Starting phenix.real_space_refine on Sat Aug 8 21:23:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsz_61787/08_2026/9jsz_61787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsz_61787/08_2026/9jsz_61787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jsz_61787/08_2026/9jsz_61787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsz_61787/08_2026/9jsz_61787.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsz_61787/08_2026/9jsz_61787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsz_61787/08_2026/9jsz_61787.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 P 147 5.49 5 Mg 4 5.21 5 S 95 5.16 5 C 19008 2.51 5 N 5415 2.21 5 O 6103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30772 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3723 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 442} Chain breaks: 1 Chain: "B" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3275 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3704 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 439} Chain breaks: 1 Chain: "N" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3146 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "O" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "L" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 385 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "H" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "E" Number of atoms: 3715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3715 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 441} Chain breaks: 1 Chain: "F" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3275 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3704 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 439} Chain breaks: 1 Chain: "J" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3146 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 373} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'RNA': 19} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "D" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.92, per 1000 atoms: 0.19 Number of scatterers: 30772 At special positions: 0 Unit cell: (174.25, 155.55, 182.75, 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) S 95 16.00 P 147 15.00 Mg 4 11.99 O 6103 8.00 N 5415 7.00 C 19008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6402 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 41 sheets defined 30.7% alpha, 14.0% beta 46 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 49 through 65 removed outlier: 4.328A pdb=" N SER A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.669A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.958A pdb=" N GLY A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.754A pdb=" N ARG A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.019A pdb=" N ILE A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 243 Processing helix chain 'A' and resid 309 through 328 removed outlier: 3.715A pdb=" N HIS A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.044A pdb=" N ASP A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.636A pdb=" N ALA A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.612A pdb=" N LYS A 483 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.817A pdb=" N ASN B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.599A pdb=" N LEU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.564A pdb=" N VAL B 226 " --> pdb=" O CYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 263 Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.502A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 383 removed outlier: 3.713A pdb=" N PHE B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 382 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.285A pdb=" N ASP B 418 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 18 No H-bonds generated for 'chain 'M' and resid 16 through 18' Processing helix chain 'M' and resid 23 through 32 Processing helix chain 'M' and resid 49 through 64 Processing helix chain 'M' and resid 105 through 113 Processing helix chain 'M' and resid 117 through 139 removed outlier: 3.876A pdb=" N ALA M 121 " --> pdb=" O ASP M 117 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL M 122 " --> pdb=" O HIS M 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 159 removed outlier: 3.568A pdb=" N LEU M 155 " --> pdb=" O PRO M 151 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 190 Processing helix chain 'M' and resid 201 through 206 removed outlier: 4.013A pdb=" N ILE M 205 " --> pdb=" O TRP M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 243 removed outlier: 3.543A pdb=" N ARG M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 328 Processing helix chain 'M' and resid 343 through 358 Processing helix chain 'M' and resid 429 through 439 Processing helix chain 'M' and resid 455 through 468 removed outlier: 3.665A pdb=" N ALA M 461 " --> pdb=" O PRO M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 484 removed outlier: 3.727A pdb=" N LYS M 483 " --> pdb=" O ASP M 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 26 removed outlier: 3.673A pdb=" N GLY N 12 " --> pdb=" O ASN N 8 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 91 Processing helix chain 'N' and resid 138 through 142 removed outlier: 4.189A pdb=" N LEU N 141 " --> pdb=" O VAL N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 196 Processing helix chain 'N' and resid 220 through 226 removed outlier: 3.880A pdb=" N SER N 223 " --> pdb=" O SER N 220 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU N 224 " --> pdb=" O ALA N 221 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE N 225 " --> pdb=" O CYS N 222 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 241 removed outlier: 4.133A pdb=" N LEU N 241 " --> pdb=" O LYS N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 245 through 262 Processing helix chain 'N' and resid 271 through 275 removed outlier: 3.599A pdb=" N ALA N 275 " --> pdb=" O ASP N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 366 Processing helix chain 'N' and resid 367 through 378 removed outlier: 4.231A pdb=" N LEU N 371 " --> pdb=" O LYS N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 420 removed outlier: 3.584A pdb=" N TRP N 420 " --> pdb=" O GLU N 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 23 through 32 Processing helix chain 'E' and resid 49 through 63 removed outlier: 3.602A pdb=" N GLU E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 118 through 139 removed outlier: 3.889A pdb=" N GLY E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 160 removed outlier: 3.926A pdb=" N VAL E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 201 through 206 removed outlier: 4.479A pdb=" N ILE E 205 " --> pdb=" O TRP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 243 Processing helix chain 'E' and resid 308 through 328 removed outlier: 3.822A pdb=" N HIS E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 358 removed outlier: 3.517A pdb=" N ASP E 348 " --> pdb=" O ASP E 344 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 439 Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.720A pdb=" N ALA E 461 " --> pdb=" O PRO E 457 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 25 Processing helix chain 'F' and resid 83 through 89 removed outlier: 3.953A pdb=" N ALA F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.519A pdb=" N ALA F 142 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 