Starting phenix.real_space_refine on Sun Sep 13 21:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n3z_48863/09_2026/9n3z_48863.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n3z_48863/09_2026/9n3z_48863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n3z_48863/09_2026/9n3z_48863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n3z_48863/09_2026/9n3z_48863.map" model { file = "/net/cci-nas-00/data/ceres_data/9n3z_48863/09_2026/9n3z_48863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n3z_48863/09_2026/9n3z_48863.cif" } resolution = 3.04 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= 0.004 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 154 5.49 5 S 105 5.16 5 C 15398 2.51 5 N 4502 2.21 5 O 5055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 25215 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1890 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 224} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1715 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 202} 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: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2488 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2513 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2485 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2489 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2089 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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': 11, 'rna2p_pyr': 12, 'rna3p_pur': 26, 'rna3p_pyr': 12} Link IDs: {'rna2p': 23, 'rna3p': 37} Chain: "J" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 974 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 953 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "L" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4521 Classifications: {'peptide': 604} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 32, 'TRANS': 571} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 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 219 SG CYS A 30 39.733 29.804 21.780 1.00126.81 S ATOM 241 SG CYS A 33 43.016 28.582 21.506 1.00125.11 S ATOM 488 SG CYS A 66 40.760 26.918 19.397 1.00137.14 S ATOM 519 SG CYS A 69 41.930 26.753 23.339 1.00139.84 S Time building chain proxies: 5.20, per 1000 atoms: 0.21 Number of scatterers: 25215 At special positions: 0 Unit cell: (107.483, 149.143, 176.638, 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 105 16.00 P 154 15.00 O 5055 8.00 N 4502 7.00 C 15398 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: 2.57 Conformation dependent library (CDL) restraints added in 913.1 milliseconds 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 30 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 66 " Number of angles added : 6 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5254 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 39 sheets defined 39.4% alpha, 18.2% beta 40 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.694A pdb=" N ILE A 7 " --> pdb=" O PRO A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 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 163 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 218 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'B' and resid 22 through 40 Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.998A pdb=" N TYR B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 137 through 147 removed outlier: 3.767A pdb=" N ILE B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.835A pdb=" N CYS B 175 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.525A pdb=" N ALA C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.804A pdb=" N GLU C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG C 158 " --> pdb=" O ASN C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 200 through 223 removed outlier: 3.854A pdb=" N ALA C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 removed outlier: 3.661A pdb=" N VAL C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.470A 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 90 removed outlier: 3.738A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 105 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.582A pdb=" N LEU D 186 " --> pdb=" O ASP D 183 " (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: 3.815A pdb=" N GLU E 157 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.505A pdb=" N VAL E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 221 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 319 through 331 Processing helix chain 'E' and resid 334 through 343 removed outlier: 4.413A 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 153 through 157 removed outlier: 3.620A pdb=" N GLU F 157 " --> pdb=" O THR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 200 through 222 Processing helix chain 'F' and resid 268 through 281 removed outlier: 3.827A pdb=" N LYS F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 331 Processing helix chain 'F' and resid 334 through 343 removed outlier: 4.327A pdb=" N PHE F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 82 removed outlier: 3.699A pdb=" N VAL G 82 " --> pdb=" O MET G 78 " (cutoff:3.500A) 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: 3.940A pdb=" N GLU G 157 " --> pdb=" O THR G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 281 removed outlier: 3.978A pdb=" N LYS G 281 " --> pdb=" O LEU G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 319 through 332 Processing helix chain 'G' and resid 335 through 343 Processing helix chain 'H' and resid 15 through 28 Processing helix chain 'H' and resid 31 through 40 Processing helix chain 'H' and resid 71 through 95 removed outlier: 3.595A pdb=" N GLN H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 131 through 138 Processing helix chain 'H' and resid 143 through 164 removed outlier: 3.830A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 231 Processing helix chain 'L' and resid 132 through 137 removed outlier: 3.960A pdb=" N VAL L 136 " --> pdb=" O GLY L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 154 Processing helix chain 'L' and resid 166 through 182 removed outlier: 3.634A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 204 removed outlier: 3.618A pdb=" N TRP L 195 " --> pdb=" O LEU L 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP L 203 " --> pdb=" O ASN L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 234 removed outlier: 3.582A pdb=" N THR L 227 " --> pdb=" O SER L 223 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU L 229 " --> pdb=" O GLN L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 