ideal model delta sinusoidal sigma weight residual 200.00 36.18 163.82 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C I 20 " pdb=" C1' C I 20 " pdb=" N1 C I 20 " pdb=" C2 C I 20 " ideal model delta sinusoidal sigma weight residual -128.00 34.46 -162.46 1 1.70e+01 3.46e-03 6.49e+01 dihedral pdb=" O4' C I 55 " pdb=" C1' C I 55 " pdb=" N1 C I 55 " pdb=" C2 C I 55 " ideal model delta sinusoidal sigma weight residual -160.00 -55.88 -104.12 1 1.50e+01 4.44e-03 5.31e+01 ... (remaining 15414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3834 0.126 - 0.251: 133 0.251 - 0.377: 6 0.377 - 0.503: 59 0.503 - 0.628: 86 Chirality restraints: 4118 Sorted by residual: chirality pdb=" P DT K 27 " pdb=" OP1 DT K 27 " pdb=" OP2 DT K 27 " pdb=" O5' DT K 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" P DA J 31 " pdb=" OP1 DA J 31 " pdb=" OP2 DA J 31 " pdb=" O5' DA J 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.74e+00 chirality pdb=" P DG J 38 " pdb=" OP1 DG J 38 " pdb=" OP2 DG J 38 " pdb=" O5' DG J 38 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.54e+00 ... (remaining 4115 not shown) Planarity restraints: 4119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 75 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.62e+00 pdb=" NE ARG B 75 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 75 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 75 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 75 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 56 " 0.239 9.50e-02 1.11e+02 1.07e-01 7.05e+00 pdb=" NE ARG B 56 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 56 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 56 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 56 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 11 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO D 12 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 12 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 12 " 0.037 5.00e-02 4.00e+02 ... (remaining 4116 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6231 2.80 - 3.33: 23613 3.33 - 3.85: 46635 3.85 - 4.38: 53056 4.38 - 4.90: 86063 Nonbonded interactions: 215598 Sorted by model distance: nonbonded pdb=" OG1 THR E 154 " pdb=" O MET E 169 " model vdw 2.276 3.040 nonbonded pdb=" O GLU B 92 " pdb=" ND1 HIS B 96 " model vdw 2.278 3.120 nonbonded pdb=" O2' A I 35 " pdb=" C5' U I 36 " model vdw 2.279 3.440 nonbonded pdb=" OG1 THR F 24 " pdb=" O GLY F 27 " model vdw 2.281 3.040 nonbonded pdb=" O ASP D 265 " pdb=" OD1 ASP D 265 " model vdw 2.286 3.040 ... (remaining 215593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 219 or resid 240 through 344)) selection = (chain 'D' and (resid 1 through 219 or resid 240 through 265 or (resid 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 through 344)) selection = (chain 'E' and (resid 1 through 219 or resid 240 through 265 or (resid 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 through 344)) selection = (chain 'F' and (resid 1 through 219 or resid 240 through 265 or (resid 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 through 344)) } 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: 12.360 Set stop_for_unknowns flag: 0.010 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26064 Z= 0.399 Angle : 1.057 14.579 36095 Z= 0.584 Chirality : 0.111 0.628 4118 Planarity : 0.007 0.125 4119 Dihedral : 20.839 179.753 10183 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 0.78 % Allowed : 20.16 % Favored : 79.06 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 2858 helix: -0.50 (0.15), residues: 1063 sheet: -0.50 (0.24), residues: 448 loop : -1.63 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 209 TYR 0.036 0.002 TYR D 47 PHE 0.029 0.002 PHE C 129 TRP 0.021 0.002 TRP B 179 HIS 0.008 0.001 HIS L 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.40 (26060) covalent geometry : angle 1.05166 / 0.58 (36089) hydrogen bonds : bond 0.17313 / 11.81 ( 1049) hydrogen bonds : angle 8.19645 / 5.77 ( 2889) metal coordination : bond 0.01872 / 0.84 ( 4) metal coordination : angle 8.22387 / 3.