Starting phenix.real_space_refine on Sun May 18 15:12:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbl_16544/05_2025/8cbl_16544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbl_16544/05_2025/8cbl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbl_16544/05_2025/8cbl_16544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbl_16544/05_2025/8cbl_16544.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbl_16544/05_2025/8cbl_16544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbl_16544/05_2025/8cbl_16544.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.67, per 1000 atoms: 0.73 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: 4.75 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 6.29 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: 7.19 Time building geometry restraints manager: 5.54 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: 5.200 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 51.960 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (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 TRP 0.010 0.001 TRP E 587 HIS 0.042 0.001 HIS E 724 PHE 0.014 0.001 PHE E 77 TYR 0.020 0.001 TYR F 135 ARG 0.002 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.15383 ( 823) hydrogen bonds : angle 6.66433 ( 2290) metal coordination : bond 0.39713 ( 2) covalent geometry : bond 0.00362 (17761) covalent geometry : angle 0.55374 (24489) *********************** 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 : 1.676 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: 0.6668 (p0) REVERT: E 83 TYR cc_start: 0.6638 (m-80) cc_final: 0.5594 (m-80) REVERT: E 370 LEU cc_start: 0.7765 (tp) cc_final: 0.7152 (tp) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 1.1907 time to fit residues: 639.8007 Evaluate side-chains 318 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 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 434 GLN E 461 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 HIS F 247 ASN F 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.071715 restraints weight = 45501.882| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.32 r_work: 0.2815 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17763 Z= 0.191 Angle : 0.717 10.729 24489 Z= 0.356 Chirality : 0.044 0.314 2882 Planarity : 0.005 0.045 2847 Dihedral : 15.946 153.894 3629 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.40 % Allowed : 14.27 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (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 TRP 0.020 0.002 TRP E 587 HIS 0.016 0.002 HIS E 724 PHE 0.034 0.002 PHE E 521 TYR 0.016 0.002 TYR E 663 ARG 0.010 0.001 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 823) hydrogen bonds : angle 5.31611 ( 2290) metal coordination : bond 0.01114 ( 2) covalent geometry : bond 0.00419 (17761) covalent geometry : angle 0.71687 (24489) *********************** 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 404 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 365 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9637 (OUTLIER) cc_final: 0.9399 (ttpp) REVERT: A 119 ASP cc_start: 0.8926 (m-30) cc_final: 0.8516 (m-30) REVERT: A 135 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8503 (tp30) REVERT: A 143 GLN cc_start: 0.9064 (mp10) cc_final: 0.8732 (mp10) REVERT: B 41 ASP cc_start: 0.8678 (t0) cc_final: 0.8451 (t0) REVERT: C 104 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8728 (pttm) REVERT: C 135 GLU cc_start: 0.8931 (tp30) cc_final: 0.8499 (tp30) REVERT: C 232 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8759 (mt-10) REVERT: D 113 ASP cc_start: 0.9213 (m-30) cc_final: 0.9010 (m-30) REVERT: E 77 PHE cc_start: 0.9167 (p90) cc_final: 0.8925 (p90) REVERT: E 101 LYS cc_start: 0.8727 (tppt) cc_final: 0.7923 (tppt) REVERT: E 109 PHE cc_start: 0.9328 (m-80) cc_final: 0.9117 (m-80) REVERT: E 115 TRP cc_start: 0.9351 (t-100) cc_final: 0.9105 (t-100) REVERT: E 239 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8125 (mp) REVERT: E 316 PHE cc_start: 0.9048 (m-80) cc_final: 0.8487 (m-80) REVERT: E 326 PHE cc_start: 0.9119 (m-10) cc_final: 0.8803 (m-80) REVERT: E 349 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9155 (mt) REVERT: E 445 GLU cc_start: 0.9297 (tp30) cc_final: 0.9081 (tp30) REVERT: E 449 GLU cc_start: 0.8953 (pt0) cc_final: 0.8557 (pt0) REVERT: E 564 ARG