245 Processing helix chain 'L' and resid 267 through 276 removed outlier: 3.627A pdb=" N LEU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 303 Processing helix chain 'L' and resid 305 through 309 Processing helix chain 'L' and resid 316 through 331 Processing helix chain 'L' and resid 362 through 371 Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 391 through 414 Processing helix chain 'L' and resid 427 through 440 removed outlier: 3.959A pdb=" N ALA L 431 " --> pdb=" O GLU L 427 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS L 433 " --> pdb=" O ILE L 429 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY L 440 " --> pdb=" O VAL L 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 468 removed outlier: 4.036A pdb=" N GLY L 468 " --> pdb=" O ASP L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 502 Processing helix chain 'L' and resid 520 through 527 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 542 through 546 removed outlier: 3.519A pdb=" N THR L 545 " --> pdb=" O PRO L 542 " (cutoff:3.500A) Processing helix chain 'L' and resid 563 through 581 Processing helix chain 'L' and resid 592 through 602 Processing helix chain 'L' and resid 602 through 607 Processing helix chain 'L' and resid 620 through 632 Processing helix chain 'L' and resid 641 through 647 removed outlier: 3.820A pdb=" N THR L 646 " --> pdb=" O GLY L 642 " (cutoff:3.500A) Processing helix chain 'L' and resid 658 through 662 Processing helix chain 'L' and resid 680 through 690 Processing helix chain 'L' and resid 691 through 709 removed outlier: 3.738A pdb=" N ILE L 695 " --> pdb=" O GLY L 691 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG L 709 " --> pdb=" O GLN L 705 " (cutoff:3.500A) Processing helix chain 'L' and resid 725 through 731 removed outlier: 3.968A pdb=" N TYR L 729 " --> pdb=" O ASP L 725 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY L 731 " --> pdb=" O ARG L 727 " (cutoff:3.500A) Processing helix chain 'L' and resid 735 through 746 removed outlier: 3.885A pdb=" N TYR L 745 " --> pdb=" O ILE L 741 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS L 746 " --> pdb=" O LEU L 742 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 4.125A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 140 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.639A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 130 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 8 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 134 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN B 3 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS B 5 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 167 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR B 7 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE B 165 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 9 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 15 Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 146 removed outlier: 7.047A pdb=" N GLN C 2 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU C 305 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU C 4 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 303 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR C 6 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.696A pdb=" N ASN C 21 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU C 250 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 41 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N VAL C 252 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 50 Processing sheet with id=AB3, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.513A pdb=" N GLY C 315 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 144 through 146 Processing sheet with id=AB5, first strand: chain 'D' and resid 144 through 146 removed outlier: 6.841A pdb=" N GLU D 4 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL D 303 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR D 6 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.962A pdb=" N ASN D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLU D 250 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 41 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL D 252 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 146 Processing sheet with id=AB9, first strand: chain 'E' and resid 144 through 146 removed outlier: 5.990A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.983A pdb=" N ASN E 21 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLU E 250 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 41 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL E 252 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 53 removed outlier: 7.574A pdb=" N VAL E 56 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 134 through 135 Processing sheet with id=AC4, first strand: chain 'E' and resid 311 through 312 Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 146 Processing sheet with id=AC6, first strand: chain 'F' and resid 144 through 146 removed outlier: 3.508A pdb=" N GLY F 302 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 21 through 23 removed outlier: 4.093A pdb=" N ASN F 21 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 45 through 53 removed outlier: 3.526A pdb=" N LYS F 58 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 52 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 311 through 312 Processing sheet with id=AD1, first strand: chain 'G' and resid 144 through 146 Processing sheet with id=AD2, first strand: chain 'G' and resid 144 through 146 removed outlier: 3.561A pdb=" N GLY G 302 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG G 8 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE G 300 " --> pdb=" O ARG G 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.881A pdb=" N ASN G 21 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 53 removed outlier: 6.965A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 174 through 176 Processing sheet with id=AD6, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.939A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN H 102 " --> pdb=" O ASP H 9 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 111 through 122 removed outlier: 4.969A pdb=" N ASN H 205 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TYR H 117 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU H 203 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N LEU H 119 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL H 201 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR H 121 " --> pdb=" O