Processing helix chain 'F' and resid 244 through 261 removed outlier: 3.951A pdb=" N GLN F 248 " --> pdb=" O ASP F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 3.814A pdb=" N LEU F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA F 360 " --> pdb=" O ALA F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 360' Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.447A pdb=" N ASP F 366 " --> pdb=" O LYS F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 382 removed outlier: 3.674A pdb=" N LEU F 382 " --> pdb=" O TRP F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 4.225A pdb=" N ASP F 418 " --> pdb=" O VAL F 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 31 Processing helix chain 'I' and resid 49 through 66 removed outlier: 3.939A pdb=" N SER I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY I 66 " --> pdb=" O THR I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.720A pdb=" N THR I 101 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 113 Processing helix chain 'I' and resid 117 through 139 removed outlier: 3.767A pdb=" N ALA I 121 " --> pdb=" O ASP I 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY I 139 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 Processing helix chain 'I' and resid 182 through 189 Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 225 through 243 removed outlier: 3.768A pdb=" N ASN I 232 " --> pdb=" O GLY I 228 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR I 235 " --> pdb=" O TRP I 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER I 236 " --> pdb=" O ASN I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 328 removed outlier: 3.780A pdb=" N HIS I 326 " --> pdb=" O ALA I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 358 removed outlier: 3.827A pdb=" N ALA I 347 " --> pdb=" O LYS I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 440 Processing helix chain 'I' and resid 455 through 469 Processing helix chain 'I' and resid 480 through 484 removed outlier: 3.572A pdb=" N LYS I 483 " --> pdb=" O ASP I 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 26 removed outlier: 4.004A pdb=" N LEU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 140 through 144 removed outlier: 3.669A pdb=" N ALA J 143 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU J 144 " --> pdb=" O LEU J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 140 through 144' Processing helix chain 'J' and resid 185 through 195 Processing helix chain 'J' and resid 244 through 263 Processing helix chain 'J' and resid 354 through 366 Processing helix chain 'J' and resid 367 through 382 removed outlier: 3.501A pdb=" N LEU J 371 " --> pdb=" O LYS J 367 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL J 375 " --> pdb=" O LEU J 371 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE J 376 " --> pdb=" O ARG J 372 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.887A pdb=" N THR A 387 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.619A pdb=" N ARG A 248 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 103 removed outlier: 5.636A pdb=" N ILE A 42 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 97 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 44 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY A 99 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 46 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A 101 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A 48 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 103 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N VAL A 145 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS A 43 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 147 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLY A 45 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA A 146 " --> pdb=" O GLN A 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.660A pdb=" N PHE A 282 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 280 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS A 259 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU A 337 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 261 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 334 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 365 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 336 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 367 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS A 338 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 4.267A pdb=" N GLU B 162 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.668A pdb=" N ALA B 44 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG B 55 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL B 46 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 53 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE B 97 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA B 58 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 99 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B 60 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR B 101 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS B 62 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL B 98 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 111 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.821A pdb=" N TYR B 335 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 328 " --> pdb=" O TYR B 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 291 removed outlier: 5.616A pdb=" N PHE B 289 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA B 300 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 291 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.637A pdb=" N PHE B 306 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 317 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 5 through 7 removed outlier: 6.379A pdb=" N VAL M 334 " --> pdb=" O ASP M 363 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL M 365 " --> pdb=" O VAL M 334 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE M 336 " --> pdb=" O VAL M 365 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL M 367 " --> pdb=" O ILE M 336 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS M 338 " --> pdb=" O VAL M 367 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS M 259 " --> pdb=" O PHE M 335 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU M 337 " --> pdb=" O CYS M 259 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL M 261 " --> pdb=" O LEU M 337 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA M 258 " --> pdb=" O ASP M 283 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP M 283 " --> pdb=" O ALA M 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER M 264 " --> pdb=" O SER M 277 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE M 282 " --> pdb=" O VAL M 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL M 290 " --> pdb=" O PHE M 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 20 through 21 removed outlier: 3.592A pdb=" N ARG M 248 " --> pdb=" O GLU M 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 93 through 95 removed outlier: 5.976A pdb=" N ILE M 42 " --> pdb=" O GLU M 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 93 through 95 removed outlier: 5.976A pdb=" N ILE M 42 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA M 146 " --> pdb=" O GLN M 198 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL M 200 " --> pdb=" O ALA M 146 