Starting phenix.real_space_refine on Sun Jun 15 08:48:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbl_16544/06_2025/8cbl_16544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbl_16544/06_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_16544/06_2025/8cbl_16544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbl_16544/06_2025/8cbl_16544.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbl_16544/06_2025/8cbl_16544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbl_16544/06_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-5710/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: 12.85, per 1000 atoms: 0.74 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: 5.07 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: 6.90 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: 7.21 Time building geometry restraints manager: 5.97 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: 6.870 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: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 54.970 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.060 ------------------------------------------------------------------------------- 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 : 1.720 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: 1.2507 time to fit residues: 671.0323 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 : 1.813 ------------------------------------------------------------------------------- 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 = 0.071716 restraints weight = 45501.792| |-----------------------------------------------------------------------------| 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 10.730 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 5.31610 ( 2290) metal coordination : bond 0.01113 ( 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 : 1.949 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: 0.8515 (m-30) REVERT: A 135 GLU cc_start: 0.8851 (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: 0.8679 (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: 0.9011 (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: 0.9350 (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: 0.9156 (mt) REVERT: E 445 GLU cc_start: 0.9297 (tp30) cc_final: 0.9080 (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: 1.2390 time to fit residues: 529.7833 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 : 2.031 ------------------------------------------------------------------------------- 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: 2.9990 chunk 197 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 178 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.100013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.073369 restraints weight = 45520.110| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.35 r_work: 0.2856 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17763 Z= 0.136 Angle : 0.678 11.617 24489 Z= 0.337 Chirality : 0.043 0.256 2882 Planarity : 0.005 0.045 2847 Dihedral : 15.761 162.789 3629 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 16.48 % Favored : 80.93 % 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: 1.88 (0.18), residues: 852 sheet: -0.30 (0.28), residues: 322 loop : -0.45 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 587 HIS 0.005 0.001 HIS E 644 PHE 0.031 0.002 PHE F 97 TYR 0.024 0.002 TYR E 59 ARG 0.010 0.001 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 823) hydrogen bonds : angle 5.12607 ( 2290) metal coordination : bond 0.00373 ( 2) covalent geometry : bond 0.00301 (17761) covalent geometry : angle 0.67799 (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 409 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8886 (m-30) cc_final: 0.8670 (m-30) REVERT: A 135 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8530 (tp30) REVERT: A 142 ASP cc_start: 0.8813 (t0) cc_final: 0.8580 (t0) REVERT: A 143 GLN cc_start: 0.9076 (mp10) cc_final: 