HIS H 199 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N HIS H 199 " --> pdb=" O TYR H 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 111 through 122 removed outlier: 4.969A pdb=" N ASN H 205 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TYR H 117 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU H 203 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N LEU H 119 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL H 201 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N TYR H 121 " --> pdb=" O HIS H 199 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N HIS H 199 " --> pdb=" O TYR H 121 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA H 200 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 178 " --> pdb=" O ALA H 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE H 202 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS H 176 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL H 204 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER H 174 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 211 through 213 Processing sheet with id=AE1, first strand: chain 'L' and resid 213 through 214 removed outlier: 6.613A pdb=" N THR L 213 " --> pdb=" O LEU L 314 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL L 185 " --> pdb=" O ILE L 313 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS L 315 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL L 187 " --> pdb=" O CYS L 315 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU L 355 " --> pdb=" O THR L 507 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL L 509 " --> pdb=" O LEU L 355 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL L 357 " --> pdb=" O VAL L 509 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL L 157 " --> pdb=" O LEU L 508 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER L 510 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA L 159 " --> pdb=" O SER L 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 372 through 375 removed outlier: 3.660A 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: 6.441A pdb=" N LEU L 550 " --> pdb=" O LEU L 721 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL L 723 " --> pdb=" O LEU L 550 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS L 552 " --> pdb=" O VAL L 723 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU L 668 " --> pdb=" O TRP L 722 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2733 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6735 1.33 - 1.46: 6321 1.46 - 1.58: 12508 1.58 - 1.70: 306 1.70 - 1.83: 193 Bond restraints: 26063 Sorted by residual: bond pdb=" C1' DC J 23 " pdb=" N1 DC J 23 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.13e+01 bond pdb=" C3' DC K 17 " pdb=" O3' DC K 17 " ideal model delta sigma weight residual 1.435 1.493 -0.058 1.30e-02 5.92e+03 2.01e+01 bond pdb=" C1' DT J 25 " pdb=" N1 DT J 25 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" C3' DT K 16 " pdb=" O3' DT K 16 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" C LYS L 393 " pdb=" N PRO L 394 " ideal model delta sigma weight residual 1.334 1.388 -0.053 1.51e-02 4.39e+03 1.25e+01 ... (remaining 26058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 34835 2.55 - 5.10: 969 5.10 - 7.66: 267 7.66 - 10.21: 13 10.21 - 12.76: 2 Bond angle restraints: 36086 Sorted by residual: angle pdb=" N GLU H 142 " pdb=" CA GLU H 142 " pdb=" C GLU H 142 " ideal model delta sigma weight residual 114.62 107.22 7.40 1.14e+00 7.69e-01 4.22e+01 angle pdb=" CA ASP H 86 " pdb=" CB ASP H 86 " pdb=" CG ASP H 86 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" N VAL L 476 " pdb=" CA VAL L 476 " pdb=" C VAL L 476 " ideal model delta sigma weight residual 108.53 101.61 6.92 1.22e+00 6.72e-01 3.22e+01 angle pdb=" C TYR L 592 " pdb=" CA TYR L 592 " pdb=" CB TYR L 592 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" O5' DT J 36 " pdb=" C5' DT J 36 " pdb=" C4' DT J 36 " ideal model delta sigma weight residual 109.40 113.60 -4.20 8.00e-01 1.56e+00 2.76e+01 ... (remaining 36081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.84: 14295 32.84 - 65.69: 1037 65.69 - 98.53: 72 98.53 - 131.38: 5 131.38 - 164.22: 12 Dihedral angle restraints: 15421 sinusoidal: 7220 harmonic: 8201 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 38.49 161.51 1 1.50e+01 4.44e-03 8.31e+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 34.99 -162.99 1 1.70e+01 3.46e-03 6.50e+01 dihedral pdb=" C3' G I 43 " pdb=" C4' G I 43 " pdb=" O4' G I 43 " pdb=" C1' G I 43 " ideal model delta sinusoidal sigma weight residual 20.00 -19.68 39.68 1 8.00e+00 1.56e-02 3.46e+01 ... (remaining 15418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3862 0.125 - 0.249: 154 0.249 - 0.374: 4 0.374 - 0.499: 60 0.499 - 0.623: 43 Chirality restraints: 4123 Sorted by residual: chirality pdb=" P DC K 12 " pdb=" OP1 DC K 12 " pdb=" OP2 DC K 12 " pdb=" O5' DC K 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.71e+00 chirality pdb=" P DT K 36 " pdb=" OP1 DT K 36 " pdb=" OP2 DT K 36 " pdb=" O5' DT K 36 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" P DG J 34 " pdb=" OP1 DG J 34 " pdb=" OP2 DG J 34 " pdb=" O5' DG J 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.95e+00 ... (remaining 4120 not shown) Planarity restraints: 4124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 176 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C PRO B 176 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO B 176 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP B 177 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 181 " -0.236 9.50e-02 1.11e+02 1.06e-01 6.87e+00 pdb=" NE ARG D 181 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 181 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 181 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 181 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 68 " -0.221 9.50e-02 1.11e+02 9.92e-02 6.35e+00 pdb=" NE ARG A 68 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 68 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 68 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 68 " -0.005 2.00e-02 2.50e+03 ... (remaining 4121 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4435 2.77 - 3.30: 23970 3.30 - 3.84: 46296 3.84 - 4.37: 53068 4.37 - 4.90: 86851 Nonbonded interactions: 214620 Sorted by model distance: nonbonded pdb=" OG1 THR F 24 " pdb=" O GLY F 27 " model vdw 2.240 3.040 nonbonded pdb=" O MET E 139 " pdb=" O2' C I 17 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR E 24 " pdb=" OD1 ASP E 26 " model vdw 2.296 3.040 nonbonded pdb=" O SER A 53 " pdb=" OG SER A 53 " model vdw 2.304 3.040 nonbonded pdb=" OG SER D 117 " pdb=" OD1 ASP D 119 " model vdw 2.307 3.040 ... (remaining 214615 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 220 or (resid 221 and (name N or name CA or name \ C or name O or name CB )) 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 'D' and (resid 1 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name CB )) 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 221 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 221 or resid 240 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: 13.