Starting phenix.real_space_refine on Wed Mar 4 23:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbl_16544/03_2026/8cbl_16544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbl_16544/03_2026/8cbl_16544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cbl_16544/03_2026/8cbl_16544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbl_16544/03_2026/8cbl_16544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbl_16544/03_2026/8cbl_16544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbl_16544/03_2026/8cbl_16544.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 1.134 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 94 5.49 5 S 86 5.16 5 C 10566 2.51 5 N 3025 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17260 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5400 Classifications: {'peptide': 692} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 648} Chain breaks: 1 Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2442 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 8, 'TRANS': 285} Chain: "T" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1823 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 21, 'rna3p': 64} Chain breaks: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.17 Number of scatterers: 17260 At special positions: 0 Unit cell: (102.364, 121.272, 165.608, 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 86 16.00 P 94 15.00 O 3488 8.00 N 3025 7.00 C 10566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 666.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 900 " pdb="ZN ZN E 900 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 900 " - pdb=" ND1 HIS E 724 " 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3658 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 14 sheets defined 49.9% alpha, 13.0% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.698A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.406A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.874A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.601A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.634A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.809A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.861A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.439A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.709A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.639A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.591A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.766A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 137 removed outlier: 3.648A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.406A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.838A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.575A pdb=" N GLY D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.481A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.645A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 90 through 98 removed outlier: 3.513A pdb=" N LEU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.708A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 270 through 281 removed outlier: 3.979A pdb=" N ILE E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.674A pdb=" N LEU E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 322 Proline residue: E 319 - end of helix removed outlier: 4.101A pdb=" N GLU E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 330 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 362 removed outlier: 4.111A pdb=" N PHE E 361 " --> pdb=" O TRP E 357 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY E 362 " --> pdb=" O MET E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 393 removed outlier: 3.720A pdb=" N LEU E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE E 392 " --> pdb=" O GLN E 388 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 455 through 470 Processing helix chain 'E' and resid 473 through 477 removed outlier: 3.706A pdb=" N LYS E 476 " --> pdb=" O PRO E 473 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 473 through 477' Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 554 through 570 removed outlier: 3.547A pdb=" N ILE E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.714A pdb=" N LYS E 585 " --> pdb=" O PRO E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'E' and resid 607 through 611 Processing helix chain 'E' and resid 618 through 632 removed outlier: 3.622A pdb=" N CYS E 632 " --> pdb=" O LEU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 677 Processing helix chain 'E' and resid 693 through 701 Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 760 through 762 No H-bonds generated for 'chain 'E' and resid 760 through 762' Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 794 Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 126 through 168 removed outlier: 3.815A pdb=" N GLU F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 182 through 202 Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.706A pdb=" N MET F 215 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 237 removed outlier: 3.587A pdb=" N ASN F 237 " --> pdb=" O TRP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 Processing