0.8716 (mp10) REVERT: A 160 GLU cc_start: 0.9004 (pm20) cc_final: 0.8602 (pm20) REVERT: B 41 ASP cc_start: 0.8677 (t0) cc_final: 0.8393 (t70) REVERT: C 104 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8848 (pttm) REVERT: C 232 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8871 (mt-10) REVERT: D 28 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8884 (mt-10) REVERT: D 113 ASP cc_start: 0.9177 (m-30) cc_final: 0.8914 (m-30) REVERT: E 77 PHE cc_start: 0.9269 (p90) cc_final: 0.8924 (p90) REVERT: E 101 LYS cc_start: 0.8483 (tppt) cc_final: 0.8149 (tppt) REVERT: E 115 TRP cc_start: 0.9320 (t-100) cc_final: 0.9013 (t-100) REVERT: E 239 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.7497 (tp) REVERT: E 280 ASP cc_start: 0.8595 (m-30) cc_final: 0.8053 (p0) REVERT: E 316 PHE cc_start: 0.8961 (m-80) cc_final: 0.8386 (m-80) REVERT: E 326 PHE cc_start: 0.9111 (m-10) cc_final: 0.8835 (m-80) REVERT: E 424 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7679 (tptp) REVERT: E 445 GLU cc_start: 0.9310 (tp30) cc_final: 0.9041 (tp30) REVERT: E 547 LEU cc_start: 0.8807 (tp) cc_final: 0.8604 (tt) REVERT: E 561 GLN cc_start: 0.9550 (mm-40) cc_final: 0.9183 (mm-40) REVERT: E 564 ARG cc_start: 0.9681 (ttm-80) cc_final: 0.9383 (tmm-80) REVERT: E 685 HIS cc_start: 0.9025 (t70) cc_final: 0.8784 (t70) REVERT: E 771 PHE cc_start: 0.8780 (m-10) cc_final: 0.8516 (m-10) REVERT: E 774 ASP cc_start: 0.9064 (t70) cc_final: 0.8584 (t70) REVERT: E 778 MET cc_start: 0.9332 (mmm) cc_final: 0.8833 (mmm) REVERT: E 781 ARG cc_start: 0.8573 (ptp-110) cc_final: 0.8273 (ptp-170) REVERT: E 782 ARG cc_start: 0.9384 (mtm110) cc_final: 0.9176 (ptp-110) REVERT: F 114 GLU cc_start: 0.9346 (pm20) cc_final: 0.8882 (pm20) outliers start: 42 outliers final: 17 residues processed: 389 average time/residue: 1.1396 time to fit residues: 500.5055 Evaluate side-chains 323 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 47 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 3 optimal weight: 0.0270 chunk 189 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 109 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.6642 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.100003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073049 restraints weight = 45983.511| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.38 r_work: 0.2857 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17763 Z= 0.136 Angle : 0.683 11.826 24489 Z= 0.337 Chirality : 0.043 0.262 2882 Planarity : 0.005 0.048 2847 Dihedral : 15.666 174.984 3629 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.64 % Allowed : 18.82 % 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: 0.80 (0.19), residues: 1992 helix: 1.87 (0.18), residues: 853 sheet: -0.41 (0.27), residues: 335 loop : -0.45 (0.23), residues: 804 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 0.030 0.002 PHE F 97 TYR 0.018 0.002 TYR E 354 ARG 0.005 0.000 ARG E 360 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 823) hydrogen bonds : angle 5.04740 ( 2290) metal coordination : bond 0.00221 ( 2) covalent geometry : bond 0.00308 (17761) covalent geometry : angle 0.68274 (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 384 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 1.744 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: 0.8997 (m-30) cc_final: 0.8568 (m-30) REVERT: A 135 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8594 (tp30) REVERT: A 143 GLN cc_start: 0.9086 (mp10) cc_final: 0.8723 (mp10) REVERT: A 160 GLU cc_start: 0.9036 (pm20) cc_final: 0.8587 (pm20) REVERT: A 211 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7524 (tp30) REVERT: B 28 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8782 (mt-10) REVERT: B 70 ASP cc_start: 0.9269 (m-30) cc_final: 0.9059 (m-30) REVERT: C 79 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9085 (mtpp) REVERT: C 104 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8750 (pttm) REVERT: C 232 