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE M 148 " --> pdb=" O VAL M 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 375 through 376 Processing sheet with id=AB7, first strand: chain 'N' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'N' and resid 77 through 79 removed outlier: 3.639A pdb=" N PHE N 77 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'N' and resid 327 through 330 removed outlier: 4.728A pdb=" N TRP N 334 " --> pdb=" O LEU N 171 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET N 402 " --> pdb=" O THR N 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 205 through 207 Processing sheet with id=AC3, first strand: chain 'N' and resid 303 through 306 Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.737A pdb=" N LYS E 394 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 334 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL E 365 " --> pdb=" O VAL E 334 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE E 336 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N CYS E 259 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU E 337 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 261 " --> pdb=" O LEU E 337 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ALA E 258 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP E 283 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY E 262 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC6, first strand: chain 'E' and resid 94 through 95 removed outlier: 5.995A pdb=" N ILE E 42 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 145 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA E 146 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.415A pdb=" N ARG F 55 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASN F 48 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET F 53 " --> pdb=" O ASN F 48 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N ILE F 97 " --> pdb=" O MET F 56 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA F 58 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL F 99 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN F 60 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR F 101 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 163 through 164 Processing sheet with id=AC9, first strand: chain 'F' and resid 335 through 337 removed outlier: 3.821A pdb=" N MET F 402 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 176 through 179 Processing sheet with id=AD2, first strand: chain 'F' and resid 204 through 206 Processing sheet with id=AD3, first strand: chain 'F' and resid 268 through 269 removed outlier: 3.529A pdb=" N GLY F 268 " --> pdb=" O TYR F 277 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 276 " --> pdb=" O PHE F 323 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE F 323 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 319 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER F 304 " --> pdb=" O ARG F 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 268 through 269 removed outlier: 3.529A pdb=" N GLY F 268 " --> pdb=" O TYR F 277 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 276 " --> pdb=" O PHE F 323 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE F 323 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.795A pdb=" N LYS I 394 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL I 334 " --> pdb=" O ASP I 363 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL I 365 " --> pdb=" O VAL I 334 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE I 336 " --> pdb=" O VAL I 365 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL I 367 " --> pdb=" O ILE I 336 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS I 338 " --> pdb=" O VAL I 367 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS I 259 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU I 337 " --> pdb=" O CYS I 259 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL I 261 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 19 through 21 removed outlier: 3.946A pdb=" N HIS I 19 " --> pdb=" O PHE I 15 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 93 through 95 removed outlier: 8.870A pdb=" N VAL I 145 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS I 43 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE I 147 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY I 45 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA I 149 " --> pdb=" O GLY I 45 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL I 47 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA I 146 " --> pdb=" O GLN I 198 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL I 200 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE I 148 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 264 through 266 removed outlier: 3.661A pdb=" N TYR I 266 " --> pdb=" O PHE I 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 282 through 283 Processing sheet with id=AE1, first strand: chain 'I' and resid 375 through 376 Processing sheet with id=AE2, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.581A pdb=" N ALA J 58 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL J 99 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN J 60 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR J 101 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYS J 62 " --> pdb=" O TYR J 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 76 through 79 Processing sheet with id=AE4, first strand: chain 'J' and resid 276 through 277 removed outlier: 3.677A pdb=" N PHE J 323 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP J 334 " --> pdb=" O LEU J 171 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU J 171 " --> pdb=" O TRP J 334 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET J 402 " --> pdb=" O THR J 172 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 204 through 206 removed outlier: 3.705A pdb=" N SER J 213 " --> pdb=" O TYR J 178 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR J 178 " --> pdb=" O SER J 213 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE J 179 " --> pdb=" O GLU J 232 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 119 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8946 1.34 - 1.46: 6755 1.46 - 1.58: 15623 1.58 - 1.70: 286 1.70 - 1.82: 174 Bond restraints: 31784 Sorted by residual: bond pdb=" C3' DT P 18 " pdb=" C2' DT P 18 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.67e+01 bond pdb=" C1' DT P 3 " pdb=" N1 DT P 3 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.10e+01 bond pdb=" C3' DT L 18 " pdb=" O3' DT L 18 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C3' DG D 17 " pdb=" C2' DG D 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 ... (remaining 31779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 42413 2.21 - 4.41: 1084 4.41 - 6.62: 120 6.62 - 8.82: 32 8.82 - 11.03: 11 Bond angle restraints: 43660 Sorted by residual: angle pdb=" O4' DG L 9 " pdb=" C4' DG L 9 " pdb=" C3' DG L 9 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 angle pdb=" C3' DT L 18 " pdb=" O3' DT L 18 " pdb=" P DA L 19 " ideal model delta sigma weight residual 119.70 125.48 -5.78 1.20e+00 6.94e-01 2.32e+01 angle pdb=" O2 C C 4 " pdb=" C2 C C 4 " pdb=" N3 C C 4 " ideal model delta sigma weight residual 121.90 118.64 3.26 7.00e-01 2.04e+00 2.18e+01 angle pdb=" N1 C G 7 " pdb=" C6 C G 7 " pdb=" C5 C G 7 " ideal model delta sigma weight residual 121.00 123.29 -2.29 5.00e-01 