cc_start: 0.9716 (ttm-80) cc_final: 0.9433 (ptm160) REVERT: E 667 THR cc_start: 0.7713 (t) cc_final: 0.7385 (m) REVERT: E 781 ARG cc_start: 0.8896 (ptp-110) cc_final: 0.8621 (ptp-110) outliers start: 39 outliers final: 19 residues processed: 381 average time/residue: 1.1464 time to fit residues: 491.2035 Evaluate side-chains 329 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 53 LYS 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 349 LEU 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 641 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 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 134 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072944 restraints weight = 45585.995| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.35 r_work: 0.2843 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2763 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= 0.138 Angle : 0.676 11.233 24489 Z= 0.336 Chirality : 0.043 0.256 2882 Planarity : 0.005 0.046 2847 Dihedral : 15.763 162.296 3629 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.64 % Allowed : 16.48 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1992 helix: 1.88 (0.18), residues: 853 sheet: -0.30 (0.28), residues: 322 loop : -0.44 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 587 HIS 0.005 0.001 HIS E 724 PHE 0.030 0.002 PHE F 97 TYR 0.023 0.002 TYR E 59 ARG 0.009 0.001 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 823) hydrogen bonds : angle 5.13232 ( 2290) metal coordination : bond 0.00372 ( 2) covalent geometry : bond 0.00307 (17761) covalent geometry : angle 0.67571 (24489) *********************** 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 408 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 365 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8892 (m-30) cc_final: 0.8550 (m-30) REVERT: A 135 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8547 (tp30) REVERT: A 142 ASP cc_start: 0.8822 (t0) cc_final: 0.8588 (t0) REVERT: A 143 GLN cc_start: 0.9084 (mp10) cc_final: 0.8719 (mp10) REVERT: A 160 GLU cc_start: 0.9004 (pm20) cc_final: 0.8619 (pm20) REVERT: A 211 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 41 ASP cc_start: 0.8679 (t0) cc_final: 0.8400 (t70) REVERT: B 113 ASP cc_start: 0.8974 (m-30) cc_final: 0.8771 (m-30) REVERT: C 104 LYS cc_start: 0.9157 (ptpp) cc_final: 0.8848 (pttm) REVERT: C 232 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8872 (mt-10) REVERT: D 28 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8888 (mt-10) REVERT: D 113 ASP cc_start: 0.9180 (m-30) cc_final: 0.8916 (m-30) REVERT: D 211 GLU cc_start: 0.7748 (pp20) cc_final: 0.7521 (tm-30) REVERT: E 77 PHE cc_start: 0.9289 (p90) cc_final: 0.8951 (p90) REVERT: E 97 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8967 (tm-30) REVERT: E 101 LYS cc_start: 0.8524 (tppt) cc_final: 0.8164 (tppt) REVERT: E 115 TRP cc_start: 0.9342 (t-100) cc_final: 0.9029 (t-100) REVERT: E 239 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7530 (tp) REVERT: E 280 ASP cc_start: 0.8614 (m-30) cc_final: 0.8070 (p0) REVERT: E 316 PHE cc_start: 0.8985 (m-80) cc_final: 0.8413 (m-80) REVERT: E 326 PHE cc_start: 0.9126 (m-10) cc_final: 0.8799 (m-80) REVERT: E 424 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7704 (tptp) REVERT: E 445 GLU cc_start: 0.9321 (tp30) cc_final: 0.9022 (tp30) REVERT: E 449 GLU cc_start: 0.9010 (pt0) cc_final: 0.8595 (pt0) REVERT: E 518 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8513 (tm-30) REVERT: E 561 GLN cc_start: 0.9580 (mm-40) cc_final: 0.9188 (mm-40) REVERT: E 564 ARG cc_start: 0.9702 (ttm-80) cc_final: 0.9458 (ttm-80) REVERT: E 685 HIS cc_start: 0.9046 (t70) cc_final: 0.8794 (t70) REVERT: E 771 PHE cc_start: 0.8813 (m-10) cc_final: 0.8543 (m-10) outliers start: 43 outliers final: 19 residues processed: 387 average time/residue: 1.1040 time to fit residues: 482.6212 Evaluate side-chains 331 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 D residue 206 LEU Chi-restraints excluded: chain E residue 57 THR 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 424 LYS 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 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 185 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 189 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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 = 0.3663 r_free = 0.3663 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072771 restraints weight = 46017.047| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.35 r_work: 0.2843 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3072 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 : 0.679 10.894 24489 Z= 0.338 Chirality : 0.043 0.263 2882 Planarity : 0.005 0.048 2847 Dihedral : 15.682 174.180 3629 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.89 % Allowed : 18.57 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1992 helix: 1.89 (0.18), residues: 853 sheet: -0.35 (0.28), residues: 323 loop : -0.44 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 587 HIS 0.007 0.001 HIS E 749 PHE 0.031 0.002 PHE E 361 TYR 0.020 0.002 TYR E 354 ARG 0.008 0.000 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 823) hydrogen bonds : angle 5.06747 ( 2290) metal coordination : bond 0.00225 ( 2) covalent geometry : bond 0.00323 (17761) covalent geometry : angle 0.67946 (24489) *********************** 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 385 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8911 (m-30) cc_final: 0.8693 (m-30) REVERT: A 135 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8594 (tp30) REVERT: A 143 GLN cc_start: 0.9101 (mp10) cc_final: 0.8732 (mp10) REVERT: A 160 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: B 28 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8797 (mt-10) REVERT: B 70 ASP cc_start: 0.9269 (m-30) cc_final: 0.9044 (m-30) REVERT: C 104 LYS cc_start: 0.9180 (ptpp) cc_final: 0.8760 (pttm) REVERT: C 232 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8809 (mt-10) REVERT: D 113 ASP cc_start: 0.9177 (m-30) cc_final: 0.8904 (m-30) REVERT: D 211 GLU cc_start: 0.7785 (pp20) cc_final: 0.7539 (tm-30) REVERT: E 77 PHE cc_start: 0.9288 (p90) cc_final: 0.8932 (p90) REVERT: E 101 LYS cc_start: 0.8556 (tppt) cc_final: 0.8150 (tppt) REVERT: E 104 ARG cc_start: 0.8755 (mpp80) cc_final: 0.8506 (mtm-85) REVERT: E 115 TRP cc_start: 0.9350 (t-100) cc_final: 0.9079 (t-100) REVERT: E 239 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7719 (pp) REVERT: E 243 PHE cc_start: 0.8266 (m-10) cc_final: 0.7937 (m-10) REVERT: E 280 ASP cc_start: 0.8699 (m-30) cc_final: 0.8118 (p0) REVERT: E 326 PHE cc_start: 0.9162 (m-10) cc_final: 0.8811 (m-10) REVERT: E 412 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.6492 (mp) REVERT: E 445 GLU cc_start: 0.9334 (tp30) cc_final: 0.9062 (tp30) REVERT: E 449 GLU cc_start: 0.9021 (pt0) cc_final: 0.8631 (pt0) REVERT: E 482 GLU cc_start: 0.7819 (mp0) cc_final: 0.7571 (mp0) REVERT: E 521 PHE cc_start: 0.8858 (t80) cc_final: 0.8258 (t80) REVERT: E 577 LEU cc_start: 0.9648 (mp) cc_final: 0.9363 (mt) REVERT: E 721 MET cc_start: 0.9475 (tpp) cc_final: 0.9240 (tpp) REVERT: E 750 MET cc_start: 0.8249 (mtp) cc_final: 0.8022 (mtp) REVERT: E 771 PHE cc_start: 0.8855 (m-10) cc_final: 0.8449 (m-10) REVERT: E 778 MET cc_start: 0.9379 (mmm) cc_final: 0.9163 (mmm) REVERT: F 146 ARG cc_start: 0.9406 (tpp-160) cc_final: 0.8945 (mmp80) REVERT: F 251 ASP cc_start: 0.8993 (m-30) cc_final: 0.8521 (t0) REVERT: F 314 ASP cc_start: 0.9132 (p0) cc_final: 0.8492 (p0) outliers start: 47 outliers final: 21 residues processed: 365 average time/residue: 1.0488 time to fit residues: 436.3006 Evaluate side-chains 319 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 145 GLU 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 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 506 ILE 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 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 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 = 0.3646 r_free = 0.3646 target = 0.098127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.071427 restraints weight = 46584.575| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.34 r_work: 0.2826 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3281 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= 0.170 Angle : 0.685 10.418 24489 Z= 0.342 Chirality : 0.043 0.302 2882 Planarity : 0.005 0.052 2847 Dihedral : 15.666 175.262 3629 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.08 % Allowed : 19.56 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1992 helix: 1.91 (0.18), residues: 854 sheet: -0.61 (0.28), residues: 320 loop : -0.46 