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8830 (mt-10) REVERT: D 113 ASP cc_start: 0.9161 (m-30) cc_final: 0.8892 (m-30) REVERT: E 77 PHE cc_start: 0.9279 (p90) cc_final: 0.8847 (p90) REVERT: E 115 TRP cc_start: 0.9341 (t-100) cc_final: 0.9058 (t-100) REVERT: E 239 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8115 (mt) REVERT: E 243 PHE cc_start: 0.8246 (m-10) cc_final: 0.7927 (m-10) REVERT: E 280 ASP cc_start: 0.8689 (m-30) cc_final: 0.8126 (p0) REVERT: E 326 PHE cc_start: 0.9145 (m-10) cc_final: 0.8806 (m-80) REVERT: E 361 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7341 (t80) REVERT: E 412 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.6368 (mm) REVERT: E 445 GLU cc_start: 0.9295 (tp30) cc_final: 0.9030 (tp30) REVERT: E 449 GLU cc_start: 0.8913 (pt0) cc_final: 0.8456 (pt0) REVERT: E 482 GLU cc_start: 0.7822 (mp0) cc_final: 0.7576 (mp0) REVERT: E 577 LEU cc_start: 0.9645 (mp) cc_final: 0.9365 (mt) REVERT: E 750 MET cc_start: 0.8161 (mtp) cc_final: 0.7912 (mtp) REVERT: E 771 PHE cc_start: 0.8810 (m-10) cc_final: 0.8504 (m-10) REVERT: E 774 ASP cc_start: 0.9153 (t70) cc_final: 0.8830 (t70) REVERT: E 778 MET cc_start: 0.9397 (mmm) cc_final: 0.9147 (mmm) REVERT: E 780 GLU cc_start: 0.9270 (pp20) cc_final: 0.8960 (pp20) REVERT: E 781 ARG cc_start: 0.8605 (ptp-110) cc_final: 0.8403 (ptp-110) REVERT: E 782 ARG cc_start: 0.9406 (mtm110) cc_final: 0.9111 (ptp-110) REVERT: F 146 ARG cc_start: 0.9403 (tpp-160) cc_final: 0.8937 (mmp80) REVERT: F 251 ASP cc_start: 0.8989 (m-30) cc_final: 0.8512 (t0) outliers start: 43 outliers final: 19 residues processed: 365 average time/residue: 1.1480 time to fit residues: 472.7420 Evaluate side-chains 326 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 A residue 225 SER Chi-restraints excluded: chain C residue 79 LYS 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 361 PHE Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 195 optimal weight: 2.9990 chunk 133 optimal weight: 0.0470 chunk 116 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.100280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073731 restraints weight = 46096.797| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.36 r_work: 0.2867 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17763 Z= 0.137 Angle : 0.696 11.473 24489 Z= 0.345 Chirality : 0.043 0.323 2882 Planarity : 0.005 0.049 2847 Dihedral : 15.582 173.465 3629 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.01 % Allowed : 19.62 % 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: 0.80 (0.19), residues: 1992 helix: 1.88 (0.18), residues: 853 sheet: -0.43 (0.27), residues: 334 loop : -0.46 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 433 HIS 0.005 0.001 HIS E 383 PHE 0.028 0.002 PHE F 97 TYR 0.017 0.001 TYR E 354 ARG 0.004 0.000 ARG E 785 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 823) hydrogen bonds : angle 4.99973 ( 2290) metal coordination : bond 0.00334 ( 2) covalent geometry : bond 0.00311 (17761) covalent geometry : angle 0.69583 (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 370 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 1.904 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: 0.8923 (m-30) cc_final: 0.8559 (m-30) REVERT: A 143 GLN cc_start: 0.9107 (mp10) cc_final: 0.8734 (mp10) REVERT: A 160 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: B 70 ASP cc_start: 0.9271 (m-30) cc_final: 0.9010 (m-30) REVERT: B 249 GLU cc_start: 0.8726 (tp30) cc_final: 0.8504 (tp30) REVERT: C 104 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8803 (pttm) REVERT: C 140 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.8798 (pp20) REVERT: C 232 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8813 (mt-10) REVERT: D 28 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8859 (mt-10) REVERT: D 113 ASP cc_start: 0.9147 (m-30) cc_final: 0.8876 (m-30) REVERT: D 211 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7403 (tp30) REVERT: E 56 ASN cc_start: 0.8514 (t0) cc_final: 0.8233 (t0) REVERT: E 75 TYR cc_start: 0.8084 (t80) cc_final: 0.7823 (t80) REVERT: E 115 TRP cc_start: 0.9334 (t-100) cc_final: 0.9127 (t-100) REVERT: E 239 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.7827 (pp) REVERT: E 243 PHE cc_start: 0.8263 (m-10) cc_final: 0.7773 (m-10) REVERT: E 280 ASP cc_start: 0.8679 (m-30) cc_final: 0.8107 (p0) REVERT: E 326 PHE cc_start: 0.9095 (m-10) cc_final: 0.8873 (m-10) REVERT: E 361 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7271 (t80) REVERT: E 426 GLN cc_start: 0.9269 (tt0) cc_final: 0.8872 (tt0) REVERT: E 445 GLU cc_start: 0.9311 (tp30) cc_final: 0.9034 (tp30) REVERT: E 449 GLU cc_start: 0.8965 (pt0) cc_final: 0.8591 (pt0) REVERT: E 452 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8822 (tm-30) REVERT: E 564 ARG cc_start: 0.9701 (ttm-80) cc_final: 0.9322 (ptp-170) REVERT: E 577 LEU cc_start: 0.9619 (mp) cc_final: 0.9322 (tp) REVERT: E 639 THR cc_start: 0.9088 (p) cc_final: 0.8745 (t) REVERT: E 651 CYS cc_start: 0.8438 (t) cc_final: 0.7912 (p) REVERT: E 771 PHE cc_start: 0.8811 (m-10) cc_final: 0.8327 (m-10) REVERT: E 774 ASP cc_start: 0.9142 (t70) cc_final: 0.8767 (t0) REVERT: F 146 ARG cc_start: 0.9408 (tpp-160) cc_final: 0.8963 (mmp80) REVERT: F 251 ASP cc_start: 0.8984 (m-30) cc_final: 0.8509 (t0) outliers start: 49 outliers final: 20 residues processed: 350 average time/residue: 1.0560 time to fit residues: 421.2766 Evaluate side-chains 311 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 361 PHE Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 42 optimal weight: 0.2980 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 149 optimal weight: 0.0060 chunk 61 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072019 restraints weight = 46140.365| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.35 r_work: 0.2834 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17763 Z= 0.173 Angle : 0.704 11.957 24489 Z= 0.351 Chirality : 0.044 0.332 2882 Planarity : 0.005 0.050 2847 Dihedral : 15.580 170.495 3629 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 20.60 % Favored : 76.38 % 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: 0.74 (0.19), residues: 1992 helix: 1.85 (0.18), residues: 862 sheet: -0.57 (0.28), residues: 320 loop : -0.48 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 433 HIS 0.007 0.001 HIS E 749 PHE 0.037 0.002 PHE E 77 TYR 0.017 0.002 TYR F 137 ARG 0.004 0.000 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 823) hydrogen bonds : angle 5.00986 ( 2290) metal coordination : bond 0.00754 ( 2) covalent geometry : bond 0.00393 (17761) covalent geometry : angle 0.70375 (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 347 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: A 142 ASP cc_start: 0.8941 (t0) cc_final: 0.8705 (t0) REVERT: A 143 GLN cc_start: 0.9119 (mp10) cc_final: 0.8732 (mp10) REVERT: A 160 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: B 28 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8809 (mt-10) REVERT: B 249 GLU cc_start: 0.8773 (tp30) cc_final: 0.8544 (tp30) REVERT: C 104 LYS cc_start: 0.9190 (ptpp) cc_final: 0.8707 (pttt) REVERT: C 140 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.8841 (pp20) REVERT: D 113 ASP cc_start: 0.9155 (m-30) cc_final: 0.8862 (m-30) REVERT: E 56 ASN cc_start: 0.8596 (t0) cc_final: 0.8275 (t0) REVERT: E 75 TYR cc_start: 0.8144 (t80) cc_final: 0.7914 (t80) REVERT: E 101 LYS cc_start: 0.8837 (tppt) cc_final: 0.8474 (tppt) REVERT: E 179 THR cc_start: 0.8563 (p) cc_final: 0.8097 (t) REVERT: E 239 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7927 (pp) REVERT: E 243 PHE cc_start: 0.8308 (m-10) cc_final: 0.7760 (m-10) REVERT: E 280 ASP cc_start: 0.8679 (m-30) cc_final: 0.8064 (p0) REVERT: E 326 PHE cc_start: 0.9155 (m-10) cc_final: 0.8752 (m-80) REVERT: E 445 GLU cc_start: 0.9320 (tp30) cc_final: 0.9032 (tp30) REVERT: E 449 GLU cc_start: 0.8993 (pt0) cc_final: 0.8609 (pt0) REVERT: E 452 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8827 (tm-30) REVERT: E 577 LEU cc_start: 0.9638 (mp) cc_final: 0.9392 (tp) REVERT: E 771 PHE cc_start: 0.8861 (m-10) cc_final: 0.8433 (m-10) REVERT: E 774 ASP cc_start: 0.9106 (t70) cc_final: 0.8608 (t0) REVERT: E 778 MET cc_start: 0.9398 (mmm) cc_final: 0.9150 (mmm) REVERT: F 146 ARG cc_start: 0.9409 (tpp-160) cc_final: 0.8957 (mmp80) REVERT: F 251 ASP cc_start: 0.8983 (m-30) cc_final: 0.8523 (t0) outliers start: 49 outliers final: 25 residues processed: 326 average time/residue: 1.1152 time to fit residues: 414.6396 Evaluate side-chains 306 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 A residue 259 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 140 GLU 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 239 LEU 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 383 HIS 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 644 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.0470 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 162 optimal weight: 0.2980 chunk 173 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 GLN E 531 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073812 restraints weight = 45409.963| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.33 r_work: 0.2874 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3653 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= 0.135 Angle : 0.721 13.234 24489 Z= 0.358 Chirality : 0.043 0.343 2882 Planarity : 0.005 0.053 2847 Dihedral : 15.504 166.144 3629 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.64 % Allowed : 21.53 % Favored : 75.83 % 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: 0.72 (0.19), residues: 1992 helix: 1.87 (0.18), residues: 856 sheet: -0.61 (0.29), residues: 318 loop : -0.51 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 433 HIS 0.005 0.001 HIS E 644 PHE 0.034 0.002 PHE E 77 TYR 0.019 0.001 TYR E 59 ARG 0.003 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 823) hydrogen bonds : angle 4.90774 ( 2290) metal coordination : bond 0.01660 ( 2) covalent geometry : bond 0.00304 (17761) covalent geometry : angle 0.72107 (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 341 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8700 (m-30) REVERT: A 142 ASP cc_start: 0.8934 (t0) cc_final: 0.8667 (t0) REVERT: A 143 GLN cc_start: 0.9128 (mp10) cc_final: 0.8730 (mp10) REVERT: A 160 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8590 (pm20) REVERT: B 249 GLU cc_start: 0.8745 (tp30) cc_final: 0.8543 (tp30) REVERT: C 104 LYS cc_start: 0.9188 (ptpp) cc_final: 0.8808 (pttm) REVERT: C 140 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.8833 (pp20) REVERT: D 28 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8872 (mt-10) REVERT: D 113 ASP cc_start: 0.9101 (m-30) cc_final: 0.8826 (m-30) REVERT: E 56 ASN cc_start: 0.8557 (t0) cc_final: 0.8216 (t0) REVERT: E 101 LYS cc_start: 0.8803 (tppt) cc_final: 0.8522 (tppt) REVERT: E 179 THR cc_start: 0.8542 (p) cc_final: 0.8049 (t) REVERT: E 239 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7919 (pp) REVERT: E 243 PHE cc_start: 0.8162 (m-10) cc_final: 0.7510 (m-10) REVERT: E 280 ASP cc_start: 0.8653 (m-30) cc_final: 0.8044 (p0) REVERT: E 326 PHE cc_start: 0.9029 (m-10) cc_final: 0.8774 (m-80) REVERT: E 420 GLU cc_start: 0.9224 (mp0) cc_final: 0.9006 (mp0) REVERT: E 445 GLU cc_start: 0.9329 (tp30) cc_final: 0.8884 (tp30) REVERT: E 449 GLU cc_start: 0.9012 (pt0) cc_final: 0.8465 (pt0) REVERT: E 452 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8835 (tm-30) REVERT: E 533 ASP cc_start: 0.9105 (p0) cc_final: 0.8641 (t0) REVERT: E 577 LEU cc_start: 0.9602 (mp) cc_final: 0.9340 (tp) REVERT: E 639 THR cc_start: 0.9172 (p) cc_final: 0.8917 (t) REVERT: E 723 ASN cc_start: 0.9788 (t0) cc_final: 0.9312 (p0) REVERT: E 771 PHE cc_start: 0.8773 (m-10) cc_final: 0.8337 (m-10) REVERT: E 774 ASP cc_start: 0.9085 (t70) cc_final: 0.8546 (t0) REVERT: E 778 MET cc_start: 0.9401 (mmm) cc_final: 0.9182 (mmm) REVERT: F 115 GLU cc_start: 0.9216 (pm20) cc_final: 