4.00e+00 2.09e+01 angle pdb=" C2 C G 7 " pdb=" N1 C G 7 " pdb=" C6 C G 7 " ideal model delta sigma weight residual 120.30 118.50 1.80 4.00e-01 6.25e+00 2.03e+01 ... (remaining 43655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 17504 33.53 - 67.06: 1273 67.06 - 100.59: 105 100.59 - 134.12: 1 134.12 - 167.65: 3 Dihedral angle restraints: 18886 sinusoidal: 8901 harmonic: 9985 Sorted by residual: dihedral pdb=" CA ASN F 167 " pdb=" C ASN F 167 " pdb=" N MET F 168 " pdb=" CA MET F 168 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA TYR J 349 " pdb=" C TYR J 349 " pdb=" N ALA J 350 " pdb=" CA ALA J 350 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA MET E 403 " pdb=" C MET E 403 " pdb=" N PRO E 404 " pdb=" CA PRO E 404 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 18883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3497 0.050 - 0.100: 920 0.100 - 0.150: 317 0.150 - 0.200: 21 0.200 - 0.250: 9 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CB ILE I 456 " pdb=" CA ILE I 456 " pdb=" CG1 ILE I 456 " pdb=" CG2 ILE I 456 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL E 319 " pdb=" CA VAL E 319 " pdb=" CG1 VAL E 319 " pdb=" CG2 VAL E 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 4761 not shown) Planarity restraints: 5124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 323 " -0.029 2.00e-02 2.50e+03 3.20e-02 1.79e+01 pdb=" CG PHE F 323 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE F 323 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE F 323 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 323 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 323 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE F 323 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 118 " -0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO F 119 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO F 119 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 119 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 118 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO B 119 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " -0.042 5.00e-02 4.00e+02 ... (remaining 5121 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 147 2.45 - 3.06: 17823 3.06 - 3.67: 48523 3.67 - 4.29: 66816 4.29 - 4.90: 110331 Nonbonded interactions: 243640 Sorted by model distance: nonbonded pdb=" OP3 A G 1 " pdb="MG MG G 101 " model vdw 1.837 2.170 nonbonded pdb=" OP1 A C 3 " pdb="MG MG C 101 " model vdw 2.058 2.170 nonbonded pdb=" OP3 A O 1 " pdb="MG MG M 501 " model vdw 2.062 2.170 nonbonded pdb=" OP3 A K 1 " pdb="MG MG I 501 " model vdw 2.067 2.170 nonbonded pdb=" OP2 A K 1 " pdb="MG MG I 501 " model vdw 2.083 2.170 ... (remaining 243635 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' and (resid 2 through 160 or resid 180 through 485)) selection = (chain 'E' and (resid 2 through 160 or resid 180 through 485)) selection = (chain 'I' and resid 2 through 485) selection = (chain 'M' and resid 2 through 485) } ncs_group { reference = (chain 'B' and (resid 7 through 145 or resid 161 through 384 or resid 400 throug \ h 424)) selection = (chain 'F' and (resid 7 through 145 or resid 161 through 384 or resid 400 throug \ h 424)) selection = (chain 'J' and (resid 7 through 384 or resid 400 through 424)) selection = (chain 'N' and (resid 7 through 384 or resid 400 through 424)) } ncs_group { reference = (chain 'C' and resid 1 through 18) selection = (chain 'G' and resid 1 through 18) selection = chain 'K' selection = (chain 'O' and resid 1 through 18) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.640 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.004 0.066 31784 Z= 0.252 Angle : 0.799 11.028 43660 Z= 0.501 Chirality : 0.051 0.250 4764 Planarity : 0.006 0.100 5124 Dihedral : 20.690 167.648 12484 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 1.02 % Allowed : 38.16 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.13), residues: 3425 helix: -0.82 (0.16), residues: 914 sheet: -1.25 (0.20), residues: 659 loop : -2.65 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 102 TYR 0.030 0.002 TYR F 79 PHE 0.070 0.002 PHE F 323 TRP 0.051 0.002 TRP J 212 HIS 0.006 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.25 (31784) covalent geometry : angle 0.79907 / 0.50 (43660) hydrogen bonds : bond 0.15630 / 10.88 ( 995) hydrogen bonds : angle 7.28914 / 5.18 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 1.123 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 306 TYR cc_start: 0.5183 (p90) cc_final: 0.4887 (p90) REVERT: B 48 ASN cc_start: 0.7592 (t0) cc_final: 0.7026 (t0) REVERT: B 194 LEU cc_start: 0.7991 (mt) cc_final: 0.7658 (pt) REVERT: E 470 TYR cc_start: 0.6232 (p90) cc_final: 0.5982 (p90) REVERT: F 375 VAL cc_start: 0.6464 (t) cc_final: 0.5923 (p) REVERT: J 187 ARG cc_start: 0.5341 (OUTLIER) cc_final: 0.4965 (mpt90) outliers start: 30 outliers final: 6 residues processed: 325 average time/residue: 0.1871 time to fit residues: 101.1618 Evaluate side-chains 243 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain J residue 187 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS M 304 HIS M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 446 ASN F 103 GLN I 181 ASN I 280 GLN J 321 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.087800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.072905 restraints weight = 139151.989| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.43 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 31784 Z= 0.180 Angle : 0.621 8.913 43660 Z= 0.334 Chirality : 0.043 0.197 4764 Planarity : 0.005 0.085 5124 Dihedral : 16.148 149.963 5740 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 5.03 % Allowed : 33.84 % Favored : 61.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.14), residues: 3425 helix: 0.27 (0.17), residues: 926 sheet: -1.27 (0.20), residues: 661 loop : -2.59 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 229 TYR 0.015 0.001 TYR N 344 PHE 0.018 0.002 PHE N 211 TRP 0.025 0.001 TRP F 212 HIS 0.011 0.001 HIS J 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (31784) covalent geometry : angle 0.62138 / 0.33 (43660) hydrogen bonds : bond 0.05047 / 3.43 ( 995) hydrogen bonds : angle 5.53269 / 3.95 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 247 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 30 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: A 157 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7159 (mmt180) REVERT: A 306 TYR cc_start: 0.5792 (p90) cc_final: 0.5329 (p90) REVERT: B 13 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: B 194 LEU cc_start: 0.8783 (mt) cc_final: 0.8235 (pp) REVERT: B 251 PHE cc_start: 0.7738 (t80) cc_final: 0.7537 (t80) REVERT: M 356 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: N 61 ILE cc_start: 0.8807 (tp) cc_final: 0.8600 (tp) REVERT: N 246 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8570 (m-30) REVERT: N 379 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8231 (m-70) REVERT: E 211 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7839 (mm) REVERT: F 62 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6381 (mmmt) REVERT: F 249 ASN cc_start: 0.5875 (OUTLIER) cc_final: 0.5595 (t0) REVERT: J 211 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7238 (p90) outliers start: 148 outliers final: 83 residues processed: 372 average time/residue: 0.1773 time to fit residues: 110.7502 