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 433 HIS 0.005 0.001 HIS E 702 PHE 0.034 0.002 PHE E 521 TYR 0.019 0.001 TYR E 354 ARG 0.003 0.000 ARG E 360 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 823) hydrogen bonds : angle 5.08481 ( 2290) metal coordination : bond 0.00253 ( 2) covalent geometry : bond 0.00384 (17761) covalent geometry : angle 0.68453 (24489) *********************** 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: 50 poor density : 310 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9012 (m-30) cc_final: 0.8714 (m-30) REVERT: A 142 ASP cc_start: 0.8924 (t0) cc_final: 0.8715 (t0) REVERT: A 143 GLN cc_start: 0.9112 (mp10) cc_final: 0.8726 (mp10) REVERT: A 160 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8594 (pm20) REVERT: C 104 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8744 (pttt) REVERT: C 232 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8873 (mt-10) REVERT: D 28 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8884 (mt-10) REVERT: D 113 ASP cc_start: 0.9180 (m-30) cc_final: 0.8898 (m-30) REVERT: E 104 ARG cc_start: 0.8760 (mpp80) cc_final: 0.8554 (mpp80) REVERT: E 243 PHE cc_start: 0.8301 (m-10) cc_final: 0.7888 (m-10) REVERT: E 280 ASP cc_start: 0.8687 (m-30) cc_final: 0.8094 (p0) REVERT: E 326 PHE cc_start: 0.9117 (m-10) cc_final: 0.8846 (m-10) REVERT: E 445 GLU cc_start: 0.9351 (tp30) cc_final: 0.8958 (tp30) REVERT: E 449 GLU cc_start: 0.9070 (pt0) cc_final: 0.8669 (pt0) REVERT: E 452 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8837 (tm-30) REVERT: E 523 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9257 (mm110) REVERT: E 577 LEU cc_start: 0.9633 (mp) cc_final: 0.9369 (tp) REVERT: E 651 CYS cc_start: 0.8427 (t) cc_final: 0.7957 (p) REVERT: E 715 MET cc_start: 0.7417 (tpp) cc_final: 0.7206 (tpp) REVERT: E 750 MET cc_start: 0.8323 (mtp) cc_final: 0.7959 (mtm) REVERT: E 771 PHE cc_start: 0.8838 (m-10) cc_final: 0.8450 (m-10) REVERT: F 146 ARG cc_start: 0.9422 (tpp-160) cc_final: 0.8976 (mmp80) REVERT: F 251 ASP cc_start: 0.8994 (m-30) cc_final: 0.8517 (t0) outliers start: 50 outliers final: 26 residues processed: 339 average time/residue: 1.0840 time to fit residues: 417.4573 Evaluate side-chains 301 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 79 LYS 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 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 145 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 337 VAL 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 598 VAL Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 777 GLU Chi-restraints excluded: chain E residue 779 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** B 215 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3650 r_free = 0.3650 target = 0.098279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071849 restraints weight = 45918.071| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.32 r_work: 0.2827 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17763 Z= 0.161 Angle : 0.697 11.950 24489 Z= 0.345 Chirality : 0.043 0.327 2882 Planarity : 0.005 0.056 2847 Dihedral : 15.617 169.808 3629 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 20.54 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1992 helix: 1.88 (0.18), residues: 854 sheet: -0.67 (0.28), residues: 321 loop : -0.47 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 433 HIS 0.008 0.001 HIS E 749 PHE 0.029 0.002 PHE E 77 TYR 0.018 0.002 TYR E 354 ARG 0.003 0.000 ARG E 360 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 823) hydrogen bonds : angle 5.04696 ( 2290) metal coordination : bond 0.00623 ( 2) covalent geometry : bond 0.00365 (17761) covalent geometry : angle 0.69686 (24489) *********************** 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 346 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8709 (m-30) REVERT: A 142 ASP cc_start: 0.8969 (t0) cc_final: 0.8712 (t0) REVERT: A 143 GLN cc_start: 0.9136 (mp10) cc_final: 0.8730 (mp10) REVERT: A 160 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8569 (pm20) REVERT: B 28 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8835 (mt-10) REVERT: C 104 LYS cc_start: 0.9204 (ptpp) cc_final: 0.8828 (pttm) REVERT: E 56 ASN cc_start: 0.8598 (t0) cc_final: 0.8275 (t0) REVERT: E 179 THR cc_start: 0.8557 (p) cc_final: 0.7916 (t) REVERT: E 181 TYR cc_start: 0.8237 (m-10) cc_final: 0.7846 (m-10) REVERT: E 280 ASP cc_start: 0.8697 (m-30) cc_final: 0.8085 (p0) REVERT: E 326 PHE cc_start: 0.9105 (m-10) cc_final: 0.8848 (m-10) REVERT: E 445 GLU cc_start: 0.9348 (tp30) cc_final: 0.9057 (OUTLIER) REVERT: E 449 GLU cc_start: 0.9078 (pt0) cc_final: 0.8575 (pt0) REVERT: E 577 LEU cc_start: 0.9623 (mp) cc_final: 0.9343 (tp) REVERT: E 684 ILE cc_start: 0.8911 (pp) cc_final: 0.8687 (pp) REVERT: E 723 ASN cc_start: 0.9790 (t0) cc_final: 0.9312 (p0) REVERT: E 771 PHE cc_start: 0.8955 (m-10) cc_final: 0.8342 (m-10) REVERT: E 778 MET cc_start: 0.9536 (mmm) cc_final: 0.9294 (mmm) REVERT: F 146 ARG cc_start: 0.9428 (tpp-160) cc_final: 0.8974 (mmp80) REVERT: F 251 ASP cc_start: 0.8999 (m-30) cc_final: 0.8505 (t0) outliers start: 51 outliers final: 31 residues processed: 323 average time/residue: 1.0717 time to fit residues: 394.0606 Evaluate side-chains 306 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 119 ASP 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 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 309 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 756 ASP Chi-restraints excluded: chain E residue 777 GLU Chi-restraints excluded: chain E residue 779 GLU 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 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 197 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 523 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 = 0.3668 r_free = 0.3668 target = 0.099444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072779 restraints weight = 45448.791| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.31 r_work: 0.2859 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3637 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= 0.139 Angle : 0.721 12.494 24489 Z= 0.356 Chirality : 0.043 0.348 2882 Planarity : 0.005 0.055 2847 Dihedral : 15.529 166.284 3629 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.71 % Allowed : 22.08 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1992 helix: 1.87 (0.18), residues: 854 sheet: -0.61 (0.28), residues: 320 loop : -0.48 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 115 HIS 0.005 0.001 HIS E 644 PHE 0.027 0.002 PHE E 735 TYR 0.019 0.001 TYR E 59 ARG 0.011 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 823) hydrogen bonds : angle 4.97694 ( 2290) metal coordination : bond 0.01495 ( 2) covalent geometry : bond 0.00314 (17761) covalent geometry : angle 0.72128 (24489) *********************** 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 351 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8746 (m-30) REVERT: A 142 ASP cc_start: 0.8974 (t0) cc_final: 0.8678 (t0) REVERT: A 143 GLN cc_start: 0.9131 (mp10) cc_final: 0.8712 (mp10) REVERT: A 160 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: B 249 GLU cc_start: 0.8699 (tp30) cc_final: 0.8426 (tp30) REVERT: C 104 LYS cc_start: 0.9197 (ptpp) cc_final: 0.8819 (pttm) REVERT: C 140 GLU cc_start: 0.9342 (tt0) cc_final: 0.8782 (pp20) REVERT: C 232 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8869 (mt-10) REVERT: D 28 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8881 (mt-10) REVERT: D 118 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9174 (mp) REVERT: E 101 LYS cc_start: 0.8859 (tppt) cc_final: 0.8485 (tppt) REVERT: E 104 ARG cc_start: 0.8688 (mpp80) cc_final: 0.8423 (mpp80) REVERT: E 154 PHE cc_start: 0.9086 (p90) cc_final: 0.8270 (m-10) REVERT: E 179 THR cc_start: 0.8562 (p) cc_final: 0.8067 (t) REVERT: E 280 ASP cc_start: 0.8681 (m-30) cc_final: 0.8058 (p0) REVERT: E 326 PHE cc_start: 0.9076 (m-10) cc_final: 0.8751 (m-80) REVERT: E 445 GLU cc_start: 0.9351 (tp30) cc_final: 0.9138 (tp30) REVERT: E 449 GLU cc_start: 0.9095 (pt0) cc_final: 0.8765 (pt0) REVERT: E 452 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8851 (tm-30) REVERT: E 518 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8068 (tm-30) REVERT: E 533 ASP cc_start: 0.9103 (p0) cc_final: 0.8646 (t0) REVERT: E 577 LEU cc_start: 0.9620 (mp) cc_final: 0.9351 (tp) REVERT: E 639 THR cc_start: 0.9259 (p) cc_final: 0.8972 (t) REVERT: E 690 GLU cc_start: 0.8592 (mp0) cc_final: 0.8303 (mp0) REVERT: E 723 ASN cc_start: 0.9796 (t0) cc_final: 0.9341 (p0) REVERT: E 771 PHE cc_start: 0.8943 (m-10) cc_final: 0.8372 (m-10) REVERT: F 146 ARG cc_start: 0.9422 (tpp-160) cc_final: 0.8960 (mmp80) REVERT: F 251 ASP cc_start: 0.8962 (m-30) cc_final: 0.8473 (t0) REVERT: F 345 GLU cc_start: 0.8825 (tp30) cc_final: 0.8619 (tp30) outliers start: 44 outliers final: 23 residues processed: 329 average time/residue: 1.0412 time to fit residues: 390.9068 Evaluate side-chains 307 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 281 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 119 ASP 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 118 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 77 PHE 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 309 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 777 GLU Chi-restraints excluded: chain F residue 125 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 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 531 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 = 0.3656 r_free = 0.3656 target = 0.098550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071887 restraints weight = 45694.797| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.32 r_work: 0.2837 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17763 Z= 0.173 Angle : 0.746 12.090 24489 Z= 0.372 Chirality : 0.044 0.303 2882 Planarity : 0.005 0.051 2847 Dihedral : 15.539 166.068 3629 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.52 % Allowed : 23.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1992 helix: 1.78 (0.18), residues: 860 sheet: -0.65 (0.28), residues: 318 loop : -0.55 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 101 HIS 0.005 0.001 HIS E 749 PHE 0.029 0.002 PHE E 739 TYR 0.018 0.001 TYR E 354 ARG 0.011 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 823) hydrogen bonds : angle 5.01650 ( 2290) metal coordination : bond 0.00576 ( 2) covalent geometry : bond 0.00394 (17761) covalent geometry : angle 0.74616 (24489) *********************** 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 330 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8721 (m-30) REVERT: A 142 ASP cc_start: 0.9009 (t0) cc_final: 0.8687 (t0) REVERT: A 143 GLN cc_start: 0.9147 (mp10) cc_final: 0.8707 (mp10) REVERT: A 160 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8605 (pm20) REVERT: B 28 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8849 (mt-10) REVERT: C 104 LYS cc_start: 0.9205 (ptpp) cc_final: 0.8824 (pttm) REVERT: D 28 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8904 (mt-10) REVERT: D 118 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9173 (mp) REVERT: E 56 ASN cc_start: 0.8663 (t0) cc_final: 0.8285 (t0) REVERT: E 101 LYS cc_start: 0.8900 (tppt) cc_final: 0.8643 (tppt) REVERT: E 154 PHE cc_start: 0.9089 (p90) cc_final: 0.8251 (m-10) REVERT: E 179 THR cc_start: 0.8575 (p) cc_final: 0.8077 (t) REVERT: E 280 ASP cc_start: 0.8684 (m-30) cc_final: 0.8439 (m-30) REVERT: E 326 PHE cc_start: 0.9062 (m-10) cc_final: 0.8750 (m-10) REVERT: E 445 GLU cc_start: 0.9361 (tp30) cc_final: 0.9146 (tp30) REVERT: E 449 GLU cc_start: 0.9089 (pt0) cc_final: 0.8738 (pt0) REVERT: E 452 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8860 (tm-30) REVERT: E 533 ASP cc_start: 0.9119 (p0) cc_final: 0.8689 (t0) REVERT: E 577 LEU cc_start: 0.9612 (mp) cc_final: 0.9370 (tp) REVERT: E 723 ASN cc_start: 0.9801 (t0) cc_final: 0.9336 (p0) REVERT: E 771 PHE cc_start: 0.8977 (m-10) cc_final: 0.8376 (m-10) REVERT: E 778 MET cc_start: 0.9497 (mmm) cc_final: 0.9204 (mmm) REVERT: E 782 ARG cc_start: 0.9251 (ptp-110) cc_final: 0.8804 (ptp-110) REVERT: F 146 ARG cc_start: 0.9425 (tpp-160) cc_final: 0.8964 (mmp80) REVERT: F 251 ASP cc_start: 0.8986 (m-30) cc_final: 0.8491 (t0) REVERT: F 345 GLU cc_start: 0.8836 (tp30) cc_final: 0.8595 (tp30) outliers start: 41 outliers final: 24 residues processed: 311 average time/residue: 1.0380 time to fit residues: 368.8097 Evaluate side-chains 305 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 119 ASP 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 118 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 77 PHE 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 262 MET Chi-restraints excluded: chain E residue 401 THR 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 553 THR Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 745 VAL 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 14 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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 