helix chain 'F' and resid 277 through 282 removed outlier: 3.609A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 330 removed outlier: 3.663A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.390A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.337A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 12 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL B 89 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 14 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.423A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 148 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET C 194 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE C 150 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C 196 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN C 152 " --> pdb=" O ILE C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.395A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 167 removed outlier: 6.580A pdb=" N CYS E 136 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ARG E 166 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 138 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL E 58 " --> pdb=" O LEU E 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 178 through 185 removed outlier: 6.205A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA E 305 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL E 341 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL E 307 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET E 343 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 309 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AB3, first strand: chain 'E' and resid 602 through 605 removed outlier: 6.161A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU E 577 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER E 511 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE E 543 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 513 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU E 512 " --> pdb=" O ASN E 505 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN E 505 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU E 514 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU E 503 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 634 through 641 removed outlier: 6.465A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.603A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.99 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: 3780 1.33 - 1.45: 3938 1.45 - 1.57: 9724 1.57 - 1.69: 183 1.69 - 1.81: 136 Bond restraints: 17761 Sorted by residual: bond pdb=" CA SER E 507 " pdb=" CB SER E 507 " ideal model delta sigma weight residual 1.535 1.463 0.071 1.36e-02 5.41e+03 2.75e+01 bond pdb=" CE1 HIS E 724 " pdb=" NE2 HIS E 724 " ideal model delta sigma weight residual 1.321 1.280 0.041 1.00e-02 1.00e+04 1.67e+01 bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.579 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O3 NAD C 301 " pdb=" PA NAD C 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 17756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 23837 1.41 - 2.82: 463 2.82 - 4.22: 156 4.22 - 5.63: 25 5.63 - 7.04: 8 Bond angle restraints: 24489 Sorted by residual: angle pdb=" CA HIS E 724 " pdb=" CB HIS E 724 " pdb=" CG HIS E 724 " ideal model delta sigma weight residual 113.80 109.19 4.61 1.00e+00 1.00e+00 2.13e+01 angle pdb=" C ASN E 723 " pdb=" N HIS E 724 " pdb=" CA HIS E 724 " ideal model delta sigma weight residual 122.93 115.97 6.96 1.51e+00 4.39e-01 2.13e+01 angle pdb=" N TYR F 135 " pdb=" CA TYR F 135 " pdb=" C TYR F 135 " ideal model delta sigma weight residual 110.97 106.57 4.40 1.09e+00 8.42e-01 1.63e+01 angle pdb=" CA ARG F 181 " pdb=" C ARG F 181 " pdb=" O ARG F 181 " ideal model delta sigma weight residual 122.41 117.91 4.50 1.21e+00 6.83e-01 1.38e+01 angle pdb=" N ASP B 113 " pdb=" CA ASP B 113 " pdb=" C ASP B 113 " ideal model delta sigma weight residual 111.14 107.39 3.75 1.08e+00 8.57e-01 1.21e+01 ... (remaining 24484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.76: 10364 30.76 - 61.52: 466 61.52 - 92.28: 84 92.28 - 123.04: 5 123.04 - 153.80: 1 Dihedral angle restraints: 10920 sinusoidal: 5226 harmonic: 5694 Sorted by residual: dihedral pdb=" O4' C T 50 " pdb=" C1' C T 50 " pdb=" N1 C T 50 " pdb=" C2 C T 50 " ideal model delta sinusoidal sigma weight residual -128.00 -59.52 -68.48 1 1.70e+01 3.46e-03 2.10e+01 dihedral pdb=" CA VAL F 206 " pdb=" C VAL F 206 " pdb=" N PHE F 207 " pdb=" CA PHE F 207 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLN F 343 " pdb=" C GLN F 343 " pdb=" N TRP F 344 " pdb=" CA TRP F 344 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2295 0.042 - 0.084: 381 0.084 - 0.126: 192 0.126 - 0.169: 10 0.169 - 0.211: 4 Chirality restraints: 2882 Sorted by residual: chirality pdb=" CA TYR F 135 " pdb=" N TYR F 135 " pdb=" C TYR F 135 " pdb=" CB TYR F 135 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C2' SAH F 501 " pdb=" C1' SAH F 501 " pdb=" C3' SAH F 501 " pdb=" O2' SAH F 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" C3' G T 49 " pdb=" C4' G T 49 " pdb=" O3' G T 49 " pdb=" C2' G T 49 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 