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.7941 (tp30) cc_final: 0.7511 (tp30) REVERT: B 50 TYR cc_start: 0.8522 (m-10) cc_final: 0.8245 (m-10) REVERT: B 142 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6792 (mp0) REVERT: H 102 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7741 (mm-40) REVERT: H 120 GLN cc_start: 0.9104 (mt0) cc_final: 0.8805 (mm110) REVERT: A 77 MET cc_start: 0.8095 (tmm) cc_final: 0.7841 (tmt) REVERT: A 179 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8648 (mmmm) REVERT: C 2 GLN cc_start: 0.8145 (mp10) cc_final: 0.7923 (mp10) REVERT: C 340 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 150 TYR cc_start: 0.8525 (m-80) cc_final: 0.8205 (m-80) REVERT: E 279 LEU cc_start: 0.8657 (mp) cc_final: 0.8453 (mm) REVERT: F 168 MET cc_start: 0.5262 (mmm) cc_final: 0.4873 (mmm) REVERT: G 139 MET cc_start: 0.8814 (tpp) cc_final: 0.8413 (mtt) REVERT: G 145 MET cc_start: 0.8451 (mtm) cc_final: 0.8140 (mtm) REVERT: L 326 MET cc_start: 0.8884 (tpp) cc_final: 0.8675 (tpt) REVERT: L 384 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8905 (tt) outliers start: 18 outliers final: 4 residues processed: 269 average time/residue: 0.6994 time to fit residues: 214.1929 Evaluate side-chains 173 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain C residue 331 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain L residue 384 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN B 84 GLN H 15 HIS A 201 GLN C 187 ASN D 92 ASN E 309 GLN G 92 ASN L 350 HIS L 373 HIS ** L 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.047298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.038911 restraints weight = 174126.971| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.48 r_work: 0.3163 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26064 Z= 0.195 Angle : 0.732 11.796 36095 Z= 0.384 Chirality : 0.049 0.370 4118 Planarity : 0.005 0.061 4119 Dihedral : 22.611 179.590 5119 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.77 % Allowed : 19.77 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 2858 helix: 0.35 (0.16), residues: 1063 sheet: -0.60 (0.24), residues: 434 loop : -1.20 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 494 TYR 0.036 0.002 TYR H 117 PHE 0.015 0.001 PHE L 626 TRP 0.045 0.002 TRP L 230 HIS 0.013 0.001 HIS L 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (26060) covalent geometry : angle 0.72891 / 0.38 (36089) hydrogen bonds : bond 0.05327 / 3.86 ( 1049) hydrogen bonds : angle 5.70907 / 4.02 ( 2889) metal coordination : bond 0.01406 / 0.63 ( 4) metal coordination : angle 4.95109 / 2.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 LYS cc_start: 0.8563 (tttp) cc_final: 0.8030 (ttpp) REVERT: B 10 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8851 (pp) REVERT: B 50 TYR cc_start: 0.8644 (m-10) cc_final: 0.8257 (m-10) REVERT: B 179 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8587 (t60) REVERT: H 102 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7886 (mm-40) REVERT: H 117 TYR cc_start: 0.8385 (m-80) cc_final: 0.8176 (m-10) REVERT: H 120 GLN cc_start: 0.9087 (mt0) cc_final: 0.8775 (mm110) REVERT: H 165 MET cc_start: 0.8301 (ttp) cc_final: 0.8035 (ttp) REVERT: A 77 MET cc_start: 0.8140 (tmm) cc_final: 0.7801 (tmm) REVERT: A 179 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8754 (mmmm) REVERT: C 2 GLN cc_start: 0.8336 (mp10) cc_final: 0.8102 (mp10) REVERT: C 63 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: C 317 THR cc_start: 0.7746 (p) cc_final: 0.7527 (t) REVERT: C 340 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8138 (tm-30) REVERT: E 80 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8953 (tppp) REVERT: E 150 TYR cc_start: 0.8508 (m-80) cc_final: 0.8137 (m-80) REVERT: F 58 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8547 (mmpt) REVERT: F 168 MET cc_start: 0.5732 (mmm) cc_final: 0.5262 (mmp) REVERT: G 139 MET cc_start: 0.9006 (tpp) cc_final: 0.8616 (mtt) REVERT: G 145 MET cc_start: 0.8750 (mtm) cc_final: 0.8431 (mtm) REVERT: G 336 LYS cc_start: 0.8928 (mppt) cc_final: 0.8667 (mppt) REVERT: L 327 MET cc_start: 0.8743 (mpt) cc_final: 0.8513 (mpt) REVERT: L 484 MET cc_start: 0.1265 (mmt) cc_final: 0.0277 (mmp) outliers start: 64 outliers final: 15 residues processed: 234 average time/residue: 0.6014 time to fit residues: 163.7927 Evaluate side-chains 192 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain L residue 230 TRP Chi-restraints excluded: chain L residue 570 CYS Chi-restraints excluded: chain L residue 705 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 279 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 271 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 193 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 276 optimal weight: 0.0670 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN L 582 