Evaluate side-chains 319 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 416 ASN Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 168 MET Chi-restraints excluded: chain N residue 246 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 379 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 191 MET Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 402 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 329 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 HIS J 379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.087476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.072553 restraints weight = 139186.695| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.45 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 31784 Z= 0.152 Angle : 0.585 9.283 43660 Z= 0.314 Chirality : 0.042 0.234 4764 Planarity : 0.005 0.077 5124 Dihedral : 16.049 147.861 5738 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 5.16 % Allowed : 33.03 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.14), residues: 3425 helix: 0.71 (0.18), residues: 927 sheet: -1.21 (0.20), residues: 654 loop : -2.54 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 157 TYR 0.022 0.001 TYR E 413 PHE 0.016 0.001 PHE N 211 TRP 0.014 0.001 TRP F 212 HIS 0.007 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (31784) covalent geometry : angle 0.58481 / 0.31 (43660) hydrogen bonds : bond 0.04544 / 3.09 ( 995) hydrogen bonds : angle 5.20515 / 3.72 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 238 time to evaluate : 1.072 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: symmetry clash REVERT: A 157 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7206 (mmt180) REVERT: A 306 TYR cc_start: 0.5730 (p90) cc_final: 0.5385 (p90) REVERT: A 403 MET cc_start: 0.8089 (mmt) cc_final: 0.7660 (mmm) REVERT: B 133 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: B 194 LEU cc_start: 0.8808 (mt) cc_final: 0.8252 (pp) REVERT: B 251 PHE cc_start: 0.7659 (t80) cc_final: 0.7453 (t80) REVERT: B 270 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.5342 (m-30) REVERT: E 185 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6510 (ppp) REVERT: E 195 PHE cc_start: 0.8370 (p90) cc_final: 0.8063 (p90) REVERT: E 211 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7831 (mm) REVERT: F 249 ASN cc_start: 0.5948 (OUTLIER) cc_final: 0.5675 (t0) REVERT: F 320 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6488 (m90) REVERT: J 187 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5551 (mpt90) REVERT: J 211 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7249 (p90) outliers start: 152 outliers final: 109 residues processed: 362 average time/residue: 0.1762 time to fit residues: 106.8624 Evaluate side-chains 339 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 222 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 416 ASN Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 371 TYR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 232 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS B 333 GLN M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 333 GLN ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 379 HIS I 21 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.083340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.068467 restraints weight = 140887.801| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 4.33 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 31784 Z= 0.327 Angle : 0.752 9.754 43660 Z= 0.402 Chirality : 0.047 0.171 4764 Planarity : 0.006 0.070 5124 Dihedral : 16.168 148.485 5732 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.03 % Favored : 87.94 % Rotamer: Outliers : 7.00 % Allowed : 31.97 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.14), residues: 3425 helix: 0.49 (0.17), residues: 938 sheet: -1.55 (0.20), residues: 627 loop : -2.69 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 221 TYR 0.020 0.002 TYR N 335 PHE 0.023 0.002 PHE I 182 TRP 0.063 0.002 TRP N 334 HIS 0.025 0.002 HIS J 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.33 (31784) covalent geometry : angle 0.75186 / 0.40 (43660) hydrogen bonds : bond 0.06221 / 4.23 ( 995) hydrogen bonds : angle 5.54739 / 3.97 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 218 time to evaluate : 1.126 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: A 26 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8233 (tp) REVERT: A 30 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 124 MET cc_start: 0.8122 (ptt) cc_final: 0.7576 (ptp) REVERT: A 157 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7163 (mtt-85) REVERT: A 306 TYR cc_start: 0.5877 (p90) cc_final: 0.5462 (p90) REVERT: A 397 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8305 (tp) REVERT: A 403 MET cc_start: 0.8092 (mmt) cc_final: 0.7656 (mmm) REVERT: B 133 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: B 251 PHE cc_start: 0.7787 (t80) cc_final: 0.7562 (t80) REVERT: B 328 GLU cc_start: 0.8013 (tt0) cc_final: 0.7676 (tp30) REVERT: B 402 MET cc_start: 0.7084 (ppp) cc_final: 0.6799 (ptt) REVERT: M 153 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8404 (tppt) REVERT: N 37 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: N 267 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6559 (pp) REVERT: N 296 LYS cc_start: 0.7411 (tppt) cc_final: 0.7052 (tppt) REVERT: N 334 TRP cc_start: 0.8219 (m100) cc_final: 0.7918 (m100) REVERT: N 379 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8334 (m-70) REVERT: E 185 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6671 (ppp) REVERT: E 195 PHE cc_start: 0.8616 (p90) cc_final: 0.8289 (p90) REVERT: E 211 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7901 (mm) REVERT: E 480 ASP cc_start: 0.8755 (p0) cc_final: 0.8208 (p0) REVERT: F 62 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6492 (mmmt) REVERT: F 249 ASN cc_start: 0.5694 (OUTLIER) cc_final: 0.5396 (t0) REVERT: F 253 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7173 (t-90) REVERT: F 307 LYS cc_start: 0.7159 (mmmm) cc_final: 0.6820 (mmmt) REVERT: F 320 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6454 (m-70) REVERT: J 187 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.5505 (mpt90) REVERT: J 211 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7212 (p90) outliers start: 206 outliers final: 141 residues processed: 391 average time/residue: 0.1695 time to fit residues: 110.7344 Evaluate side-chains 360 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 203 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 273 HIS Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 416 ASN Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 464 VAL Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 318 VAL Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain N residue 338 ILE Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 379 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 402 MET Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 342 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 302 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.084928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.070039 restraints weight = 140422.718| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.37 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31784 Z= 0.171 Angle : 0.619 10.662 43660 Z= 0.331 Chirality : 0.043 0.258 4764 Planarity : 0.004 0.063 