2879 not shown) Planarity restraints: 2847 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.045 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.010 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.023 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 724 " 0.005 2.00e-02 2.50e+03 2.70e-02 1.10e+01 pdb=" CG HIS E 724 " -0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS E 724 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS E 724 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS E 724 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS E 724 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.027 2.00e-02 2.50e+03 1.55e-02 4.79e+00 pdb=" C2N NAD B 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " -0.012 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " -0.011 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.024 2.00e-02 2.50e+03 ... (remaining 2844 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 111 2.49 - 3.09: 12999 3.09 - 3.70: 28376 3.70 - 4.30: 41708 4.30 - 4.90: 65728 Nonbonded interactions: 148922 Sorted by model distance: nonbonded pdb=" O2' G T 49 " pdb=" O5' C T 50 " model vdw 1.890 3.040 nonbonded pdb=" O2' U T 51 " pdb=" O5' U T 52 " model vdw 1.945 3.040 nonbonded pdb=" O2' A T 3 " pdb=" OP1 A T 4 " model vdw 2.056 3.040 nonbonded pdb=" O2' C T 69 " pdb=" OP2 G T 70 " model vdw 2.088 3.040 nonbonded pdb=" O2' U T 51 " pdb=" O3' U T 52 " model vdw 2.132 3.040 ... (remaining 148917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 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: 7.610 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: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.040 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 0.562 17763 Z= 0.233 Angle : 0.554 7.041 24489 Z= 0.280 Chirality : 0.040 0.211 2882 Planarity : 0.004 0.038 2847 Dihedral : 17.015 153.803 7262 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.78 (0.19), residues: 1992 helix: 1.80 (0.18), residues: 846 sheet: -0.42 (0.29), residues: 308 loop : -0.38 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.020 0.001 TYR F 135 PHE 0.014 0.001 PHE E 77 TRP 0.010 0.001 TRP E 587 HIS 0.042 0.001 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00362 (17761) covalent geometry : angle 0.55374 (24489) hydrogen bonds : bond 0.15383 ( 823) hydrogen bonds : angle 6.66433 ( 2290) metal coordination : bond 0.39713 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.483 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: C 79 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7985 (mtpp) REVERT: E 57 THR cc_start: 0.7803 (t) cc_final: 0.7442 (t) REVERT: E 69 ASP cc_start: 0.7392 (p0) cc_final: 0.6669 (p0) REVERT: E 83 TYR cc_start: 0.6638 (m-80) cc_final: 0.5521 (m-80) REVERT: E 370 LEU cc_start: 0.7764 (tp) cc_final: 0.7152 (tp) outliers start: 0 outliers final: 1 residues processed: 479 average time/residue: 0.5845 time to fit residues: 312.2247 Evaluate side-chains 316 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 633 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 146 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN C 260 GLN D 152 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 461 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN F 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.098606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.072099 restraints weight = 45336.013| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.32 r_work: 0.2818 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17763 Z= 0.184 Angle : 0.722 10.326 24489 Z= 0.356 Chirality : 0.044 0.304 2882 Planarity : 0.005 0.046 2847 Dihedral : 15.947 153.664 3631 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.40 % Allowed : 13.90 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.84 (0.19), residues: 1992 helix: 1.90 (0.18), residues: 851 sheet: -0.40 (0.29), residues: 293 loop : -0.43 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 781 TYR 0.017 0.002 TYR E 663 PHE 0.030 0.002 PHE F 97 TRP 0.020 0.002 TRP E 587 HIS 0.019 0.002 HIS E 724 Details of bonding type rmsd covalent geometry : bond 0.00414 (17761) covalent geometry : angle 0.72151 (24489) hydrogen bonds : bond 0.04903 ( 823) hydrogen bonds : angle 5.34095 ( 2290) metal coordination : bond 0.00483 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 364 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8916 (m-30) cc_final: 0.8648 (m-30) REVERT: A 135 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8487 (tp30) REVERT: A 143 GLN cc_start: 0.9057 (mp10) cc_final: 0.8727 (mp10) REVERT: B 41 ASP cc_start: 0.8673 (t0) cc_final: 0.8175 (t0) REVERT: C 135 GLU cc_start: 0.8935 (tp30) cc_final: 0.8479 (tp30) REVERT: C 232 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8776 (mt-10) REVERT: D 113 ASP cc_start: 0.9205 (m-30) cc_final: 0.8997 (m-30) REVERT: E 77 PHE cc_start: 0.9171 (p90) cc_final: 0.8947 (p90) REVERT: E 98 HIS cc_start: 0.8811 (m90) cc_final: 0.8532 (m90) REVERT: E 101 LYS cc_start: 0.8713 (tppt) cc_final: 0.8113 (tppt) REVERT: E 109 PHE cc_start: 0.9324 (m-80) cc_final: 0.9116 (m-80) REVERT: E 115 TRP cc_start: 