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 30.050 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 0.067 26067 Z= 0.382 Angle : 1.063 34.524 36092 Z= 0.587 Chirality : 0.096 0.623 4123 Planarity : 0.007 0.106 4124 Dihedral : 20.729 164.220 10167 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.08 % Allowed : 19.78 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2868 helix: -0.39 (0.15), residues: 1043 sheet: -0.52 (0.24), residues: 467 loop : -1.37 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 449 TYR 0.037 0.002 TYR A 79 PHE 0.026 0.003 PHE H 175 TRP 0.020 0.002 TRP A 67 HIS 0.011 0.002 HIS H 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.38 (26063) covalent geometry : angle 1.03910 / 0.59 (36086) hydrogen bonds : bond 0.16555 / 11.24 ( 1068) hydrogen bonds : angle 8.08339 / 5.73 ( 2931) metal coordination : bond 0.02100 / 1.01 ( 4) metal coordination : angle 17.36802 / 9.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8420 (m-80) cc_final: 0.7716 (m-10) REVERT: C 103 TYR cc_start: 0.9194 (m-80) cc_final: 0.8966 (m-80) REVERT: C 340 GLN cc_start: 0.9374 (tt0) cc_final: 0.9043 (tm-30) REVERT: D 139 MET cc_start: 0.7795 (mtt) cc_final: 0.7563 (mtt) REVERT: E 45 MET cc_start: 0.8783 (ppp) cc_final: 0.8417 (ppp) REVERT: E 145 MET cc_start: 0.8225 (mtp) cc_final: 0.7990 (mtp) REVERT: F 168 MET cc_start: 0.6636 (mmm) cc_final: 0.5836 (mmm) REVERT: G 45 MET cc_start: 0.9080 (ptm) cc_final: 0.8680 (ptm) REVERT: G 47 TYR cc_start: 0.9032 (m-80) cc_final: 0.8598 (m-10) REVERT: G 80 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8850 (mmtp) REVERT: H 42 MET cc_start: 0.9034 (mmm) cc_final: 0.8655 (mmm) REVERT: H 165 MET cc_start: 0.8241 (ptm) cc_final: 0.7967 (ptp) REVERT: L 265 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7337 (mt) REVERT: L 270 GLU cc_start: 0.9251 (tp30) cc_final: 0.9037 (tm-30) REVERT: L 327 MET cc_start: 0.9318 (mmp) cc_final: 0.9095 (mmm) REVERT: L 359 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8141 (mm-30) REVERT: L 670 ILE cc_start: 0.9594 (mp) cc_final: 0.9248 (tt) outliers start: 25 outliers final: 8 residues processed: 246 average time/residue: 0.1811 time to fit residues: 69.2705 Evaluate side-chains 174 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 224 HIS Chi-restraints excluded: chain L residue 265 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN A 122 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN C 2 GLN C 68 ASN E 214 ASN E 284 ASN E 309 GLN F 306 ASN L 263 HIS ** L 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN L 323 HIS ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 552 HIS L 702 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.047455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034119 restraints weight = 153982.417| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.31 r_work: 0.2852 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26067 Z= 0.257 Angle : 0.743 22.844 36092 Z= 0.383 Chirality : 0.048 0.362 4123 Planarity : 0.005 0.052 4124 Dihedral : 22.180 173.254 5115 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.95 % Allowed : 17.66 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2868 helix: 0.60 (0.16), residues: 1075 sheet: -0.54 (0.24), residues: 434 loop : -1.06 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 155 TYR 0.026 0.002 TYR A 79 PHE 0.018 0.002 PHE E 133 TRP 0.014 0.002 TRP H 212 HIS 0.006 0.001 HIS L 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 (26063) covalent geometry : angle 0.72406 / 0.38 (36086) hydrogen bonds : bond 0.05174 / 3.44 ( 1068) hydrogen bonds : angle 5.72619 / 3.99 ( 2931) metal coordination : bond 0.02426 / 1.17 ( 4) metal coordination : angle 12.99316 / 6.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 172 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8695 (m-80) cc_final: 0.8113 (m-80) REVERT: C 340 GLN cc_start: 0.9385 (tt0) cc_final: 0.9058 (tm-30) REVERT: E 45 MET cc_start: 0.8719 (ppp) cc_final: 0.8355 (ppp) REVERT: E 70 MET cc_start: 0.9412 (mmm) cc_final: 0.9161 (tpp) REVERT: E 145 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: E 169 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8460 (ttt) REVERT: E 175 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: G 45 MET cc_start: 0.9041 (ptm) cc_final: 0.8554 (ptm) REVERT: G 47 TYR cc_start: 0.9014 (m-80) cc_final: 0.8571 (m-10) REVERT: G 90 LYS cc_start: 0.9232 (ptpt) cc_final: 0.8877 (ptpp) REVERT: G 139 MET cc_start: 0.9128 (tpp) cc_final: 0.8878 (mmm) REVERT: G 169 MET cc_start: 0.8890 (ppp) cc_final: 0.8462 (ppp) REVERT: H 42 MET cc_start: 0.8896 (mmm) cc_final: 0.8380 (mmm) REVERT: L 170 MET cc_start: 0.9397 (tpp) cc_final: 0.9023 (tpp) REVERT: L 201 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7908 (ttm) REVERT: L 230 TRP cc_start: 0.9023 (m-90) cc_final: 0.8755 (m-90) REVERT: L 265 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7340 (mt) REVERT: L 270 GLU cc_start: 0.9344 (tp30) cc_final: 0.9071 (tm-30) REVERT: L 327 MET cc_start: 0.9391 (mmp) cc_final: 0.9111 (mmm) outliers start: 68 outliers final: 29 residues processed: 223 average time/residue: 0.1673 time to fit residues: 59.0115 Evaluate side-chains 192 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 524 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 146 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 594 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.047208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033825 restraints weight = 152987.148| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.31 r_work: 0.2839 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26067 Z= 0.188 Angle : 0.644 12.904 36092 Z= 0.338 Chirality : 0.045 0.351 4123 Planarity : 0.004 0.050 4124 Dihedral : 22.029 169.866 5111 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.69 % Allowed : 17.74 % Favored : 79.57 % 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: -0.27 (0.16), residues: 2868 helix: 1.00 (0.16), residues: 1076 sheet: -0.53 (0.23), residues: 438 loop : -1.00 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 180 TYR 0.025 0.001 TYR A 79 PHE 0.013 0.001 PHE E 133 TRP 0.013 0.001 TRP H 212 HIS 0.005 0.001 HIS G 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (26063) covalent geometry : angle 0.63898 / 0.34 (36086) hydrogen bonds : bond 0.04488 / 3.09 ( 1068) hydrogen bonds : angle 5.41435 / 3.80 ( 2931) metal coordination : bond 0.01139 / 0.55 ( 4) metal coordination : angle 6.38242 / 3.