5124 Dihedral : 16.093 145.966 5732 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.10 % Favored : 89.87 % Rotamer: Outliers : 6.25 % Allowed : 32.82 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 3425 helix: 0.69 (0.17), residues: 940 sheet: -1.41 (0.20), residues: 636 loop : -2.61 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.031 0.002 TYR E 398 PHE 0.020 0.002 PHE E 275 TRP 0.015 0.001 TRP J 420 HIS 0.010 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (31784) covalent geometry : angle 0.61914 / 0.33 (43660) hydrogen bonds : bond 0.04747 / 3.21 ( 995) hydrogen bonds : angle 5.22120 / 3.73 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 224 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 124 MET cc_start: 0.7973 (ptt) cc_final: 0.7460 (ptp) REVERT: A 255 GLU cc_start: 0.8250 (pt0) cc_final: 0.8047 (pt0) REVERT: A 306 TYR cc_start: 0.5690 (p90) cc_final: 0.5361 (p90) REVERT: A 397 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 403 MET cc_start: 0.8109 (mmt) cc_final: 0.7688 (mmm) REVERT: B 133 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: B 194 LEU cc_start: 0.8884 (mt) cc_final: 0.8583 (mt) REVERT: B 222 CYS cc_start: 0.8578 (m) cc_final: 0.8238 (p) REVERT: B 328 GLU cc_start: 0.7896 (tt0) cc_final: 0.7631 (tp30) REVERT: B 402 MET cc_start: 0.7097 (ppp) cc_final: 0.6871 (ptt) REVERT: B 421 VAL cc_start: 0.2952 (OUTLIER) cc_final: 0.2752 (t) REVERT: M 153 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8330 (tppt) REVERT: N 56 MET cc_start: 0.7593 (pmm) cc_final: 0.7100 (pmm) REVERT: N 246 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: N 267 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6647 (pp) REVERT: N 296 LYS cc_start: 0.7450 (tppt) cc_final: 0.7133 (tppt) REVERT: N 334 TRP cc_start: 0.8214 (m100) cc_final: 0.7925 (m100) REVERT: E 183 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6355 (ttp80) REVERT: E 185 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6542 (ppp) REVERT: E 195 PHE cc_start: 0.8522 (p90) cc_final: 0.8173 (p90) REVERT: E 211 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7792 (mm) REVERT: F 62 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6380 (mmmt) REVERT: F 253 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7247 (t-90) REVERT: F 320 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6698 (m90) REVERT: I 114 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6619 (mmtt) REVERT: J 187 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5612 (mpt90) REVERT: J 211 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7107 (p90) outliers start: 184 outliers final: 122 residues processed: 380 average time/residue: 0.1663 time to fit residues: 106.0790 Evaluate side-chains 355 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 217 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 466 GLU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 246 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 318 VAL Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 321 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 470 TYR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 36 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 HIS J 17 ASN J 215 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.081212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066347 restraints weight = 142855.423| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.30 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 31784 Z= 0.399 Angle : 0.846 12.068 43660 Z= 0.445 Chirality : 0.050 0.292 4764 Planarity : 0.006 0.078 5124 Dihedral : 16.278 149.788 5732 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.43 % Favored : 86.54 % Rotamer: Outliers : 7.61 % Allowed : 31.80 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.13), residues: 3425 helix: 0.22 (0.17), residues: 937 sheet: -1.87 (0.20), residues: 625 loop : -2.86 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 157 TYR 0.032 0.003 TYR E 398 PHE 0.028 0.003 PHE J 214 TRP 0.022 0.002 TRP A 201 HIS 0.028 0.002 HIS J 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.40 (31784) covalent geometry : angle 0.84564 / 0.44 (43660) hydrogen bonds : bond 0.06942 / 4.74 ( 995) hydrogen bonds : angle 5.81503 / 4.17 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 204 time to evaluate : 1.088 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 30 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: A 124 MET cc_start: 0.8231 (ptt) cc_final: 0.7756 (ptp) REVERT: A 157 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7659 (mmt90) REVERT: A 249 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8448 (ptt-90) REVERT: A 281 MET cc_start: 0.8223 (pmm) cc_final: 0.7978 (pmm) REVERT: A 306 TYR cc_start: 0.5775 (p90) cc_final: 0.5467 (p90) REVERT: A 397 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 403 MET cc_start: 0.8144 (mmt) cc_final: 0.7706 (mmm) REVERT: B 222 CYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8203 (p) REVERT: B 402 MET cc_start: 0.7195 (ppp) cc_final: 0.6955 (ptt) REVERT: M 153 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8416 (tppt) REVERT: N 246 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: N 267 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6685 (pp) REVERT: N 296 LYS cc_start: 0.7462 (tppt) cc_final: 0.7126 (tppt) REVERT: N 334 TRP cc_start: 0.8364 (m100) cc_final: 0.7793 (m100) REVERT: N 378 TRP cc_start: 0.8693 (t60) cc_final: 0.8409 (t60) REVERT: E 185 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6678 (ppp) REVERT: E 195 PHE cc_start: 0.8633 (p90) cc_final: 0.8319 (p90) REVERT: E 211 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7883 (mm) REVERT: E 284 GLU cc_start: 0.8829 (tt0) cc_final: 0.8546 (tm-30) REVERT: E 446 ASN cc_start: 0.6526 (OUTLIER) cc_final: 0.6323 (t0) REVERT: E 480 ASP cc_start: 0.8877 (p0) cc_final: 0.8375 (p0) REVERT: F 253 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7183 (t-90) REVERT: F 306 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7821 (t80) REVERT: F 307 LYS cc_start: 0.8272 (tppp) cc_final: 0.7891 (mmmt) REVERT: F 320 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.7118 (m-70) REVERT: I 114 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6738 (mmtt) REVERT: I 268 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: J 187 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5609 (mpt90) REVERT: J 211 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7102 (p90) REVERT: J 354 PHE cc_start: 0.8968 (m-80) cc_final: 0.8698 (m-80) outliers start: 224 outliers final: 158 residues processed: 396 average time/residue: 0.1656 time to fit residues: 110.7315 Evaluate side-chains 368 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 193 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 466 GLU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 246 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 267 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 318 VAL Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain N residue 338 ILE Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 405 TYR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 470 TYR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 PHE Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 185 MET Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 352 HIS Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 18 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN F 60 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.085059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.070192 restraints weight = 139566.920| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.37 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31784 Z= 0.131 Angle : 0.618 9.521 43660 Z= 0.329 Chirality : 0.043 0.211 4764 Planarity : 0.005 0.076 5124 Dihedral : 16.113 147.817 5732 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % Rotamer: Outliers : 4.99 % Allowed : 33.84 % Favored : 61.