GLN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 705 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.045524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.036961 restraints weight = 172611.791| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.40 r_work: 0.3089 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26064 Z= 0.180 Angle : 0.693 10.963 36095 Z= 0.363 Chirality : 0.047 0.363 4118 Planarity : 0.005 0.065 4119 Dihedral : 22.456 179.880 5114 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.38 % Allowed : 19.16 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 2858 helix: 0.69 (0.16), residues: 1064 sheet: -0.66 (0.23), residues: 436 loop : -1.10 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 330 TYR 0.026 0.002 TYR L 300 PHE 0.014 0.001 PHE L 626 TRP 0.022 0.001 TRP L 230 HIS 0.004 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (26060) covalent geometry : angle 0.69055 / 0.36 (36089) hydrogen bonds : bond 0.04461 / 3.16 ( 1049) hydrogen bonds : angle 5.35137 / 3.76 ( 2889) metal coordination : bond 0.01294 / 0.57 ( 4) metal coordination : angle 4.56920 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 179 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8872 (pp) REVERT: B 50 TYR cc_start: 0.8756 (m-10) cc_final: 0.8396 (m-10) REVERT: B 179 TRP cc_start: 0.9161 (OUTLIER) cc_final: 0.8475 (t60) REVERT: H 79 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8676 (OUTLIER) REVERT: H 120 GLN cc_start: 0.9016 (mt0) cc_final: 0.8679 (mm110) REVERT: A 77 MET cc_start: 0.8155 (tmm) cc_final: 0.7855 (tmm) REVERT: A 122 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: C 2 GLN cc_start: 0.8457 (mp10) cc_final: 0.8174 (mp10) REVERT: C 78 MET cc_start: 0.9087 (ttm) cc_final: 0.8743 (mtm) REVERT: C 169 MET cc_start: 0.8298 (tpt) cc_final: 0.7870 (tpp) REVERT: C 340 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8254 (tm-30) REVERT: E 150 TYR cc_start: 0.8589 (m-80) cc_final: 0.8143 (m-80) REVERT: E 182 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7993 (ptt) REVERT: F 216 LYS cc_start: 0.9656 (OUTLIER) cc_final: 0.9419 (ttmt) REVERT: G 139 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8834 (mtt) REVERT: G 145 MET cc_start: 0.8828 (mtm) cc_final: 0.8542 (mtm) REVERT: L 582 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7566 (pp30) REVERT: L 606 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (mm) outliers start: 78 outliers final: 29 residues processed: 235 average time/residue: 0.6025 time to fit residues: 165.6343 Evaluate side-chains 203 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain L residue 230 TRP Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 294 CYS Chi-restraints excluded: chain L residue 562 ASP Chi-restraints excluded: chain L residue 570 CYS Chi-restraints excluded: chain L residue 582 GLN Chi-restraints excluded: chain L residue 606 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 6 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN H 120 GLN C 92 ASN C 110 ASN C 209 GLN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN L 220 ASN L 225 GLN L 334 ASN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.042488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.033849 restraints weight = 173459.618| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.28 r_work: 0.2954 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 26064 Z= 0.316 Angle : 0.775 10.377 36095 Z= 0.405 Chirality : 0.050 0.411 4118 Planarity : 0.005 0.064 4119 Dihedral : 22.526 179.586 5114 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 3.42 % Allowed : 19.46 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2858 helix: 0.70 (0.16), residues: 1072 sheet: -0.71 (0.23), residues: 450 loop : -1.11 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 20 TYR 0.046 0.002 TYR H 117 PHE 0.020 0.002 PHE F 133 TRP 0.023 0.002 TRP L 230 HIS 0.015 0.001 HIS L 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.32 (26060) covalent geometry : angle 0.77231 / 0.40 (36089) hydrogen bonds : bond 0.05164 / 3.68 ( 1049) hydrogen bonds : angle 5.35280 / 3.75 ( 2889) metal coordination : bond 0.01746 / 0.78 ( 4) metal coordination : angle 5.15551 / 2.