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8741 (m-80) cc_final: 0.8155 (m-80) REVERT: C 340 GLN cc_start: 0.9399 (tt0) cc_final: 0.9197 (tm-30) REVERT: D 175 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: E 145 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8513 (mtp) REVERT: E 169 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8455 (ttt) REVERT: E 175 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: G 45 MET cc_start: 0.9049 (ptm) cc_final: 0.8536 (ptm) REVERT: G 47 TYR cc_start: 0.9010 (m-80) cc_final: 0.8544 (m-10) REVERT: G 139 MET cc_start: 0.9130 (tpp) cc_final: 0.8890 (mmm) REVERT: G 145 MET cc_start: 0.9077 (mtm) cc_final: 0.8858 (mtm) REVERT: G 169 MET cc_start: 0.8873 (ppp) cc_final: 0.8462 (ppp) REVERT: H 42 MET cc_start: 0.8956 (mmm) cc_final: 0.8469 (mmm) REVERT: L 170 MET cc_start: 0.9402 (tpp) cc_final: 0.9108 (tpp) REVERT: L 201 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7923 (ttm) REVERT: L 265 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7257 (tp) REVERT: L 270 GLU cc_start: 0.9311 (tp30) cc_final: 0.9008 (tp30) REVERT: L 327 MET cc_start: 0.9392 (mmp) cc_final: 0.9123 (mmm) outliers start: 62 outliers final: 25 residues processed: 208 average time/residue: 0.1687 time to fit residues: 56.0322 Evaluate side-chains 187 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 406 MET Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 524 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN E 284 ASN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 297 GLN ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.046283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.032896 restraints weight = 153587.626| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.25 r_work: 0.2799 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26067 Z= 0.221 Angle : 0.650 12.442 36092 Z= 0.340 Chirality : 0.045 0.355 4123 Planarity : 0.004 0.048 4124 Dihedral : 21.995 171.512 5110 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.04 % Allowed : 17.92 % Favored : 79.05 % 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: -0.08 (0.16), residues: 2868 helix: 1.18 (0.17), residues: 1078 sheet: -0.47 (0.25), residues: 419 loop : -0.89 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 180 TYR 0.023 0.002 TYR A 79 PHE 0.017 0.002 PHE E 133 TRP 0.013 0.002 TRP G 258 HIS 0.005 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (26063) covalent geometry : angle 0.64797 / 0.34 (36086) hydrogen bonds : bond 0.04268 / 2.92 ( 1068) hydrogen bonds : angle 5.21615 / 3.68 ( 2931) metal coordination : bond 0.01554 / 0.76 ( 4) metal coordination : angle 4.41129 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 159 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8815 (m-80) cc_final: 0.8077 (m-10) REVERT: A 198 GLN cc_start: 0.8844 (pm20) cc_final: 0.8644 (pp30) REVERT: B 212 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8833 (m-70) REVERT: C 340 GLN cc_start: 0.9405 (tt0) cc_final: 0.9197 (tm-30) REVERT: D 47 TYR cc_start: 0.9029 (m-80) cc_final: 0.8679 (m-80) REVERT: D 175 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: E 78 MET cc_start: 0.9215 (ttm) cc_final: 0.8896 (mtp) REVERT: E 169 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8537 (ttt) REVERT: E 175 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: F 182 MET cc_start: 0.8922 (mmm) cc_final: 0.8585 (mmm) REVERT: G 45 MET cc_start: 0.9102 (ptm) cc_final: 0.8764 (ptm) REVERT: G 46 MET cc_start: 0.8901 (ttp) cc_final: 0.8641 (ptm) REVERT: G 90 LYS cc_start: 0.9307 (ptpt) cc_final: 0.8990 (ptpp) REVERT: G 139 MET cc_start: 0.9125 (tpp) cc_final: 0.8886 (mmm) REVERT: G 145 MET cc_start: 0.9123 (mtm) cc_final: 0.8915 (mtm) REVERT: G 169 MET cc_start: 0.8863 (ppp) cc_final: 0.8408 (ppp) REVERT: G 282 MET cc_start: 0.9074 (tpp) cc_final: 0.8683 (tpp) REVERT: H 42 MET cc_start: 0.8992 (mmm) cc_final: 0.8528 (mmm) REVERT: L 170 MET cc_start: 0.9362 (tpp) cc_final: 0.8880 (tpp) REVERT: L 201 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7998 (ttm) REVERT: L 265 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7569 (mt) REVERT: L 270 GLU cc_start: 0.9311 (tp30) cc_final: 0.9063 (tm-30) REVERT: L 327 MET cc_start: 0.9400 (mmp) cc_final: 0.9064 (mmt) outliers start: 70 outliers final: 36 residues processed: 210 average time/residue: 0.1611 time to fit residues: 54.9053 Evaluate side-chains 197 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 524 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 269 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN F 2 GLN ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 594 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 = 0.3439 r_free = 0.3439 target = 0.046631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.033300 restraints weight = 152021.667| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.26 r_work: 0.2816 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26067 Z= 0.154 Angle : 0.606 12.273 36092 Z= 0.319 Chirality : 0.043 0.343 4123 Planarity : 0.004 0.049 4124 Dihedral : 21.924 170.709 5110 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.73 % Allowed : 18.61 % Favored : 78.66 % 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: 0.04 (0.16), residues: 2868 helix: 1.31 (0.17), residues: 1080 sheet: -0.43 (0.25), residues: 418 loop : -0.84 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.033 0.001 TYR L 307 PHE 0.014 0.001 PHE H 175 TRP 0.012 0.001 TRP G 258 HIS 0.007 0.001 HIS L 480 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (26063) covalent geometry : angle 0.60430 / 0.32 (36086) hydrogen bonds : bond 0.03951 / 2.71 ( 1068) hydrogen bonds : angle 5.08071 / 3.59 ( 2931) metal coordination : bond 0.00938 / 0.46 ( 4) metal coordination : angle 3.84054 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8810 (m-80) cc_final: 0.8081 (m-10) REVERT: C 340 GLN cc_start: 0.9407 (tt0) cc_final: 0.9203 (tm-30) REVERT: D 175 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: E 2 GLN cc_start: 0.8772 (mp10) cc_final: 0.8263 (mp10) REVERT: E 70 