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3425 helix: 0.76 (0.17), residues: 935 sheet: -1.57 (0.20), residues: 660 loop : -2.60 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 377 TYR 0.021 0.001 TYR E 413 PHE 0.018 0.001 PHE E 275 TRP 0.018 0.001 TRP J 420 HIS 0.010 0.001 HIS F 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (31784) covalent geometry : angle 0.61766 / 0.33 (43660) hydrogen bonds : bond 0.04344 / 2.95 ( 995) hydrogen bonds : angle 5.17794 / 3.71 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 225 time to evaluate : 1.108 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 30 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: A 124 MET cc_start: 0.8010 (ptt) cc_final: 0.7572 (ptp) REVERT: A 255 GLU cc_start: 0.8256 (pt0) cc_final: 0.8037 (pt0) REVERT: A 281 MET cc_start: 0.8154 (pmm) cc_final: 0.7936 (pmm) REVERT: A 306 TYR cc_start: 0.5646 (p90) cc_final: 0.5343 (p90) REVERT: A 397 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 403 MET cc_start: 0.8094 (mmt) cc_final: 0.7723 (mmm) REVERT: A 433 LEU cc_start: 0.9073 (mt) cc_final: 0.8658 (mt) REVERT: B 222 CYS cc_start: 0.8548 (m) cc_final: 0.8159 (p) REVERT: B 328 GLU cc_start: 0.7948 (tt0) cc_final: 0.7651 (tp30) REVERT: B 402 MET cc_start: 0.7077 (ppp) cc_final: 0.6763 (ptt) REVERT: M 153 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8317 (tppt) REVERT: N 246 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8498 (m-30) REVERT: N 296 LYS cc_start: 0.7517 (tppt) cc_final: 0.7098 (tppt) REVERT: N 334 TRP cc_start: 0.8256 (m100) cc_final: 0.7844 (m100) REVERT: E 183 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6469 (ttp80) REVERT: E 195 PHE cc_start: 0.8409 (p90) cc_final: 0.8073 (p90) REVERT: E 475 GLU cc_start: 0.8185 (tt0) cc_final: 0.7863 (tt0) REVERT: F 62 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6598 (mmmt) REVERT: F 215 HIS cc_start: 0.3307 (OUTLIER) cc_final: 0.2956 (t-90) REVERT: F 253 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7322 (t70) REVERT: F 306 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7857 (t80) REVERT: F 414 ARG cc_start: 0.3707 (OUTLIER) cc_final: 0.2246 (ptp-170) REVERT: J 211 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7214 (p90) REVERT: J 354 PHE cc_start: 0.8873 (m-80) cc_final: 0.8596 (m-80) outliers start: 147 outliers final: 100 residues processed: 351 average time/residue: 0.1792 time to fit residues: 105.8136 Evaluate side-chains 319 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 208 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 466 GLU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 246 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 318 VAL Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 306 PHE Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 212 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 345 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 190 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 321 optimal weight: 0.0170 chunk 9 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 112 optimal weight: 0.0170 chunk 283 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.085251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.070390 restraints weight = 139559.974| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.37 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31784 Z= 0.131 Angle : 0.604 11.370 43660 Z= 0.319 Chirality : 0.042 0.238 4764 Planarity : 0.004 0.066 5124 Dihedral : 15.998 147.109 5728 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.99 % Favored : 89.99 % Rotamer: Outliers : 4.08 % Allowed : 35.24 % Favored : 60.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.14), residues: 3425 helix: 0.88 (0.18), residues: 933 sheet: -1.40 (0.20), residues: 652 loop : -2.55 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 183 TYR 0.020 0.001 TYR E 413 PHE 0.016 0.001 PHE E 275 TRP 0.016 0.001 TRP J 420 HIS 0.007 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (31784) covalent geometry : angle 0.60404 / 0.32 (43660) hydrogen bonds : bond 0.04224 / 2.87 ( 995) hydrogen bonds : angle 5.04642 / 3.62 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 222 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: A 124 MET cc_start: 0.7975 (ptt) cc_final: 0.7543 (ptp) REVERT: A 185 MET cc_start: 0.7965 (pmm) cc_final: 0.7159 (pmm) REVERT: A 255 GLU cc_start: 0.8223 (pt0) cc_final: 0.7990 (pt0) REVERT: A 306 TYR cc_start: 0.5665 (p90) cc_final: 0.5315 (p90) REVERT: A 403 MET cc_start: 0.8050 (mmt) cc_final: 0.7684 (mmm) REVERT: A 433 LEU cc_start: 0.9125 (mt) cc_final: 0.8849 (mt) REVERT: B 328 GLU cc_start: 0.7964 (tt0) cc_final: 0.7688 (tp30) REVERT: B 402 MET cc_start: 0.7063 (ppp) cc_final: 0.6779 (ptt) REVERT: M 153 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8315 (tppt) REVERT: N 296 LYS cc_start: 0.7538 (tppt) cc_final: 0.7149 (tppt) REVERT: N 334 TRP cc_start: 0.8275 (m100) cc_final: 0.7909 (m100) REVERT: E 185 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6315 (ppp) REVERT: E 195 PHE cc_start: 0.8387 (p90) cc_final: 0.8071 (p90) REVERT: E 211 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7681 (mm) REVERT: E 475 GLU cc_start: 0.8243 (tt0) cc_final: 0.7887 (tt0) REVERT: F 62 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6533 (mmmt) REVERT: F 232 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8475 (tm-30) REVERT: F 306 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7896 (t80) REVERT: F 307 LYS cc_start: 0.8324 (tppp) cc_final: 0.8095 (tppt) REVERT: F 414 ARG cc_start: 0.3748 (OUTLIER) cc_final: 0.2286 (ptp-170) REVERT: I 114 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.6770 (mmtt) REVERT: J 211 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6814 (p90) REVERT: J 354 PHE cc_start: 0.8871 (m-80) cc_final: 0.8595 (m-80) outliers start: 120 outliers final: 93 residues processed: 323 average time/residue: 0.1880 time to fit residues: 101.4236 Evaluate side-chains 317 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 215 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 318 VAL Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 306 PHE Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 212 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 345 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 41 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 282 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** 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 = 0.3838 r_free = 0.3838 target = 0.084004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.069202 restraints weight = 140752.977| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.32 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31784 Z= 0.193 Angle : 0.645 11.483 43660 Z= 0.339 Chirality : 0.043 0.180 4764 Planarity : 0.004 0.060 5124 Dihedral : 