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 168 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8979 (pp) REVERT: B 50 TYR cc_start: 0.8877 (m-10) cc_final: 0.8456 (m-10) REVERT: B 179 TRP cc_start: 0.9320 (OUTLIER) cc_final: 0.8710 (t60) REVERT: H 39 MET cc_start: 0.8937 (tpp) cc_final: 0.8578 (tpt) REVERT: H 120 GLN cc_start: 0.9012 (mt0) cc_final: 0.8668 (mm-40) REVERT: C 2 GLN cc_start: 0.8849 (mp10) cc_final: 0.8487 (mp10) REVERT: C 78 MET cc_start: 0.9177 (ttm) cc_final: 0.8830 (mtm) REVERT: C 340 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8484 (tm-30) REVERT: D 64 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8433 (pp) REVERT: D 282 MET cc_start: 0.8989 (mmm) cc_final: 0.8675 (tpp) REVERT: E 182 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8185 (ptt) REVERT: F 46 MET cc_start: 0.8291 (pp-130) cc_final: 0.7997 (ptt) REVERT: F 343 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8839 (tp-100) REVERT: G 80 LYS cc_start: 0.9148 (tppt) cc_final: 0.8853 (mmmt) REVERT: G 139 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8959 (mtt) REVERT: G 141 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: G 145 MET cc_start: 0.8956 (mtm) cc_final: 0.8705 (mtm) REVERT: L 327 MET cc_start: 0.8814 (mpt) cc_final: 0.8605 (mpt) REVERT: L 381 MET cc_start: 0.8661 (ttt) cc_final: 0.8452 (tpt) REVERT: L 484 MET cc_start: 0.2823 (OUTLIER) cc_final: 0.1388 (mmp) REVERT: L 513 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8942 (tt) outliers start: 79 outliers final: 28 residues processed: 225 average time/residue: 0.6129 time to fit residues: 160.0021 Evaluate side-chains 194 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain L residue 294 CYS Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 570 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 74 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN D 63 GLN D 309 GLN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.042348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.033742 restraints weight = 171047.313| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.24 r_work: 0.2948 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26064 Z= 0.208 Angle : 0.693 12.367 36095 Z= 0.362 Chirality : 0.047 0.370 4118 Planarity : 0.005 0.045 4119 Dihedral : 22.484 178.857 5114 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.12 % Allowed : 20.46 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2858 helix: 0.86 (0.16), residues: 1070 sheet: -0.59 (0.24), residues: 414 loop : -1.01 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 218 TYR 0.024 0.002 TYR L 300 PHE 0.015 0.001 PHE F 133 TRP 0.056 0.001 TRP L 230 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (26060) covalent geometry : angle 0.69126 / 0.36 (36089) hydrogen bonds : bond 0.04364 / 3.13 ( 1049) hydrogen bonds : angle 5.15339 / 3.60 ( 2889) metal coordination : bond 0.01424 / 0.64 ( 4) metal coordination : angle 4.27064 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8949 (pp) REVERT: B 50 TYR cc_start: 0.8913 (m-10) cc_final: 0.8573 (m-10) REVERT: B 74 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8704 (ttpm) REVERT: B 179 TRP cc_start: 0.9312 (OUTLIER) cc_final: 0.8601 (t60) REVERT: H 120 GLN cc_start: 0.8957 (mt0) cc_final: 0.8592 (mm-40) REVERT: H 165 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8711 (ttp) REVERT: C 2 GLN cc_start: 0.8852 (mp10) cc_final: 0.8483 (mp10) REVERT: C 78 MET cc_start: 0.9171 (ttm) cc_final: 0.8831 (mtm) REVERT: C 124 MET cc_start: 0.9250 (mtp) cc_final: 0.9040 (mtt) REVERT: C 330 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8873 (mp) REVERT: D 145 MET cc_start: 0.8440 (mpp) cc_final: 0.8043 (mtm) REVERT: D 282 MET cc_start: 0.8998 (mmm) cc_final: 0.8685 (tpp) REVERT: F 46 MET cc_start: 0.8456 (pp-130) cc_final: 0.8189 (ptt) REVERT: F 343 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8870 (tp-100) REVERT: G 80 LYS cc_start: 0.9151 (tppt) cc_final: 0.8877 (mmmt) REVERT: G 139 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8870 (mmt) REVERT: G 141 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: G 145 MET cc_start: 0.8942 (mtm) cc_final: 0.8646 (mtm) REVERT: L 202 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9400 (tmmt) REVERT: L 327 MET cc_start: 0.8680 (mpt) cc_final: 0.8473 (mpt) REVERT: L 484 MET cc_start: 0.3217 (OUTLIER) cc_final: 0.1794 (mmp) REVERT: L 606 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (mm) REVERT: L 728 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9143 (mp) outliers start: 72 outliers final: 25 residues processed: 220 average time/residue: 0.6245 time to fit residues: 160.0611 Evaluate side-chains 196 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain L residue 202 LYS Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 