0.9349 (t-100) cc_final: 0.9098 (t-100) REVERT: E 239 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7541 (tp) REVERT: E 316 PHE cc_start: 0.9041 (m-80) cc_final: 0.8477 (m-80) REVERT: E 326 PHE cc_start: 0.9100 (m-10) cc_final: 0.8818 (m-80) REVERT: E 442 ASN cc_start: 0.9359 (t0) cc_final: 0.9156 (t0) REVERT: E 449 GLU cc_start: 0.8991 (pt0) cc_final: 0.8668 (pt0) REVERT: E 667 THR cc_start: 0.7672 (t) cc_final: 0.7338 (m) REVERT: E 781 ARG cc_start: 0.8902 (ptp-110) cc_final: 0.8625 (ptp-110) REVERT: F 114 GLU cc_start: 0.9314 (pm20) cc_final: 0.8828 (pm20) outliers start: 39 outliers final: 18 residues processed: 380 average time/residue: 0.5712 time to fit residues: 242.8968 Evaluate side-chains 327 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 595 CYS Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 20 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 71 optimal weight: 0.0270 chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 GLN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.099854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.073160 restraints weight = 46192.265| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.38 r_work: 0.2844 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17763 Z= 0.139 Angle : 0.679 11.431 24489 Z= 0.337 Chirality : 0.043 0.257 2882 Planarity : 0.005 0.046 2847 Dihedral : 15.760 162.451 3629 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 16.36 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.83 (0.19), residues: 1992 helix: 1.86 (0.18), residues: 852 sheet: -0.27 (0.28), residues: 315 loop : -0.46 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 785 TYR 0.024 0.002 TYR E 59 PHE 0.037 0.002 PHE F 97 TRP 0.021 0.002 TRP E 587 HIS 0.007 0.001 HIS E 98 Details of bonding type rmsd covalent geometry : bond 0.00310 (17761) covalent geometry : angle 0.67875 (24489) hydrogen bonds : bond 0.04300 ( 823) hydrogen bonds : angle 5.15465 ( 2290) metal coordination : bond 0.00461 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 362 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8855 (m-30) cc_final: 0.8641 (m-30) REVERT: A 135 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8542 (tp30) REVERT: A 142 ASP cc_start: 0.8818 (t0) cc_final: 0.8590 (t0) REVERT: A 143 GLN cc_start: 0.9082 (mp10) cc_final: 0.8717 (mp10) REVERT: A 160 GLU cc_start: 0.8999 (pm20) cc_final: 0.8563 (pm20) REVERT: B 41 ASP cc_start: 0.8685 (t0) cc_final: 0.8403 (t70) REVERT: C 104 LYS cc_start: 0.9188 (ptpp) cc_final: 0.8967 (pttt) REVERT: C 232 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8872 (mt-10) REVERT: D 28 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8898 (mt-10) REVERT: D 113 ASP cc_start: 0.9180 (m-30) cc_final: 0.8918 (m-30) REVERT: D 211 GLU cc_start: 0.7745 (pp20) cc_final: 0.7522 (tm-30) REVERT: E 77 PHE cc_start: 0.9241 (p90) cc_final: 0.9009 (p90) REVERT: E 101 LYS cc_start: 0.8614 (tppt) cc_final: 0.8076 (tppt) REVERT: E 115 TRP cc_start: 0.9337 (t-100) cc_final: 0.9023 (t-100) REVERT: E 239 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7516 (tp) REVERT: E 280 ASP cc_start: 0.8607 (m-30) cc_final: 0.8079 (p0) REVERT: E 316 PHE cc_start: 0.8992 (m-80) cc_final: 0.8423 (m-80) REVERT: E 326 PHE cc_start: 0.9139 (m-10) cc_final: 0.8822 (m-80) REVERT: E 442 ASN cc_start: 0.9349 (t0) cc_final: 0.9060 (t0) REVERT: E 445 GLU cc_start: 0.9281 (tp30) cc_final: 0.9018 (tp30) REVERT: E 449 GLU cc_start: 0.8991 (pt0) cc_final: 0.8653 (pt0) REVERT: E 518 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8447 (tm-30) REVERT: E 569 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9050 (tp) REVERT: E 685 HIS cc_start: 0.9029 (t70) cc_final: 0.8776 (t70) REVERT: E 771 PHE cc_start: 0.8782 (m-10) cc_final: 0.8519 (m-10) REVERT: E 774 ASP cc_start: 0.9048 (t70) cc_final: 0.8780 (t70) REVERT: E 778 MET cc_start: 0.9304 (mmm) cc_final: 0.8868 (mmm) REVERT: E 781 ARG cc_start: 0.8609 (ptp-110) cc_final: 0.8174 (ptp-170) REVERT: E 782 ARG cc_start: 0.9393 (mtm110) cc_final: 0.9150 (ptp-110) outliers start: 42 outliers final: 18 residues processed: 382 average time/residue: 0.5474 time to fit residues: 235.2942 Evaluate side-chains 327 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 205 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 170 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 147 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN ** E 644 HIS ** 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 = 0.3646 r_free = 0.3646 target = 0.098418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071709 restraints weight = 46221.261| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.36 r_work: 0.2830 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17763 Z= 0.164 Angle : 0.677 8.704 24489 Z= 0.339 Chirality : 0.043 0.264 2882 Planarity : 0.005 0.048 2847 Dihedral : 15.701 173.137 3629 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.77 % Allowed : 18.57 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.84 (0.19), residues: 1992 helix: 1.87 (0.18), residues: 853 sheet: -0.28 (0.28), residues: 318 loop : -0.45 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 785 TYR 0.022 