0.9011 (pm20) REVERT: F 146 ARG cc_start: 0.9406 (tpp-160) cc_final: 0.8942 (mmp80) REVERT: F 251 ASP cc_start: 0.8986 (m-30) cc_final: 0.8497 (t0) REVERT: F 345 GLU cc_start: 0.8802 (tp30) cc_final: 0.8596 (tp30) outliers start: 43 outliers final: 23 residues processed: 320 average time/residue: 1.1697 time to fit residues: 427.8513 Evaluate side-chains 306 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 140 GLU 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 77 PHE Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 262 MET 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 414 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 683 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 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 = 0.3657 r_free = 0.3657 target = 0.098544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071824 restraints weight = 45704.583| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.30 r_work: 0.2843 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17763 Z= 0.178 Angle : 0.737 11.515 24489 Z= 0.371 Chirality : 0.044 0.317 2882 Planarity : 0.005 0.054 2847 Dihedral : 15.507 167.522 3629 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.28 % Allowed : 22.82 % Favored : 74.91 % 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: 0.68 (0.19), residues: 1992 helix: 1.84 (0.18), residues: 860 sheet: -0.67 (0.28), residues: 323 loop : -0.52 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 101 HIS 0.005 0.001 HIS E 702 PHE 0.029 0.002 PHE E 77 TYR 0.029 0.002 TYR E 329 ARG 0.012 0.001 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 823) hydrogen bonds : angle 4.98354 ( 2290) metal coordination : bond 0.00907 ( 2) covalent geometry : bond 0.00404 (17761) covalent geometry : angle 0.73725 (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 331 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9011 (t0) cc_final: 0.8686 (t0) REVERT: A 143 GLN cc_start: 0.9138 (mp10) cc_final: 0.8702 (mp10) REVERT: A 160 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: B 28 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8836 (mt-10) REVERT: C 104 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8817 (pttm) REVERT: C 140 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.8839 (pp20) REVERT: D 28 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8912 (mt-10) REVERT: E 56 ASN cc_start: 0.8611 (t0) cc_final: 0.8232 (t0) REVERT: E 179 THR cc_start: 0.8586 (p) cc_final: 0.8097 (t) REVERT: E 280 ASP cc_start: 0.8654 (m-30) cc_final: 0.8411 (m-30) REVERT: E 326 PHE cc_start: 0.9099 (m-10) cc_final: 0.8733 (m-80) REVERT: E 445 GLU cc_start: 0.9361 (tp30) cc_final: 0.9124 (OUTLIER) REVERT: E 449 GLU cc_start: 0.9051 (pt0) cc_final: 0.8622 (pt0) REVERT: E 452 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8858 (tm-30) REVERT: E 533 ASP cc_start: 0.9126 (p0) cc_final: 0.8684 (t0) REVERT: E 577 LEU cc_start: 0.9597 (mp) cc_final: 0.9362 (tp) REVERT: E 690 GLU cc_start: 0.8596 (mp0) cc_final: 0.8208 (mp0) REVERT: E 723 ASN cc_start: 0.9782 (t0) cc_final: 0.9282 (p0) REVERT: E 771 PHE cc_start: 0.8809 (m-10) cc_final: 0.8321 (m-10) REVERT: E 774 ASP cc_start: 0.9174 (t70) cc_final: 0.8055 (t0) REVERT: E 778 MET cc_start: 0.9440 (mmm) cc_final: 0.9055 (mmm) REVERT: F 146 ARG cc_start: 0.9416 (tpp-160) cc_final: 0.8954 (mmp80) REVERT: F 251 ASP cc_start: 0.8984 (m-30) cc_final: 0.8486 (t0) REVERT: F 345 GLU cc_start: 0.8841 (tp30) cc_final: 0.8624 (tp30) outliers start: 37 outliers final: 24 residues processed: 314 average time/residue: 1.0644 time to fit residues: 382.5119 Evaluate side-chains 299 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 C residue 140 GLU 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 337 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 486 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 135 optimal weight: 0.0570 chunk 88 optimal weight: 0.0870 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 393 