606 LEU Chi-restraints excluded: chain L residue 728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 237 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 HIS ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN E 81 HIS ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.042464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.033846 restraints weight = 172353.502| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.26 r_work: 0.2954 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26064 Z= 0.160 Angle : 0.674 12.915 36095 Z= 0.351 Chirality : 0.046 0.355 4118 Planarity : 0.004 0.045 4119 Dihedral : 22.372 178.197 5114 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.16 % Allowed : 20.72 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2858 helix: 1.03 (0.16), residues: 1071 sheet: -0.55 (0.24), residues: 414 loop : -0.95 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 218 TYR 0.016 0.001 TYR G 22 PHE 0.014 0.001 PHE L 626 TRP 0.032 0.001 TRP L 230 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (26060) covalent geometry : angle 0.67190 / 0.35 (36089) hydrogen bonds : bond 0.04079 / 2.94 ( 1049) hydrogen bonds : angle 4.95921 / 3.47 ( 2889) metal coordination : bond 0.01062 / 0.47 ( 4) metal coordination : angle 3.86840 / 1.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 167 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8927 (pp) REVERT: B 50 TYR cc_start: 0.8915 (m-10) cc_final: 0.8527 (m-10) REVERT: B 74 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8755 (ttpm) REVERT: B 179 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.8635 (t60) REVERT: H 31 GLN cc_start: 0.9117 (mp10) cc_final: 0.8862 (pm20) REVERT: H 39 MET cc_start: 0.8973 (tpp) cc_final: 0.8656 (tpt) REVERT: H 120 GLN cc_start: 0.8931 (mt0) cc_final: 0.8558 (mm-40) REVERT: H 165 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8668 (ttp) REVERT: C 78 MET cc_start: 0.9164 (ttm) cc_final: 0.8854 (mtm) REVERT: C 124 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9027 (mtt) REVERT: C 330 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (mp) REVERT: C 340 GLN cc_start: 0.8938 (tt0) cc_final: 0.8687 (tm-30) REVERT: D 145 MET cc_start: 0.8423 (mpp) cc_final: 0.8222 (mtm) REVERT: E 182 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (ptp) REVERT: F 46 MET cc_start: 0.8481 (pp-130) cc_final: 0.8243 (ptt) REVERT: F 343 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8881 (tp-100) REVERT: G 80 LYS cc_start: 0.9144 (tppt) cc_final: 0.8853 (mmmt) REVERT: G 139 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8565 (mmt) REVERT: G 141 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: G 145 MET cc_start: 0.8919 (mtm) cc_final: 0.8598 (mtm) REVERT: G 336 LYS cc_start: 0.8900 (mppt) cc_final: 0.8693 (ttmm) REVERT: G 340 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8643 (mm110) REVERT: L 327 MET cc_start: 0.8664 (mpt) cc_final: 0.8395 (mpt) REVERT: L 484 MET cc_start: 0.3171 (OUTLIER) cc_final: 0.2371 (mmp) REVERT: L 513 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8831 (tt) REVERT: L 580 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8159 (t) REVERT: L 728 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9151 (mp) outliers start: 73 outliers final: 29 residues processed: 224 average time/residue: 0.6037 time to fit residues: 157.4965 Evaluate side-chains 203 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 169 MET Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain L residue 400 LYS Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 570 CYS Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 728 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 34 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 253 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 HIS D 309 GLN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.041240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.032634 restraints weight = 171649.580| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.20 r_work: 0.2901 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26064 Z= 0.238 Angle : 0.736 17.526 36095 Z= 0.379 Chirality : 0.048 0.404 4118 Planarity : 0.005 0.048 4119 Dihedral : 22.353 179.142 5113 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.38 % Allowed : 20.94 % Favored : 75.68 % 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 are not related in a simple way. whole: -0.20 (0.16), residues: 2858 helix: 1.06 (0.16), residues: 1064 sheet: -0.54 (0.24), residues: 424 loop : -0.92 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 8 TYR 0.017 0.002 TYR D 47 PHE 0.019 0.002 PHE H 69 TRP 0.082 0.002 TRP L 230 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.24 (26060) covalent geometry : angle 0.73498 / 0.38 (36089) hydrogen bonds : bond 0.04552 / 3.27 ( 1049) hydrogen bonds : angle 5.03773 / 3.53 ( 2889) metal coordination : bond 0.01379 / 0.62 ( 4) metal coordination : angle 3.68883 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 165 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8953 (pp) REVERT: B 15 MET cc_start: 0.8689 (mmt) cc_final: 0.8273 (mmm) REVERT: B 50 TYR cc_start: 0.8990 (m-10) cc_final: 0.8619 (m-10) REVERT: B 179 TRP cc_start: 0.9385 (OUTLIER) cc_final: 0.8807 (t60) REVERT: H 39 MET cc_start: 0.8961 (tpp) cc_final: 0.8629 (tpt) REVERT: H 79 ASP cc_start: 0.9188 (m-30) cc_final: 0.8917 (p0) REVERT: H 120 GLN cc_start: 0.8917 (mt0) cc_final: 0.8540 (mm-40) REVERT: H 165 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8632 (ptm) REVERT: A 179 LYS cc_start: 0.9483 (mmtp) cc_final: 0.9162 (mmtm) REVERT: C 78 MET cc_start: 0.9209 (ttm) cc_final: 0.8878 (mtm) REVERT: C 168 MET cc_start: 0.8164 (mmt) cc_final: 0.7852 (mmt) REVERT: C 330 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.9011 (mp) REVERT: C 340 GLN cc_start: 0.9036 (tt0) cc_final: 0.8775 (tm-30) REVERT: D 282 MET cc_start: 0.9052 (tpt) cc_final: 0.8693 (tpp) REVERT: E 182 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8208 (ptt) REVERT: F 343 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8898 (tp-100) REVERT: G 80 LYS cc_start: 0.9173 (tppt) cc_final: 0.8779 (mmmt) REVERT: G 139 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8908 (mtt) REVERT: G 141 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: G 145 MET cc_start: 0.8982 (mtm) cc_final: 0.8700 (mtm) REVERT: L 327 MET cc_start: 0.8704 (mpt) cc_final: 0.8419 (mpt) REVERT: L 484 MET cc_start: 0.3766 (OUTLIER) cc_final: 0.2774 (mmp) REVERT: L 513 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8827 (tt) REVERT: L 728 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9160 (mp) REVERT: L 745 TYR cc_start: 0.7825 (m-80) cc_final: 0.7620 (m-80) outliers start: 78 outliers final: 33 residues processed: 219 average time/residue: 0.5778 time to fit residues: 147.8572 Evaluate side-chains 203 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 570 CYS Chi-restraints excluded: chain L residue 728 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 58 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 275 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 285 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN F 306 ASN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.041010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.032404 restraints weight = 171880.928| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.20 r_work: 0.2892 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26064 Z= 0.224 Angle : 0.718 14.104 36095 Z= 0.372 Chirality : 0.048 0.432 4118 Planarity : 0.004 0.047 4119 Dihedral : 22.342 179.709 5113 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.47 % Allowed : 22.02 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2858 helix: 1.11 (0.17), residues: 1071 sheet: -0.45 (0.24), residues: 421 loop : -0.90 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 8 TYR 0.017 0.001 TYR D 47 PHE 0.015 0.001 PHE F 133 TRP 0.056 0.002 TRP L 230 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (26060) covalent geometry : angle 0.71691 / 0.37 (36089) hydrogen bonds : bond 0.04400 / 3.17 ( 1049) hydrogen bonds : angle 4.99686 / 3.51 ( 2889) metal coordination : bond 0.01311 / 0.60 ( 4) metal coordination : angle 3.47375 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8893 (pp) REVERT: B 50 TYR cc_start: 0.9010 (m-10) cc_final: 0.8655 (m-10) REVERT: B 74 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8842 (ttpp) REVERT: B 179 TRP cc_start: 0.9371 (OUTLIER) cc_final: 0.8775 (t60) REVERT: H 31 GLN cc_start: 0.9274 (mp10) cc_final: 0.9050 (pm20) REVERT: H 39 MET cc_start: 0.8952 (tpp) cc_final: 0.8630 (tpt) REVERT: H 120 GLN cc_start: 0.8908 (mt0) cc_final: 0.8529 (mm-40) REVERT: H 165 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8641 (ptm) REVERT: A 179 LYS cc_start: 0.9488 (mmtp) cc_final: 0.9165 (mmtm) REVERT: C 78 MET cc_start: 0.9220 (ttm) cc_final: 0.8861 (mtm) REVERT: C 168 MET cc_start: 0.8243 (mmt) cc_final: 0.7871 (mmt) REVERT: C 340 GLN cc_start: 0.9079 (tt0) cc_final: 0.8762 (tm-30) REVERT: D 181 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7317 (tpt90) REVERT: D 282 MET cc_start: 0.9104 (tpt) cc_final: 0.8663 (tpp) REVERT: E 282 MET cc_start: 0.8900 (mmm) cc_final: 0.8582 (mmp) REVERT: G 80 LYS cc_start: 0.9189 (tppt) cc_final: 0.8771 (mmmt) REVERT: G 139 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8631 (mmt) REVERT: G 141 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: G 145 MET cc_start: 0.9017 (mtm) cc_final: 0.8720 (mtm) REVERT: L 327 MET cc_start: 0.8579 (mpt) cc_final: 0.8304 (mpt) REVERT: L 484 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.2889 (mmp) REVERT: L 513 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8812 (tt) REVERT: L 580 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8302 (t) REVERT: L 728 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9175 (mp) REVERT: L 745 TYR cc_start: 0.7845 (m-80) cc_final: 0.7633 (m-80) outliers start: 57 outliers final: 25 residues processed: 206 average time/residue: 0.5952 time to fit residues: 143.2069 Evaluate side-chains 191 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 570 CYS Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 728 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 126 optimal weight: 2.9990 chunk 202 optimal weight: 0.2980 chunk 164 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 263 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN F 306 ASN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.041692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.033080 restraints weight = 171840.717| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.23 r_work: 0.2925 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26064 Z= 0.139 Angle : 0.692 13.521 36095 Z= 0.358 Chirality : 0.046 0.361 4118 Planarity : 0.004 0.044 4119 Dihedral : 22.276 177.447 5113 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.95 % Allowed : 22.71 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 2858 helix: 1.17 (0.17), residues: 1078 sheet: -0.29 (0.24), residues: 415 loop : -0.88 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 180 TYR 0.014 0.001 TYR A 79 PHE 0.014 0.001 PHE C 129 TRP 0.049 0.001 TRP L 230 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (26060) covalent geometry : angle 0.69100 / 0.36 (36089) hydrogen bonds : bond 0.04010 / 2.90 ( 1049) hydrogen bonds : angle 4.82780 / 3.38 ( 2889) metal coordination : bond 0.00873 / 0.39 ( 4) metal coordination : angle 3.24461 / 1.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8841 (pp) REVERT: B 15 MET cc_start: 0.8618 (mmt) cc_final: 0.8156 (mmm) REVERT: B 50 TYR cc_start: 0.8973 (m-10) cc_final: 0.8625 (m-10) REVERT: B 179 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.8632 (t60) REVERT: H 39 MET cc_start: 0.8945 (tpp) cc_final: 0.8636 (tpt) REVERT: H 165 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8697 (ptm) REVERT: A 179 LYS cc_start: 0.9490 (mmtp) cc_final: 0.9172 (mmtm) REVERT: C 78 MET cc_start: 0.9175 (ttm) cc_final: 0.8882 (mtm) REVERT: C 340 GLN cc_start: 0.9026 (tt0) cc_final: 0.8665 (tm-30) REVERT: D 282 MET cc_start: 0.9056 (tpt) cc_final: 0.8614 (tpp) REVERT: G 80 LYS cc_start: 0.9166 (tppt) cc_final: 0.8804 (mmmt) REVERT: G 139 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8504 (mmt) REVERT: G 141 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: G 145 MET cc_start: 0.8954 (mtm) cc_final: 0.8718 (mtm) REVERT: L 327 MET cc_start: 0.8601 (mpt) cc_final: 0.8311 (mpt) REVERT: L 381 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7985 (mmt) REVERT: L 484 MET cc_start: 0.3831 (OUTLIER) cc_final: 0.2872 (mmp) REVERT: L 513 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8773 (tt) REVERT: L 580 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8211 (t) REVERT: L 728 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9163 (mp) outliers start: 45 outliers final: 24 residues processed: 198 average time/residue: 0.6203 time to fit residues: 142.2313 Evaluate side-chains 191 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain L residue 294 CYS Chi-restraints excluded: chain L residue 381 MET Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 728 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 159 optimal weight: 0.0040 chunk 153 optimal weight: 4.