0.002 TYR E 354 PHE 0.036 0.002 PHE F 97 TRP 0.019 0.002 TRP E 587 HIS 0.009 0.001 HIS E 702 Details of bonding type rmsd covalent geometry : bond 0.00367 (17761) covalent geometry : angle 0.67737 (24489) hydrogen bonds : bond 0.04224 ( 823) hydrogen bonds : angle 5.13747 ( 2290) metal coordination : bond 0.00274 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8593 (tp30) REVERT: A 143 GLN cc_start: 0.9106 (mp10) cc_final: 0.8730 (mp10) REVERT: A 160 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: B 70 ASP cc_start: 0.9277 (m-30) cc_final: 0.9061 (m-30) REVERT: D 113 ASP cc_start: 0.9192 (m-30) cc_final: 0.8898 (m-30) REVERT: D 211 GLU cc_start: 0.7774 (pp20) cc_final: 0.7530 (tm-30) REVERT: E 77 PHE cc_start: 0.9311 (p90) cc_final: 0.9108 (p90) REVERT: E 101 LYS cc_start: 0.8579 (tppt) cc_final: 0.8125 (tppt) REVERT: E 104 ARG cc_start: 0.8806 (mpp80) cc_final: 0.8557 (mpp80) REVERT: E 115 TRP cc_start: 0.9353 (t-100) cc_final: 0.9128 (t-100) REVERT: E 239 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8309 (mt) REVERT: E 243 PHE cc_start: 0.8277 (m-10) cc_final: 0.7976 (m-10) REVERT: E 280 ASP cc_start: 0.8691 (m-30) cc_final: 0.8123 (p0) REVERT: E 326 PHE cc_start: 0.9149 (m-10) cc_final: 0.8770 (m-10) REVERT: E 412 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.6644 (mm) REVERT: E 442 ASN cc_start: 0.9374 (t0) cc_final: 0.9074 (t0) REVERT: E 445 GLU cc_start: 0.9292 (tp30) cc_final: 0.9023 (tp30) REVERT: E 449 GLU cc_start: 0.9040 (pt0) cc_final: 0.8667 (pt0) REVERT: E 569 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8948 (mp) REVERT: E 649 PHE cc_start: 0.8771 (m-80) cc_final: 0.8187 (m-80) REVERT: E 750 MET cc_start: 0.8323 (mtp) cc_final: 0.8109 (mtp) REVERT: E 771 PHE cc_start: 0.8847 (m-10) cc_final: 0.8579 (m-10) REVERT: E 779 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9372 (mp0) REVERT: F 146 ARG cc_start: 0.9399 (tpp-160) cc_final: 0.8928 (mmp80) REVERT: F 251 ASP cc_start: 0.8998 (m-30) cc_final: 0.8519 (t0) outliers start: 45 outliers final: 20 residues processed: 354 average time/residue: 0.5261 time to fit residues: 210.1612 Evaluate side-chains 322 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 298 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072520 restraints weight = 45826.841| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.35 r_work: 0.2843 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17763 Z= 0.140 Angle : 0.675 8.947 24489 Z= 0.337 Chirality : 0.043 0.244 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.646 175.599 3629 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.89 % Allowed : 19.80 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.81 (0.19), residues: 1992 helix: 1.91 (0.18), residues: 852 sheet: -0.43 (0.27), residues: 336 loop : -0.47 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 782 TYR 0.016 0.001 TYR E 528 PHE 0.034 0.002 PHE F 97 TRP 0.019 0.002 TRP E 587 HIS 0.004 0.001 HIS E 749 Details of bonding type rmsd covalent geometry : bond 0.00318 (17761) covalent geometry : angle 0.67542 (24489) hydrogen bonds : bond 0.04024 ( 823) hydrogen bonds : angle 5.03691 ( 2290) metal coordination : bond 0.00304 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8615 (tp30) REVERT: A 143 GLN cc_start: 0.9111 (mp10) cc_final: 0.8730 (mp10) REVERT: A 160 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8616 (pm20) REVERT: D 28 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8884 (mt-10) REVERT: D 113 ASP cc_start: 0.9154 (m-30) cc_final: 0.8866 (m-30) REVERT: E 115 TRP cc_start: 0.9338 (t-100) cc_final: 0.9104 (t-100) REVERT: E 239 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7806 (pp) REVERT: E 243 PHE cc_start: 0.8280 (m-10) cc_final: 0.7805 (m-10) REVERT: E 280 ASP cc_start: 0.8666 (m-30) cc_final: 0.8070 (p0) REVERT: E 326 PHE cc_start: 0.9107 (m-10) cc_final: 0.8754 (m-10) REVERT: E 412 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7793 (tp) REVERT: E 442 ASN cc_start: 0.9391 (t0) cc_final: 0.9090 (t0) REVERT: E 445 GLU cc_start: 0.9325 (tp30) cc_final: 0.9033 (tp30) REVERT: E 449 GLU cc_start: 0.9063 (pt0) cc_final: 0.8570 (pt0) REVERT: E 569 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8957 (mp) REVERT: E 577 LEU cc_start: 0.9622 (mp) cc_final: 0.9360 (tp) REVERT: E 649 PHE cc_start: 0.8800 (m-80) cc_final: 0.8227 (m-80) REVERT: E 651 CYS cc_start: 0.8453 (t) cc_final: 0.8050 (p) REVERT: E 696 GLU cc_start: 0.9296 (mp0) cc_final: 0.8996 (mp0) REVERT: E 771 PHE cc_start: 0.9022 (m-10) cc_final: 0.8491 (m-10) REVERT: E 775 ILE cc_start: 0.9703 (mt) cc_final: 0.9472 (pp) REVERT: E 780 GLU cc_start: 0.9274 (pp20) cc_final: 0.8842 (pp20) REVERT: F 146 ARG cc_start: 0.9399 (tpp-160) cc_final: 0.8949 (mmp80) REVERT: F 251 ASP cc_start: 0.8985 (m-30) cc_final: 0.8491 (t0) outliers start: 47 outliers final: 21 residues processed: 340 average time/residue: 0.5128 time to fit residues: 197.9798 Evaluate side-chains 304 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 191 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 GLN E 531 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072611 restraints weight = 45690.433| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.34 