MET cc_start: 0.9368 (mmm) cc_final: 0.8757 (mmm) REVERT: E 168 MET cc_start: 0.8218 (mmm) cc_final: 0.7841 (tpp) REVERT: E 175 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: E 282 MET cc_start: 0.8813 (tpp) cc_final: 0.8174 (tpp) REVERT: F 182 MET cc_start: 0.8915 (mmm) cc_final: 0.8586 (mmm) REVERT: G 45 MET cc_start: 0.9161 (ptm) cc_final: 0.8861 (ptm) REVERT: G 46 MET cc_start: 0.8906 (ttp) cc_final: 0.8572 (ptm) REVERT: G 90 LYS cc_start: 0.9288 (ptpt) cc_final: 0.8984 (ptpp) REVERT: G 139 MET cc_start: 0.9084 (tpp) cc_final: 0.8860 (mmm) REVERT: G 145 MET cc_start: 0.9093 (mtm) cc_final: 0.8838 (mtm) REVERT: G 169 MET cc_start: 0.8846 (ppp) cc_final: 0.8419 (ppp) REVERT: G 282 MET cc_start: 0.9079 (tpp) cc_final: 0.8800 (tpp) REVERT: G 340 GLN cc_start: 0.9102 (mt0) cc_final: 0.8857 (mm-40) REVERT: H 42 MET cc_start: 0.9051 (mmm) cc_final: 0.8594 (mmm) REVERT: L 170 MET cc_start: 0.9359 (tpp) cc_final: 0.8911 (tpp) REVERT: L 201 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8050 (ttm) REVERT: L 252 LEU cc_start: 0.8734 (mp) cc_final: 0.8533 (mp) REVERT: L 265 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7484 (mt) REVERT: L 270 GLU cc_start: 0.9313 (tp30) cc_final: 0.8990 (tm-30) REVERT: L 327 MET cc_start: 0.9383 (mmp) cc_final: 0.9020 (mmt) REVERT: L 745 TYR cc_start: 0.8840 (m-80) cc_final: 0.8510 (t80) outliers start: 63 outliers final: 34 residues processed: 209 average time/residue: 0.1792 time to fit residues: 60.1622 Evaluate side-chains 191 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 524 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 228 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 150 optimal weight: 0.4980 chunk 262 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN F 30 ASN F 247 ASN ** L 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.045895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032472 restraints weight = 153146.168| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.24 r_work: 0.2778 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26067 Z= 0.239 Angle : 0.643 12.677 36092 Z= 0.335 Chirality : 0.045 0.358 4123 Planarity : 0.004 0.048 4124 Dihedral : 21.911 172.063 5110 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.65 % Allowed : 19.22 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2868 helix: 1.29 (0.16), residues: 1091 sheet: -0.51 (0.25), residues: 427 loop : -0.85 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 180 TYR 0.025 0.002 TYR L 307 PHE 0.018 0.002 PHE E 133 TRP 0.013 0.001 TRP G 258 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (26063) covalent geometry : angle 0.64105 / 0.34 (36086) hydrogen bonds : bond 0.04121 / 2.80 ( 1068) hydrogen bonds : angle 5.08877 / 3.59 ( 2931) metal coordination : bond 0.01439 / 0.70 ( 4) metal coordination : angle 3.88121 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8883 (m-80) cc_final: 0.8285 (m-10) REVERT: B 212 HIS cc_start: 0.9195 (OUTLIER) cc_final: 0.8745 (m90) REVERT: C 309 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8947 (mm110) REVERT: C 340 GLN cc_start: 0.9444 (tt0) cc_final: 0.9174 (tm-30) REVERT: D 175 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: D 328 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8784 (pp20) REVERT: E 2 GLN cc_start: 0.8801 (mp10) cc_final: 0.8301 (mp10) REVERT: E 168 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: E 175 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: E 282 MET cc_start: 0.8944 (tpp) cc_final: 0.8319 (tpp) REVERT: G 45 MET cc_start: 0.9180 (ptm) cc_final: 0.8768 (ptm) REVERT: G 46 MET cc_start: 0.8909 (ttp) cc_final: 0.8593 (ptm) REVERT: G 47 TYR cc_start: 0.9118 (m-10) cc_final: 0.8864 (m-10) REVERT: G 90 LYS cc_start: 0.9326 (ptpt) cc_final: 0.9066 (ptpp) REVERT: G 139 MET cc_start: 0.9135 (tpp) cc_final: 0.8905 (mmm) REVERT: G 169 MET cc_start: 0.8865 (ppp) cc_final: 0.8415 (ppp) REVERT: G 282 MET cc_start: 0.9061 (tpp) cc_final: 0.8859 (tpp) REVERT: G 336 LYS cc_start: 0.9355 (ptmm) cc_final: 0.9055 (ptmm) REVERT: G 340 GLN cc_start: 0.9060 (mt0) cc_final: 0.8772 (mm-40) REVERT: H 20 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7845 (ttt180) REVERT: H 42 MET cc_start: 0.9095 (mmm) cc_final: 0.8649 (mmm) REVERT: H 167 LEU cc_start: 0.9294 (pt) cc_final: 0.9054 (pp) REVERT: L 170 MET cc_start: 0.9334 (tpp) cc_final: 0.8887 (tpp) REVERT: L 265 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7573 (mt) REVERT: L 270 GLU cc_start: 0.9255 (tp30) cc_final: 0.9053 (tm-30) REVERT: L 327 MET cc_start: 0.9408 (mmp) cc_final: 0.9114 (mmt) REVERT: L 406 MET cc_start: 0.9166 (ppp) cc_final: 0.8556 (ppp) REVERT: L 745 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8504 (t80) outliers start: 61 outliers final: 43 residues processed: 203 average time/residue: 0.1754 time to fit residues: 57.5873 Evaluate side-chains 203 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 247 ASN Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 480 HIS Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 745 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 188 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 247 ASN F 247 ASN ** L 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.046094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.032775 restraints weight = 151911.527| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.25 r_work: 0.2793 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26067 Z= 0.161 Angle : 0.618 12.336 36092 Z= 0.323 Chirality : 0.044 0.343 4123 Planarity : 0.004 0.049 4124 Dihedral : 21.854 171.299 5110 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.73 % Allowed : 19.09 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2868 helix: 1.37 (0.16), residues: 1089 sheet: -0.48 (0.25), residues: 429 loop : -0.83 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.031 0.001 TYR L 307 PHE 0.016 0.001 PHE F 246 TRP 0.014 0.001 TRP G 258 HIS 0.016 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (26063) covalent geometry : angle 0.61651 / 0.32 (36086) hydrogen bonds : bond 0.03872 / 2.65 ( 1068) hydrogen bonds : angle 5.03892 / 3.56 ( 2931) metal coordination : bond 0.00964 / 0.47 ( 4) metal coordination : angle 3.49846 / 1.