HIS ** 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 = 0.3692 r_free = 0.3692 target = 0.100999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.074241 restraints weight = 45431.718| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.36 r_work: 0.2889 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17763 Z= 0.138 Angle : 0.780 14.308 24489 Z= 0.387 Chirality : 0.045 0.415 2882 Planarity : 0.005 0.055 2847 Dihedral : 15.437 163.035 3629 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.09 % Allowed : 23.92 % Favored : 73.99 % 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: 1.76 (0.18), residues: 856 sheet: -0.57 (0.29), residues: 318 loop : -0.56 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 115 HIS 0.005 0.001 HIS E 383 PHE 0.028 0.001 PHE E 77 TYR 0.018 0.001 TYR E 354 ARG 0.011 0.000 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 823) hydrogen bonds : angle 4.90132 ( 2290) metal coordination : bond 0.00865 ( 2) covalent geometry : bond 0.00312 (17761) covalent geometry : angle 0.77998 (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 332 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8971 (t0) cc_final: 0.8620 (t0) REVERT: A 143 GLN cc_start: 0.9135 (mp10) cc_final: 0.8690 (mp10) REVERT: A 160 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8615 (pm20) REVERT: B 28 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8809 (mt-10) REVERT: B 249 GLU cc_start: 0.8729 (tp30) cc_final: 0.8511 (tp30) REVERT: C 104 LYS cc_start: 0.9194 (ptpp) cc_final: 0.8756 (pttt) REVERT: C 136 MET cc_start: 0.8886 (mtt) cc_final: 0.8636 (mtt) REVERT: C 140 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.8859 (pp20) REVERT: D 28 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8881 (mt-10) REVERT: E 56 ASN cc_start: 0.8617 (t0) cc_final: 0.8270 (t0) REVERT: E 179 THR cc_start: 0.8537 (p) cc_final: 0.8055 (t) REVERT: E 243 PHE cc_start: 0.8128 (m-10) cc_final: 0.7462 (m-10) REVERT: E 326 PHE cc_start: 0.9001 (m-10) cc_final: 0.8674 (m-80) REVERT: E 400 LEU cc_start: 0.9090 (mm) cc_final: 0.8874 (mm) REVERT: E 445 GLU cc_start: 0.9356 (tp30) cc_final: 0.9132 (tp30) REVERT: E 449 GLU cc_start: 0.9052 (pt0) cc_final: 0.8680 (pt0) REVERT: E 452 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8859 (tm-30) REVERT: E 533 ASP cc_start: 0.9093 (p0) cc_final: 0.8655 (t0) REVERT: E 577 LEU cc_start: 0.9582 (mp) cc_final: 0.9348 (tp) REVERT: E 690 GLU cc_start: 0.8554 (mp0) cc_final: 0.8153 (mp0) REVERT: E 723 ASN cc_start: 0.9767 (t0) cc_final: 0.9249 (p0) REVERT: E 771 PHE cc_start: 0.8775 (m-10) cc_final: 0.8048 (m-10) REVERT: F 146 ARG cc_start: 0.9416 (tpp-160) cc_final: 0.8948 (mmp80) REVERT: F 251 ASP cc_start: 0.8969 (m-30) cc_final: 0.8464 (t0) REVERT: F 345 GLU cc_start: 0.8874 (tp30) cc_final: 0.8590 (tm-30) outliers start: 34 outliers final: 17 residues processed: 312 average time/residue: 1.0499 time to fit residues: 376.6678 Evaluate side-chains 306 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 244 ILE 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 486 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 745 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 161 optimal weight: 0.5980 chunk 204 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 590 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 = 0.3683 r_free = 0.3683 target = 0.100572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.074196 restraints weight = 45186.267| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.31 r_work: 0.2878 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17763 Z= 0.149 Angle : 0.780 11.895 24489 Z= 0.392 Chirality : 0.045 0.342 2882 Planarity : 0.005 0.054 2847 Dihedral : 15.387 165.478 3629 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.29 % Allowed : 25.15 % Favored : 73.55 % 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 (0.20), residues: 1992 helix: 1.78 (0.18), residues: 856 sheet: -0.66 (0.29), residues: 323 loop : -0.55 