r_work: 0.2847 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17763 Z= 0.144 Angle : 0.690 10.699 24489 Z= 0.342 Chirality : 0.043 0.266 2882 Planarity : 0.005 0.049 2847 Dihedral : 15.570 170.281 3629 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.71 % Allowed : 21.40 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.83 (0.19), residues: 1992 helix: 1.94 (0.18), residues: 849 sheet: -0.45 (0.28), residues: 339 loop : -0.45 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 781 TYR 0.017 0.001 TYR F 137 PHE 0.029 0.001 PHE E 77 TRP 0.026 0.002 TRP E 433 HIS 0.007 0.001 HIS E 749 Details of bonding type rmsd covalent geometry : bond 0.00327 (17761) covalent geometry : angle 0.68980 (24489) hydrogen bonds : bond 0.04009 ( 823) hydrogen bonds : angle 4.96872 ( 2290) metal coordination : bond 0.00140 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8922 (t0) cc_final: 0.8704 (t0) REVERT: A 143 GLN cc_start: 0.9130 (mp10) cc_final: 0.8749 (mp10) REVERT: A 160 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: D 113 ASP cc_start: 0.9146 (m-30) cc_final: 0.8847 (m-30) REVERT: E 154 PHE cc_start: 0.9109 (p90) cc_final: 0.8258 (m-10) REVERT: E 179 THR cc_start: 0.8549 (p) cc_final: 0.8086 (t) REVERT: E 239 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.7870 (pp) REVERT: E 280 ASP cc_start: 0.8674 (m-30) cc_final: 0.8063 (p0) REVERT: E 326 PHE cc_start: 0.9099 (m-10) cc_final: 0.8774 (m-10) REVERT: E 412 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7632 (tp) REVERT: E 442 ASN cc_start: 0.9405 (t0) cc_final: 0.9108 (t0) REVERT: E 445 GLU cc_start: 0.9353 (tp30) cc_final: 0.9144 (tp30) REVERT: E 449 GLU cc_start: 0.9096 (pt0) cc_final: 0.8690 (pt0) REVERT: E 533 ASP cc_start: 0.9100 (p0) cc_final: 0.8555 (t70) REVERT: E 577 LEU cc_start: 0.9609 (mp) cc_final: 0.9344 (tp) REVERT: E 649 PHE cc_start: 0.8804 (m-80) cc_final: 0.8268 (m-80) REVERT: E 684 ILE cc_start: 0.8977 (pp) cc_final: 0.8762 (pp) REVERT: E 721 MET cc_start: 0.9326 (tpp) cc_final: 0.9096 (tpp) REVERT: E 723 ASN cc_start: 0.9776 (t0) cc_final: 0.9245 (p0) REVERT: E 771 PHE cc_start: 0.9058 (m-10) cc_final: 0.8509 (m-10) REVERT: F 146 ARG cc_start: 0.9405 (tpp-160) cc_final: 0.8953 (mmp80) REVERT: F 251 ASP cc_start: 0.8975 (m-30) cc_final: 0.8500 (t0) outliers start: 44 outliers final: 25 residues processed: 326 average time/residue: 0.4873 time to fit residues: 181.1970 Evaluate side-chains 302 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 46 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** 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 = 0.3670 r_free = 0.3670 target = 0.099668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073023 restraints weight = 45532.480| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.34 r_work: 0.2860 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17763 Z= 0.143 Angle : 0.719 14.023 24489 Z= 0.356 Chirality : 0.044 0.350 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.514 167.113 3629 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.52 % Allowed : 22.20 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.79 (0.19), residues: 1992 helix: 1.90 (0.18), residues: 853 sheet: -0.50 (0.28), residues: 323 loop : -0.48 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 782 TYR 0.017 0.001 TYR E 354 PHE 0.030 0.002 PHE E 719 TRP 0.024 0.002 TRP F 101 HIS 0.006 0.001 HIS E 702 Details of bonding type rmsd covalent geometry : bond 0.00325 (17761) covalent geometry : angle 0.71933 (24489) hydrogen bonds : bond 0.03981 ( 823) hydrogen bonds : angle 4.93830 ( 2290) metal coordination : bond 0.00496 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8956 (t0) cc_final: 0.8689 (t0) REVERT: A 143 GLN cc_start: 0.9135 (mp10) cc_final: 0.8731 (mp10) REVERT: A 160 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8581 (pm20) REVERT: B 28 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8811 (mt-10) REVERT: C 104 LYS cc_start: 0.9243 (ptpp) cc_final: 0.8996 (pttt) REVERT: D 113 ASP cc_start: 0.9105 (m-30) cc_final: 0.8809 (m-30) REVERT: E 101 LYS cc_start: 0.8924 (tppt) cc_final: 0.8551 (tppt) REVERT: E 104 ARG cc_start: 0.8814 (mpp80) cc_final: 0.8596 (mpp80) REVERT: E 154 PHE cc_start: 0.9119 (p90) cc_final: 0.8235 (m-10) REVERT: E 179 THR cc_start: 0.8555 (p) cc_final: 0.8066 (t) REVERT: E 239 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.7850 (pp) REVERT: E 280 ASP cc_start: 0.8662 (m-30) cc_final: 0.8051 (p0) REVERT: E 326 PHE cc_start: 0.9068 (m-10) cc_final: 0.8726 (m-10) REVERT: E 412 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.6483 (mm) REVERT: E 442 ASN cc_start: 0.9399 (t0) cc_final: 0.9095 (t0) REVERT: E 445 GLU cc_start: 0.9353 (tp30) cc_final: 0.9134 (tp30) REVERT: E 449 GLU cc_start: 0.9103 (pt0) cc_final: 0.8697 (pt0) REVERT: E 533 ASP cc_start: 0.9081 (p0) cc_final: 0.8732 (t70) REVERT: E 569 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9007 (mt) REVERT: E 577 LEU cc_start: 0.9598 (mp) cc_final: 0.9361 (tp) REVERT: E 723 ASN cc_start: 0.9802 (t0) cc_final: 0.9314 (p0) REVERT: E 771 PHE cc_start: 0.8967 (m-10) cc_final: 0.8378 (m-10) REVERT: F 146 ARG cc_start: 0.9412 (tpp-160) cc_final: 