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8859 (m-80) cc_final: 0.8269 (m-10) REVERT: C 148 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.9192 (p) REVERT: C 340 GLN cc_start: 0.9411 (tt0) cc_final: 0.9207 (tm-30) REVERT: D 168 MET cc_start: 0.8130 (mmm) cc_final: 0.7830 (mmm) REVERT: D 175 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: D 328 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8750 (pp20) REVERT: E 2 GLN cc_start: 0.8799 (mp10) cc_final: 0.8287 (mp10) REVERT: E 175 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: F 182 MET cc_start: 0.8899 (mmm) cc_final: 0.8568 (mmm) REVERT: G 45 MET cc_start: 0.9180 (ptm) cc_final: 0.8837 (ptm) REVERT: G 46 MET cc_start: 0.8976 (ttp) cc_final: 0.8710 (ptm) REVERT: G 90 LYS cc_start: 0.9307 (ptpt) cc_final: 0.9056 (ptpp) REVERT: G 139 MET cc_start: 0.9097 (tpp) cc_final: 0.8872 (mmm) REVERT: G 169 MET cc_start: 0.8825 (ppp) cc_final: 0.8460 (ppp) REVERT: G 282 MET cc_start: 0.9048 (tpp) cc_final: 0.8833 (tpp) REVERT: G 336 LYS cc_start: 0.9369 (ptmm) cc_final: 0.9065 (ptmm) REVERT: G 340 GLN cc_start: 0.9083 (mt0) cc_final: 0.8775 (mm-40) REVERT: H 20 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (ttt180) REVERT: H 42 MET cc_start: 0.9123 (mmm) cc_final: 0.8713 (mmm) REVERT: H 88 MET cc_start: 0.9460 (mmm) cc_final: 0.9004 (mtp) REVERT: H 167 LEU cc_start: 0.9264 (pt) cc_final: 0.9022 (pp) REVERT: L 170 MET cc_start: 0.9326 (tpp) cc_final: 0.8870 (tpp) REVERT: L 265 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7557 (mt) REVERT: L 270 GLU cc_start: 0.9244 (tp30) cc_final: 0.9041 (tm-30) REVERT: L 327 MET cc_start: 0.9422 (mmp) cc_final: 0.9115 (mmm) REVERT: L 406 MET cc_start: 0.9222 (ppp) cc_final: 0.8590 (ppp) REVERT: L 447 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6837 (mmt) REVERT: L 745 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8522 (t80) outliers start: 63 outliers final: 43 residues processed: 203 average time/residue: 0.1718 time to fit residues: 56.3024 Evaluate side-chains 202 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 480 HIS Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 524 ARG Chi-restraints excluded: chain L residue 594 ASN Chi-restraints excluded: chain L residue 745 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 232 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 236 optimal weight: 50.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN F 2 GLN ** L 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.045915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032603 restraints weight = 152623.959| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.24 r_work: 0.2786 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26067 Z= 0.183 Angle : 0.621 12.162 36092 Z= 0.322 Chirality : 0.044 0.346 4123 Planarity : 0.004 0.049 4124 Dihedral : 21.813 171.666 5110 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.52 % Allowed : 19.26 % Favored : 78.22 % 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: 2868 helix: 1.39 (0.17), residues: 1095 sheet: -0.42 (0.25), residues: 419 loop : -0.84 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.031 0.001 TYR L 307 PHE 0.014 0.001 PHE E 133 TRP 0.014 0.001 TRP G 258 HIS 0.007 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (26063) covalent geometry : angle 0.61978 / 0.32 (36086) hydrogen bonds : bond 0.03844 / 2.62 ( 1068) hydrogen bonds : angle 5.00573 / 3.55 ( 2931) metal coordination : bond 0.01066 / 0.52 ( 4) metal coordination : angle 3.35684 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8875 (m-80) cc_final: 0.8252 (m-10) REVERT: B 212 HIS cc_start: 0.9106 (OUTLIER) cc_final: 0.8684 (m90) REVERT: C 148 SER cc_start: 0.9459 (OUTLIER) cc_final: 0.9196 (p) REVERT: C 309 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8960 (mm110) REVERT: C 340 GLN cc_start: 0.9421 (tt0) cc_final: 0.9209 (tm-30) REVERT: D 175 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: E 2 GLN cc_start: 0.8820 (mp10) cc_final: 0.8301 (mp10) REVERT: E 175 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: E 282 MET cc_start: 0.8886 (tpp) cc_final: 0.8313 (tpp) REVERT: F 182 MET cc_start: 0.8886 (mmm) cc_final: 0.8561 (mmm) REVERT: G 45 MET cc_start: 0.9172 (ptm) cc_final: 0.8516 (ppp) REVERT: G 46 MET cc_start: 0.8966 (ttp) cc_final: 0.8564 (ptm) REVERT: G 90 LYS cc_start: 0.9316 (ptpt) cc_final: 0.9076 (ptpp) REVERT: G 139 MET cc_start: 0.9102 (tpp) cc_final: 0.8871 (mmm) REVERT: G 169 MET cc_start: 0.8817 (ppp) cc_final: 0.8406 (ppp) REVERT: G 282 MET cc_start: 0.9032 (tpp) cc_final: 0.8819 (tpp) REVERT: G 340 GLN cc_start: 0.9075 (mt0) cc_final: 0.8792 (mm-40) REVERT: H 20 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7728 (ttt180) REVERT: H 42 MET cc_start: 0.9149 (mmm) cc_final: 0.8740 (mmm) REVERT: H 88 MET cc_start: 0.9450 (mmm) cc_final: 0.9016 (mtp) REVERT: H 167 LEU cc_start: 0.9257 (pt) cc_final: 0.9017 (pp) REVERT: L 170 MET cc_start: 0.9315 (tpp) cc_final: 0.8857 (tpp) REVERT: L 265 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7494 (mt) REVERT: L 327 MET cc_start: 0.9408 (mmp) cc_final: 0.9115 (mmm) REVERT: L 406 MET cc_start: 0.9217 (ppp) cc_final: 0.8620 (ppp) REVERT: L 447 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6801 (mmt) REVERT: L 745 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8533 (t80) outliers start: 58 outliers final: 45 residues processed: 199 average time/residue: 0.1641 time to fit residues: 52.8990 Evaluate side-chains 203 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 480 HIS Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 524 ARG Chi-restraints excluded: chain L residue 594 ASN Chi-restraints excluded: chain L residue 745 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 251 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 0.0270 chunk 151 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN ** L 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 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 = 0.3432 r_free = 0.3432 target = 0.046309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033078 restraints weight = 152359.341| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.26 r_work: 0.2807 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26067 Z= 0.132 Angle : 0.617 11.848 36092 Z= 0.318 Chirality : 0.043 0.333 4123 Planarity : 0.004 0.049 4124 Dihedral : 21.755 171.426 5110 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.30 % Allowed : 19.61 % Favored : 78.09 % 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: 0.18 (0.16), residues: 2868 helix: 1.44 (0.17), residues: 1091 sheet: -0.39 (0.25), residues: 419 loop : -0.78 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.018 0.001 TYR A 79 PHE 0.014 0.001 PHE H 175 TRP 0.013 0.001 TRP G 258 HIS 0.019 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (26063) covalent geometry : angle 0.61532 / 0.32 (36086) hydrogen bonds : bond 0.03698 / 2.53 ( 1068) hydrogen bonds : angle 4.92673 / 3.50 ( 2931) metal coordination : bond 0.00717 / 0.35 ( 4) metal coordination : angle 3.12651 / 1.