15.988 147.840 5725 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.92 % Favored : 89.05 % Rotamer: Outliers : 4.28 % Allowed : 35.10 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3425 helix: 0.89 (0.18), residues: 935 sheet: -1.49 (0.20), residues: 639 loop : -2.56 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 285 TYR 0.019 0.001 TYR E 413 PHE 0.020 0.002 PHE E 275 TRP 0.056 0.002 TRP J 378 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (31784) covalent geometry : angle 0.64549 / 0.34 (43660) hydrogen bonds : bond 0.04618 / 3.14 ( 995) hydrogen bonds : angle 5.12718 / 3.67 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 211 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: A 124 MET cc_start: 0.8035 (ptt) cc_final: 0.7574 (ptp) REVERT: A 185 MET cc_start: 0.7944 (pmm) cc_final: 0.7194 (pmm) REVERT: A 306 TYR cc_start: 0.5679 (p90) cc_final: 0.5402 (p90) REVERT: A 403 MET cc_start: 0.8022 (mmt) cc_final: 0.7634 (mmm) REVERT: B 328 GLU cc_start: 0.8052 (tt0) cc_final: 0.7754 (tp30) REVERT: B 349 TYR cc_start: 0.7970 (m-80) cc_final: 0.7540 (m-80) REVERT: B 402 MET cc_start: 0.7117 (ppp) cc_final: 0.6828 (ptt) REVERT: M 153 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8341 (tppt) REVERT: M 304 HIS cc_start: 0.7931 (m90) cc_final: 0.7677 (m90) REVERT: N 296 LYS cc_start: 0.7580 (tppt) cc_final: 0.7267 (tppt) REVERT: N 334 TRP cc_start: 0.8331 (m100) cc_final: 0.7939 (m100) REVERT: E 183 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6392 (ttp80) REVERT: E 185 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6699 (ppp) REVERT: E 195 PHE cc_start: 0.8514 (p90) cc_final: 0.8240 (p90) REVERT: E 211 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7758 (mm) REVERT: E 446 ASN cc_start: 0.6418 (OUTLIER) cc_final: 0.6010 (t0) REVERT: E 475 GLU cc_start: 0.8289 (tt0) cc_final: 0.8061 (tt0) REVERT: F 62 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6553 (mmmt) REVERT: F 232 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8528 (tm-30) REVERT: F 306 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7929 (t80) REVERT: F 414 ARG cc_start: 0.3988 (OUTLIER) cc_final: 0.2503 (ptp-170) REVERT: I 114 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.6794 (mmtt) REVERT: J 211 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.6940 (p90) REVERT: J 354 PHE cc_start: 0.8860 (m-80) cc_final: 0.8582 (m-80) REVERT: J 377 MET cc_start: 0.8576 (tmm) cc_final: 0.8272 (ttt) outliers start: 126 outliers final: 103 residues processed: 323 average time/residue: 0.1666 time to fit residues: 89.7929 Evaluate side-chains 320 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 206 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 306 PHE Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 326 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** F 60 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.085169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.070369 restraints weight = 139201.664| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.35 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31784 Z= 0.135 Angle : 0.613 11.702 43660 Z= 0.321 Chirality : 0.042 0.296 4764 Planarity : 0.004 0.061 5124 Dihedral : 15.904 146.739 5725 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.04 % Favored : 89.93 % Rotamer: Outliers : 3.84 % Allowed : 35.34 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.14), residues: 3425 helix: 0.94 (0.18), residues: 934 sheet: -1.36 (0.20), residues: 653 loop : -2.51 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 183 TYR 0.020 0.001 TYR E 398 PHE 0.016 0.001 PHE N 211 TRP 0.020 0.001 TRP J 212 HIS 0.006 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (31784) covalent geometry : angle 0.61269 / 0.32 (43660) hydrogen bonds : bond 0.04082 / 2.79 ( 995) hydrogen bonds : angle 4.99418 / 3.58 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6850 Ramachandran restraints generated. 3425 Oldfield, 0 Emsley, 3425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 218 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: A 124 MET cc_start: 0.7995 (ptt) cc_final: 0.7577 (ptp) REVERT: A 132 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8716 (tm-30) REVERT: A 185 MET cc_start: 0.7938 (pmm) cc_final: 0.7277 (pmm) REVERT: A 306 TYR cc_start: 0.5722 (p90) cc_final: 0.5381 (p90) REVERT: A 403 MET cc_start: 0.8040 (mmt) cc_final: 0.7668 (mmm) REVERT: B 222 CYS cc_start: 0.8554 (m) cc_final: 0.8175 (p) REVERT: B 270 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: B 328 GLU cc_start: 0.8001 (tt0) cc_final: 0.7721 (tp30) REVERT: B 349 TYR cc_start: 0.7979 (m-80) cc_final: 0.7577 (m-80) REVERT: B 402 MET cc_start: 0.7113 (ppp) cc_final: 0.6859 (ptt) REVERT: M 153 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (tppt) REVERT: M 304 HIS cc_start: 0.7869 (m90) cc_final: 0.7664 (m90) REVERT: N 168 MET cc_start: 0.8071 (mmm) cc_final: 0.7768 (mmp) REVERT: N 296 LYS cc_start: 0.7583 (tppt) cc_final: 0.7190 (tppt) REVERT: N 334 TRP cc_start: 0.8274 (m100) cc_final: 0.7918 (m100) REVERT: E 183 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6382 (ttp80) REVERT: E 195 PHE cc_start: 0.8470 (p90) cc_final: 0.8100 (p90) REVERT: E 211 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7702 (mm) REVERT: F 62 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6449 (mmmt) REVERT: F 232 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8519 (tm-30) REVERT: F 306 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7948 (t80) REVERT: F 414 ARG cc_start: 0.3815 (OUTLIER) cc_final: 0.2369 (ptp-170) REVERT: I 114 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6899 (mmtt) REVERT: J 211 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6890 (p90) REVERT: J 354 PHE cc_start: 0.8840 (m-80) cc_final: 0.8564 (m-80) outliers start: 113 outliers final: 95 residues processed: 317 average time/residue: 0.1774 time to fit residues: 93.6944 Evaluate side-chains 315 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 210 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 306 PHE Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 134 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 3.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** 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 = 0.3840 r_free = 0.3840 target = 0.084038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.069209 restraints weight = 140855.045| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 4.34 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31784 Z= 0.191 Angle : 0.649 11.631 43660 Z= 0.339 Chirality : 0.043 0.302 4764 Planarity : 0.004 0.059 5124 Dihedral : 15.884 147.181 5725 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.98 % Favored : 88.99 % Rotamer: Outliers : 4.18 % Allowed : 34.83 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.14), residues: 3425 helix: 0.92 (0.18), residues: 935 sheet: -1.45 (0.20), residues: 640 loop : -2.52 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 377 TYR 0.022 0.001 TYR E 398 PHE 0.020 0.002 PHE E 275 TRP 0.017 0.001 TRP J 212 HIS 0.006 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (31784) covalent geometry : angle 0.64894 / 0.34 (43660) hydrogen bonds : bond 0.04620 / 3.15 ( 995) hydrogen bonds : angle 5.08316 / 3.65 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5945.03 seconds wall clock time: 103 minutes 29.81 seconds (6209.81 seconds total)