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN C 306 ASN C 340 GLN D 284 ASN F 306 ASN L 328 GLN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.040570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.031969 restraints weight = 174680.744| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.23 r_work: 0.2868 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26064 Z= 0.261 Angle : 0.753 14.197 36095 Z= 0.389 Chirality : 0.048 0.448 4118 Planarity : 0.005 0.061 4119 Dihedral : 22.303 178.488 5113 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.86 % Allowed : 22.67 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2858 helix: 1.14 (0.17), residues: 1068 sheet: -0.37 (0.24), residues: 409 loop : -0.92 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 180 TYR 0.023 0.002 TYR H 117 PHE 0.020 0.002 PHE E 14 TRP 0.042 0.002 TRP L 230 HIS 0.007 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (26060) covalent geometry : angle 0.75169 / 0.39 (36089) hydrogen bonds : bond 0.04849 / 3.48 ( 1049) hydrogen bonds : angle 4.99205 / 3.50 ( 2889) metal coordination : bond 0.01364 / 0.62 ( 4) metal coordination : angle 3.34273 / 1.68 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 15 MET cc_start: 0.8802 (mmt) cc_final: 0.8368 (mmm) REVERT: B 50 TYR cc_start: 0.9034 (m-10) cc_final: 0.8659 (m-10) REVERT: B 166 LYS cc_start: 0.8896 (tmmm) cc_final: 0.8640 (tmmm) REVERT: B 179 TRP cc_start: 0.9419 (OUTLIER) cc_final: 0.8851 (t60) REVERT: H 39 MET cc_start: 0.8939 (tpp) cc_final: 0.8635 (tpt) REVERT: H 120 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: H 165 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8730 (ptm) REVERT: A 179 LYS cc_start: 0.9485 (mmtp) cc_final: 0.9161 (mmtm) REVERT: C 78 MET cc_start: 0.9245 (ttm) cc_final: 0.8945 (mtm) REVERT: C 168 MET cc_start: 0.8218 (mmt) cc_final: 0.7918 (mmt) REVERT: C 340 GLN cc_start: 0.9106 (tt0) cc_final: 0.8789 (tm-30) REVERT: D 282 MET cc_start: 0.9188 (tpt) cc_final: 0.8779 (tpp) REVERT: F 306 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.9043 (m110) REVERT: G 80 LYS cc_start: 0.9215 (tppt) cc_final: 0.8866 (mmmt) REVERT: G 139 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8893 (mtt) REVERT: G 141 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: G 145 MET cc_start: 0.9038 (mtm) cc_final: 0.8697 (mtm) REVERT: L 319 MET cc_start: 0.9050 (tpp) cc_final: 0.8815 (tpt) REVERT: L 327 MET cc_start: 0.8651 (mpt) cc_final: 0.8359 (mpt) REVERT: L 484 MET cc_start: 0.3864 (OUTLIER) cc_final: 0.2766 (mmp) REVERT: L 513 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8779 (tt) REVERT: L 580 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8316 (t) REVERT: L 728 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9187 (mp) outliers start: 43 outliers final: 22 residues processed: 187 average time/residue: 0.6209 time to fit residues: 134.9512 Evaluate side-chains 185 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 141 GLU Chi-restraints excluded: chain L residue 294 CYS Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 474 ILE Chi-restraints excluded: chain L residue 484 MET Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 580 THR Chi-restraints excluded: chain L residue 728 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 85 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN F 106 ASN G 340 GLN ** L 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.040665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.032049 restraints weight = 173457.169| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.23 r_work: 0.2871 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 26064 Z= 0.244 Angle : 0.888 59.200 36095 Z= 0.495 Chirality : 0.047 0.446 4118 Planarity : 0.005 0.173 4119 Dihedral : 22.312 178.576 5113 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 1.65 % Allowed : 22.80 % Favored : 75.55 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2858 helix: 1.14 (0.17), residues: 1068 sheet: -0.42 (0.24), residues: 409 loop : -0.92 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 180 TYR 0.021 0.002 TYR H 117 PHE 0.020 0.002 PHE E 14 TRP 0.039 0.001 TRP L 230 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 (26060) covalent geometry : angle 0.88659 / 0.49 (36089) hydrogen bonds : bond 0.04806 / 3.45 ( 1049) hydrogen bonds : angle 4.99345 / 3.50 ( 2889) metal coordination : bond 0.01191 / 0.53 ( 4) metal coordination : angle 3.34942 / 1.69 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6838.14 seconds wall clock time: 117 minutes 47.12 seconds (7067.12 seconds total)