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 115 HIS 0.005 0.001 HIS E 383 PHE 0.030 0.002 PHE E 77 TYR 0.020 0.002 TYR F 137 ARG 0.008 0.000 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 823) hydrogen bonds : angle 4.97178 ( 2290) metal coordination : bond 0.00390 ( 2) covalent geometry : bond 0.00340 (17761) covalent geometry : angle 0.77974 (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 308 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 287 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9002 (t0) cc_final: 0.8591 (t0) REVERT: A 143 GLN cc_start: 0.9130 (mp10) cc_final: 0.8666 (mp10) REVERT: A 160 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: B 28 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8803 (mt-10) REVERT: B 249 GLU cc_start: 0.8715 (tp30) cc_final: 0.8501 (tp30) REVERT: C 104 LYS cc_start: 0.9190 (ptpp) cc_final: 0.8744 (pttt) REVERT: C 140 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.8865 (pp20) REVERT: D 28 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8870 (mt-10) REVERT: E 56 ASN cc_start: 0.8626 (t0) cc_final: 0.8282 (t0) REVERT: E 92 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8700 (pp30) REVERT: E 179 THR cc_start: 0.8554 (p) cc_final: 0.8074 (t) REVERT: E 243 PHE cc_start: 0.8139 (m-10) cc_final: 0.7426 (m-10) REVERT: E 326 PHE cc_start: 0.8995 (m-10) cc_final: 0.8678 (m-80) REVERT: E 445 GLU cc_start: 0.9373 (tp30) cc_final: 0.9150 (tp30) REVERT: E 449 GLU cc_start: 0.9069 (pt0) cc_final: 0.8701 (pt0) REVERT: E 452 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8864 (tm-30) REVERT: E 482 GLU cc_start: 0.7714 (mp0) cc_final: 0.7513 (mp0) REVERT: E 533 ASP cc_start: 0.9114 (p0) cc_final: 0.8677 (t0) REVERT: E 577 LEU cc_start: 0.9587 (mp) cc_final: 0.9376 (tp) REVERT: E 723 ASN cc_start: 0.9796 (t0) cc_final: 0.9227 (p0) REVERT: E 732 VAL cc_start: 0.8571 (p) cc_final: 0.7938 (t) REVERT: E 771 PHE cc_start: 0.8853 (m-10) cc_final: 0.7779 (m-10) REVERT: E 774 ASP cc_start: 0.8660 (p0) cc_final: 0.8407 (p0) REVERT: F 146 ARG cc_start: 0.9414 (tpp-160) cc_final: 0.8943 (mmp80) REVERT: F 251 ASP cc_start: 0.8977 (m-30) cc_final: 0.8475 (t0) REVERT: F 345 GLU cc_start: 0.8856 (tp30) cc_final: 0.8575 (tm-30) outliers start: 21 outliers final: 16 residues processed: 295 average time/residue: 1.0961 time to fit residues: 370.4719 Evaluate side-chains 292 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 140 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 244 ILE 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 486 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 644 HIS Chi-restraints excluded: chain E residue 683 LEU 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: 1.9990 chunk 50 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 117 ASN E 383 HIS E 523 GLN ** E 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN E 638 GLN ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070103 restraints weight = 45813.690| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.21 r_work: 0.2810 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17763 Z= 0.254 Angle : 0.815 13.229 24489 Z= 0.413 Chirality : 0.047 0.384 2882 Planarity : 0.005 0.054 2847 Dihedral : 15.562 170.903 3629 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.60 % Allowed : 25.09 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.19), residues: 1992 helix: 1.71 (0.18), residues: 853 sheet: -0.75 (0.28), residues: 324 loop : -0.59 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP E 115 HIS 0.007 0.002 HIS E 702 PHE 0.026 0.002 PHE E 77 TYR 0.040 0.002 TYR E 663 ARG 0.024 0.001 ARG E 782 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 823) hydrogen bonds : angle 5.18886 ( 2290) metal coordination : bond 0.01096 ( 2) covalent geometry : bond 0.00571 (17761) covalent geometry : angle 0.81455 (24489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13146.45 seconds wall clock time: 225 minutes 52.57 seconds (13552.57 seconds total)