523 GLN E 590 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 = 0.3668 r_free = 0.3668 target = 0.099382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072780 restraints weight = 45551.916| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.32 r_work: 0.2856 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17763 Z= 0.153 Angle : 0.767 14.158 24489 Z= 0.381 Chirality : 0.044 0.305 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.496 166.264 3629 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 24.29 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1992 helix: 1.71 (0.18), residues: 862 sheet: -0.60 (0.28), residues: 320 loop : -0.60 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 433 HIS 0.005 0.001 HIS E 702 PHE 0.026 0.002 PHE E 735 TYR 0.020 0.001 TYR E 354 ARG 0.010 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 823) hydrogen bonds : angle 5.01742 ( 2290) metal coordination : bond 0.00385 ( 2) covalent geometry : bond 0.00350 (17761) covalent geometry : angle 0.76712 (24489) *********************** 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 321 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: A 142 ASP cc_start: 0.9021 (t0) cc_final: 0.8669 (t0) REVERT: A 143 GLN cc_start: 0.9154 (mp10) cc_final: 0.8691 (mp10) REVERT: A 160 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: B 28 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8844 (mt-10) REVERT: B 249 GLU cc_start: 0.8681 (tp30) cc_final: 0.8426 (tp30) REVERT: C 104 LYS cc_start: 0.9213 (ptpp) cc_final: 0.8779 (pttt) REVERT: D 28 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8902 (mt-10) REVERT: E 56 ASN cc_start: 0.8649 (t0) cc_final: 0.8271 (t0) REVERT: E 92 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8737 (pp30) REVERT: E 104 ARG cc_start: 0.8687 (mpp80) cc_final: 0.7853 (ptt180) REVERT: E 154 PHE cc_start: 0.9103 (p90) cc_final: 0.8229 (m-10) REVERT: E 179 THR cc_start: 0.8564 (p) cc_final: 0.8082 (t) REVERT: E 243 PHE cc_start: 0.8191 (m-10) cc_final: 0.7573 (m-10) REVERT: E 280 ASP cc_start: 0.8683 (m-30) cc_final: 0.8441 (m-30) REVERT: E 326 PHE cc_start: 0.9052 (m-10) cc_final: 0.8721 (m-10) REVERT: E 400 LEU cc_start: 0.9128 (mm) cc_final: 0.8917 (mm) REVERT: E 445 GLU cc_start: 0.9374 (tp30) cc_final: 0.9165 (tp30) REVERT: E 449 GLU cc_start: 0.9121 (pt0) cc_final: 0.8796 (pt0) REVERT: E 452 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8869 (tm-30) REVERT: E 533 ASP cc_start: 0.9087 (p0) cc_final: 0.8678 (t0) REVERT: E 577 LEU cc_start: 0.9583 (mp) cc_final: 0.9376 (tp) REVERT: E 639 THR cc_start: 0.9267 (p) cc_final: 0.9007 (t) REVERT: E 667 THR cc_start: 0.7290 (m) cc_final: 0.7040 (m) REVERT: E 719 PHE cc_start: 0.8541 (t80) cc_final: 0.8027 (t80) REVERT: E 721 MET cc_start: 0.9030 (tpp) cc_final: 0.8722 (tpp) REVERT: E 723 ASN cc_start: 0.9781 (t0) cc_final: 0.9307 (p0) REVERT: E 732 VAL cc_start: 0.9139 (p) cc_final: 0.8883 (p) REVERT: E 771 PHE cc_start: 0.8965 (m-10) cc_final: 0.8396 (m-10) REVERT: F 146 ARG cc_start: 0.9429 (tpp-160) cc_final: 0.8956 (mmp80) REVERT: F 251 ASP cc_start: 0.8995 (m-30) cc_final: 0.8476 (t0) REVERT: F 345 GLU cc_start: 0.8862 (tp30) cc_final: 0.8631 (tp30) outliers start: 31 outliers final: 24 residues processed: 307 average time/residue: 1.0164 time to fit residues: 362.4912 Evaluate side-chains 299 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 119 ASP 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 77 PHE 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 148 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 401 THR 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 553 THR Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 745 VAL 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 161 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 155 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 157 optimal weight: 0.6980 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.100031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073373 restraints weight = 45398.103| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.33 r_work: 0.2872 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17763 Z= 0.147 Angle : 0.786 15.359 24489 Z= 0.392 Chirality : 0.045 0.340 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.436 166.080 3629 