0.8954 (mmp80) REVERT: F 251 ASP cc_start: 0.8966 (m-30) cc_final: 0.8465 (t0) outliers start: 41 outliers final: 20 residues processed: 314 average time/residue: 0.4680 time to fit residues: 168.9347 Evaluate side-chains 296 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.097114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.070546 restraints weight = 45989.140| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.30 r_work: 0.2812 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17763 Z= 0.206 Angle : 0.751 13.378 24489 Z= 0.377 Chirality : 0.044 0.269 2882 Planarity : 0.005 0.048 2847 Dihedral : 15.592 167.917 3629 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.46 % Allowed : 23.19 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.67 (0.19), residues: 1992 helix: 1.75 (0.18), residues: 866 sheet: -0.52 (0.28), residues: 322 loop : -0.52 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 782 TYR 0.020 0.002 TYR E 147 PHE 0.022 0.002 PHE E 361 TRP 0.025 0.002 TRP E 433 HIS 0.009 0.001 HIS E 749 Details of bonding type rmsd covalent geometry : bond 0.00463 (17761) covalent geometry : angle 0.75123 (24489) hydrogen bonds : bond 0.04407 ( 823) hydrogen bonds : angle 5.03969 ( 2290) metal coordination : bond 0.00628 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9031 (t0) cc_final: 0.8710 (t0) REVERT: A 143 GLN cc_start: 0.9148 (mp10) cc_final: 0.8713 (mp10) REVERT: A 160 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: B 28 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8851 (mt-10) REVERT: B 249 GLU cc_start: 0.8725 (tp30) cc_final: 0.8469 (tp30) REVERT: D 28 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8925 (mt-10) REVERT: D 160 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: E 101 LYS cc_start: 0.9066 (tppt) cc_final: 0.8813 (tppt) REVERT: E 154 PHE cc_start: 0.9126 (p90) cc_final: 0.8214 (m-10) REVERT: E 179 THR cc_start: 0.8615 (p) cc_final: 0.8131 (t) REVERT: E 280 ASP cc_start: 0.8691 (m-30) cc_final: 0.8449 (m-30) REVERT: E 326 PHE cc_start: 0.9086 (m-10) cc_final: 0.8806 (m-10) REVERT: E 412 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7695 (tp) REVERT: E 442 ASN cc_start: 0.9411 (t0) cc_final: 0.9087 (t0) REVERT: E 445 GLU cc_start: 0.9380 (tp30) cc_final: 0.9169 (tp30) REVERT: E 449 GLU cc_start: 0.9139 (pt0) cc_final: 0.8715 (pt0) REVERT: E 518 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8421 (tm-30) REVERT: E 569 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9149 (mp) REVERT: E 723 ASN cc_start: 0.9793 (t0) cc_final: 0.9301 (p0) REVERT: E 771 PHE cc_start: 0.9029 (m-10) cc_final: 0.8445 (m-10) REVERT: F 146 ARG cc_start: 0.9425 (tpp-160) cc_final: 0.8974 (mmp80) REVERT: F 251 ASP cc_start: 0.8983 (m-30) cc_final: 0.8503 (t0) outliers start: 40 outliers final: 21 residues processed: 309 average time/residue: 0.4791 time to fit residues: 169.5285 Evaluate side-chains 297 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 95 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 151 optimal weight: 0.0370 chunk 51 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 GLN E 590 GLN ** E 644 HIS ** 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 = 0.3666 r_free = 0.3666 target = 0.099233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072636 restraints weight = 45581.140| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.34 r_work: 0.2860 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17763 Z= 0.143 Angle : 0.768 13.364 24489 Z= 0.384 Chirality : 0.045 0.341 2882 Planarity : 0.005 0.049 2847 Dihedral : 15.518 165.867 3629 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 1.85 % Allowed : 24.48 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.65 (0.19), residues: 1992 helix: 1.70 (0.18), residues: 872 sheet: -0.45 (0.29), residues: 322 loop : -0.56 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 782 TYR 0.018 0.001 TYR E 354 PHE 0.020 0.001 PHE F 97 TRP 0.031 0.003 TRP E 115 HIS 0.005 0.001 HIS E 702 Details of bonding type rmsd covalent geometry : bond 0.00324 (17761) covalent geometry : angle 0.76809 (24489) hydrogen bonds : bond 0.04102 ( 823) hydrogen bonds : angle 4.98706 ( 2290) metal coordination : bond 0.00218 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8714 (m-30) cc_final: 0.8493 (m-30) REVERT: A 142 ASP cc_start: 0.8982 (t0) cc_final: 0.8625 (t0) REVERT: A 143 GLN cc_start: 0.9155 (mp10) cc_final: 0.8704 (mp10) REVERT: A 160 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8590 (pm20) REVERT: B 28 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8830 (mt-10) REVERT: B 249 GLU cc_start: 0.8702 (tp30) cc_final: 0.8459 (tp30) REVERT: C 104 LYS cc_start: 0.9248 (ptpp) cc_final: 0.9001 (pttm) REVERT: C 136 MET cc_start: 0.8941 (mtt) cc_final: 0.8669 (mtt) REVERT: D 28 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8915 (mt-10) REVERT: E 154 PHE cc_start: 0.9086 (p90) cc_final: 0.8136 (m-10) REVERT: E 179 THR cc_start: 0.8581 (p) cc_final: 0.8124 (t) REVERT: E 243 PHE cc_start: 0.8146 (m-10) cc_final: 0.7469 (m-10) REVERT: E 280 ASP cc_start: 0.8668 (m-30) cc_final: 0.8427 (m-30) REVERT: E 326 PHE cc_start: 0.9028 (m-10) cc_final: 0.8723 (m-10) REVERT: E 412 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.6529 (mm) REVERT: E 442 ASN cc_start: 0.9396 (t0) cc_final: 0.9092 (t0) REVERT: E 445 GLU cc_start: 0.9371 (tp30) cc_final: 0.9154 (tp30) REVERT: E 449 GLU cc_start: 0.9150 (pt0) cc_final: 0.8753 (pt0) REVERT: E 569 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9068 (mt) REVERT: E 690 GLU cc_start: 0.8433 (mp0) cc_final: 0.8200 (mp0) REVERT: E 721 MET cc_start: 0.9049 (tpp) cc_final: 0.8789 (tpp) REVERT: E 723 ASN cc_start: 0.9776 (t0) cc_final: 0.9264 (p0) REVERT: E 771 PHE cc_start: 0.8952 (m-10) cc_final: 0.8429 (m-10) REVERT: E 782 ARG cc_start: 0.9542 (ttp-110) cc_final: 0.8981 (ptm-80) REVERT: E 784 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8930 (tppt) REVERT: F 146 ARG cc_start: 0.9421 (tpp-160) cc_final: 0.8954 (mmp80) REVERT: F 251 ASP cc_start: 0.8992 (m-30) cc_final: 0.8474 (t0) outliers start: 30 outliers final: 18 residues processed: 300 average time/residue: 0.4793 time to fit residues: 164.2702 Evaluate side-chains 290 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 HIS Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.098233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071680 restraints weight = 45166.836| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.26 r_work: 0.2841 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17763 Z= 0.180 Angle : 0.790 15.515 24489 Z= 0.393 Chirality : 0.045 0.324 2882 Planarity : 0.005 0.047 2847 Dihedral : 15.513 167.783 3629 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 1.66 % Allowed : 25.15 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % 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: 0.59 (0.20), residues: 1992 helix: 1.68 (0.18), residues: 872 sheet: -0.56 (0.29), residues: 327 loop : -0.58 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 782 TYR 0.019 0.002 TYR E 354 PHE 0.024 0.002 PHE E 735 TRP 0.037 0.002 TRP E 115 HIS 0.007 0.001 HIS E 383 Details of bonding type rmsd covalent geometry : bond 0.00412 (17761) covalent geometry : angle 0.79039 (24489) hydrogen bonds : bond 0.04272 ( 823) hydrogen bonds : angle 5.07041 ( 2290) metal coordination : bond 0.00756 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9029 (t0) cc_final: 0.8650 (t0) REVERT: A 143 GLN cc_start: 0.9148 (mp10) cc_final: 0.8678 (mp10) REVERT: A 160 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: B 28 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8841 (mt-10) REVERT: C 104 LYS cc_start: 0.9242 (ptpp) cc_final: 0.8993 (pttm) REVERT: D 28 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8907 (mt-10) REVERT: D 160 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: E 154 PHE cc_start: 0.9041 (p90) cc_final: 0.8067 (m-10) REVERT: E 179 THR cc_start: 0.8618 (p) cc_final: 0.8150 (t) REVERT: E 243 PHE cc_start: 0.8213 (m-10) cc_final: 0.7491 (m-10) REVERT: E 280 ASP cc_start: 0.8680 (m-30) cc_final: 0.8444 (m-30) REVERT: E 326 PHE cc_start: 0.9053 (m-10) cc_final: 0.8772 (m-10) REVERT: E 412 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7604 (tp) REVERT: E 442 ASN cc_start: 0.9408 (t0) cc_final: 0.9093 (t0) REVERT: E 445 GLU cc_start: 0.9388 (tp30) cc_final: 0.9020 (tp30) REVERT: E 449 GLU cc_start: 0.9150 (pt0) cc_final: 0.8650 (pt0) REVERT: E 482 GLU cc_start: 0.7807 (mp0) cc_final: 0.7554 (mp0) REVERT: E 569 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9180 (mt) REVERT: E 668 MET cc_start: 0.7412 (pmm) cc_final: 0.6271 (mpp) REVERT: E 690 GLU cc_start: 0.8520 (mp0) cc_final: 0.8160 (mp0) REVERT: E 723 ASN cc_start: 0.9792 (t0) cc_final: 0.9250 (p0) REVERT: E 729 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: E 771 PHE cc_start: 0.8978 (m-10) cc_final: 0.8400 (m-10) REVERT: F 146 ARG cc_start: 0.9432 (tpp-160) cc_final: 0.8963 (mmp80) REVERT: F 251 ASP cc_start: 0.9008 (m-30) cc_final: 0.8495 (t0) outliers start: 27 outliers final: 16 residues processed: 285 average time/residue: 0.4858 time to fit residues: 158.3696 Evaluate side-chains 296 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 275 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 789 GLN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072944 restraints weight = 45296.394| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.30 r_work: 0.2867 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17763 Z= 0.147 Angle : 0.787 12.758 24489 Z= 0.393 Chirality : 0.045 0.341 2882 Planarity : 0.005 0.048 2847 Dihedral : 15.447 166.612 3629 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 24.97 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1992 helix: 1.64 (0.18), residues: 872 sheet: -0.48 (0.29), residues: 325 loop : -0.61 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 782 TYR 0.025 0.001 TYR E 663 PHE 0.018 0.001 PHE F 97 TRP 0.046 0.003 TRP E 115 HIS 0.005 0.001 HIS E 702 Details of bonding type rmsd covalent geometry : bond 0.00335 (17761) covalent geometry : angle 0.78734 (24489) hydrogen bonds : bond 0.04129 ( 823) hydrogen bonds : angle 5.08001 ( 2290) metal coordination : bond 0.01329 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6455.35 seconds wall clock time: 110 minutes 37.12 seconds (6637.12 seconds total)