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8877 (m-80) cc_final: 0.8256 (m-10) REVERT: D 1 MET cc_start: 0.7661 (tpp) cc_final: 0.7427 (tpp) REVERT: D 168 MET cc_start: 0.8099 (mmm) cc_final: 0.7894 (mmm) REVERT: D 175 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: E 2 GLN cc_start: 0.8801 (mp10) cc_final: 0.8294 (mp10) REVERT: E 168 MET cc_start: 0.8819 (tpp) cc_final: 0.8382 (mmm) REVERT: E 175 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: E 282 MET cc_start: 0.8805 (tpp) cc_final: 0.8281 (tpp) REVERT: F 182 MET cc_start: 0.8844 (mmm) cc_final: 0.8549 (mmm) REVERT: G 45 MET cc_start: 0.9141 (ptm) cc_final: 0.8550 (ppp) REVERT: G 46 MET cc_start: 0.8979 (ttp) cc_final: 0.8599 (ptm) REVERT: G 90 LYS cc_start: 0.9275 (ptpt) cc_final: 0.9057 (ptpp) REVERT: G 139 MET cc_start: 0.9060 (tpp) cc_final: 0.8844 (mmm) REVERT: G 169 MET cc_start: 0.8831 (ppp) cc_final: 0.8468 (ppp) REVERT: G 340 GLN cc_start: 0.9114 (mt0) cc_final: 0.8830 (mm-40) REVERT: H 42 MET cc_start: 0.9177 (mmm) cc_final: 0.8779 (mmm) REVERT: H 88 MET cc_start: 0.9424 (mmm) cc_final: 0.9015 (mtp) REVERT: H 167 LEU cc_start: 0.9246 (pt) cc_final: 0.9007 (pp) REVERT: L 170 MET cc_start: 0.9319 (tpp) cc_final: 0.8865 (tpp) REVERT: L 201 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (tmm) REVERT: L 327 MET cc_start: 0.9381 (mmp) cc_final: 0.9127 (mmm) REVERT: L 406 MET cc_start: 0.9214 (ppp) cc_final: 0.8640 (ppp) REVERT: L 447 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6785 (mmt) REVERT: L 745 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8505 (t80) outliers start: 53 outliers final: 39 residues processed: 194 average time/residue: 0.1687 time to fit residues: 52.6432 Evaluate side-chains 195 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 480 HIS Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 524 ARG Chi-restraints excluded: chain L residue 745 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 296 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 236 optimal weight: 50.0000 chunk 266 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.046229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033070 restraints weight = 152746.025| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.18 r_work: 0.2809 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26067 Z= 0.145 Angle : 0.622 13.280 36092 Z= 0.320 Chirality : 0.043 0.336 4123 Planarity : 0.004 0.090 4124 Dihedral : 21.669 172.197 5107 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.21 % Allowed : 19.65 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2868 helix: 1.43 (0.16), residues: 1091 sheet: -0.37 (0.25), residues: 419 loop : -0.76 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 20 TYR 0.018 0.001 TYR A 79 PHE 0.013 0.001 PHE H 175 TRP 0.012 0.001 TRP G 258 HIS 0.003 0.001 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (26063) covalent geometry : angle 0.62098 / 0.32 (36086) hydrogen bonds : bond 0.03687 / 2.53 ( 1068) hydrogen bonds : angle 4.88631 / 3.48 ( 2931) metal coordination : bond 0.00848 / 0.41 ( 4) metal coordination : angle 3.04020 / 1.62 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8926 (m-80) cc_final: 0.8370 (m-10) REVERT: B 212 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8775 (m90) REVERT: C 313 GLN cc_start: 0.8884 (mp10) cc_final: 0.8631 (tm-30) REVERT: D 139 MET cc_start: 0.8613 (ptp) cc_final: 0.8283 (mtm) REVERT: D 175 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: E 2 GLN cc_start: 0.8768 (mp10) cc_final: 0.8272 (mp10) REVERT: E 175 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: E 282 MET cc_start: 0.8813 (tpp) cc_final: 0.8314 (tpp) REVERT: F 182 MET cc_start: 0.8820 (mmm) cc_final: 0.8581 (mmm) REVERT: G 45 MET cc_start: 0.9135 (ptm) cc_final: 0.8662 (ppp) REVERT: G 46 MET cc_start: 0.8952 (ttp) cc_final: 0.8685 (ptm) REVERT: G 139 MET cc_start: 0.9052 (tpp) cc_final: 0.8843 (mmm) REVERT: G 169 MET cc_start: 0.8835 (ppp) cc_final: 0.8488 (ppp) REVERT: G 340 GLN cc_start: 0.9099 (mt0) cc_final: 0.8838 (mm-40) REVERT: H 42 MET cc_start: 0.9203 (mmm) cc_final: 0.8822 (mmm) REVERT: H 88 MET cc_start: 0.9410 (mmm) cc_final: 0.8995 (mtp) REVERT: H 167 LEU cc_start: 0.9247 (pt) cc_final: 0.9021 (pp) REVERT: L 170 MET cc_start: 0.9324 (tpp) cc_final: 0.8872 (tpp) REVERT: L 327 MET cc_start: 0.9337 (mmp) cc_final: 0.9100 (mmm) REVERT: L 406 MET cc_start: 0.9228 (ppp) cc_final: 0.8684 (ppp) REVERT: L 447 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6715 (mmt) REVERT: L 745 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8493 (t80) outliers start: 51 outliers final: 38 residues processed: 191 average time/residue: 0.1690 time to fit residues: 52.6379 Evaluate side-chains 190 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 293 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain L residue 201 MET Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 472 LEU Chi-restraints excluded: chain L residue 480 HIS Chi-restraints excluded: chain L residue 523 THR Chi-restraints excluded: chain L residue 524 ARG Chi-restraints excluded: chain L residue 745 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 300 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 250 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN ** L 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.046347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033094 restraints weight = 150870.484| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.23 r_work: 0.2810 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26067 Z= 0.134 Angle : 0.615 11.332 36092 Z= 0.316 Chirality : 0.043 0.332 4123 Planarity : 0.004 0.087 4124 Dihedral : 21.639 172.267 5107 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.82 % Allowed : 20.04 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2868 helix: 1.45 (0.17), residues: 1090 sheet: -0.38 (0.25), residues: 425 loop : -0.74 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 20 TYR 0.030 0.001 TYR L 307 PHE 0.014 0.001 PHE H 175 TRP 0.013 0.001 TRP G 258 HIS 0.019 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26063) covalent geometry : angle 0.61361 / 0.32 (36086) hydrogen bonds : bond 0.03633 / 2.50 ( 1068) hydrogen bonds : angle 4.85039 / 3.46 ( 2931) metal coordination : bond 0.00754 / 0.37 ( 4) metal coordination : angle 2.96423 / 1.58 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.33 seconds wall clock time: 111 minutes 33.90 seconds (6693.90 seconds total)