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.09 % Allowed : 24.66 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1992 helix: 1.69 (0.18), residues: 862 sheet: -0.57 (0.29), residues: 320 loop : -0.63 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 433 HIS 0.005 0.001 HIS E 383 PHE 0.026 0.002 PHE E 735 TYR 0.019 0.001 TYR E 354 ARG 0.011 0.000 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 823) hydrogen bonds : angle 5.00195 ( 2290) metal coordination : bond 0.00271 ( 2) covalent geometry : bond 0.00336 (17761) covalent geometry : angle 0.78619 (24489) ********************** 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 311 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 1.794 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: 0.9023 (t0) cc_final: 0.8632 (t0) REVERT: A 143 GLN cc_start: 0.9139 (mp10) cc_final: 0.8661 (mp10) REVERT: A 160 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8620 (pm20) REVERT: B 28 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8832 (mt-10) REVERT: C 104 LYS cc_start: 0.9216 (ptpp) cc_final: 0.8864 (pttm) REVERT: D 28 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8891 (mt-10) REVERT: D 64 ASP cc_start: 0.8495 (t0) cc_final: 0.8253 (t0) REVERT: E 56 ASN cc_start: 0.8644 (t0) cc_final: 0.8304 (t0) REVERT: E 92 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8798 (pp30) REVERT: E 101 LYS cc_start: 0.8907 (tppt) cc_final: 0.8552 (tppt) REVERT: E 154 PHE cc_start: 0.9126 (p90) cc_final: 0.8262 (m-10) REVERT: E 179 THR cc_start: 0.8522 (p) cc_final: 0.8046 (t) REVERT: E 243 PHE cc_start: 0.8160 (m-10) cc_final: 0.7503 (m-10) REVERT: E 280 ASP cc_start: 0.8676 (m-30) cc_final: 0.8435 (m-30) REVERT: E 326 PHE cc_start: 0.9036 (m-10) cc_final: 0.8627 (m-10) REVERT: E 400 LEU cc_start: 0.9102 (mm) cc_final: 0.8824 (mm) REVERT: E 430 ARG cc_start: 0.9328 (mpp80) cc_final: 0.9034 (mpp80) REVERT: E 445 GLU cc_start: 0.9367 (tp30) cc_final: 0.9159 (tp30) REVERT: E 449 GLU cc_start: 0.9112 (pt0) cc_final: 0.8716 (pt0) REVERT: E 533 ASP cc_start: 0.9084 (p0) cc_final: 0.8697 (t0) REVERT: E 667 THR cc_start: 0.7469 (m) cc_final: 0.7109 (m) REVERT: E 690 GLU cc_start: 0.8516 (mp0) cc_final: 0.7986 (mp0) REVERT: E 723 ASN cc_start: 0.9778 (t0) cc_final: 0.9248 (p0) REVERT: E 729 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: F 146 ARG cc_start: 0.9424 (tpp-160) cc_final: 0.8950 (mmp80) REVERT: F 251 ASP cc_start: 0.8985 (m-30) cc_final: 0.8475 (t0) REVERT: F 345 GLU cc_start: 0.8853 (tp30) cc_final: 0.8569 (tm-30) outliers start: 34 outliers final: 22 residues processed: 295 average time/residue: 1.0273 time to fit residues: 347.0701 Evaluate side-chains 290 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 79 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 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 365 THR Chi-restraints excluded: chain E residue 401 THR 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 553 THR Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 729 TYR Chi-restraints excluded: chain E residue 745 VAL 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 199 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** 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 = 0.3675 r_free = 0.3675 target = 0.099756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073038 restraints weight = 45411.820| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.33 r_work: 0.2860 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17763 Z= 0.161 Angle : 0.796 15.823 24489 Z= 0.397 Chirality : 0.045 0.335 2882 Planarity : 0.005 0.057 2847 Dihedral : 15.410 167.450 3629 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.91 % Allowed : 25.52 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1992 helix: 1.63 (0.18), residues: 863 sheet: -0.65 (0.28), residues: 323 loop : -0.61 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 115 HIS 0.005 0.001 HIS E 702 PHE 0.025 0.002 PHE E 735 TYR 0.020 0.002 TYR F 137 ARG 0.010 0.001 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 823) hydrogen bonds : angle 5.08872 ( 2290) metal coordination : bond 0.00311 ( 2) covalent geometry : bond 0.00370 (17761) covalent geometry : angle 0.79615 (24489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13264.54 seconds wall clock time: 229 minutes 20.57 seconds (13760.57 seconds total)