Starting phenix.real_space_refine on Wed May 28 08:49:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsz_61787/05_2025/9jsz_61787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsz_61787/05_2025/9jsz_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_61787/05_2025/9jsz_61787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsz_61787/05_2025/9jsz_61787.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsz_61787/05_2025/9jsz_61787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsz_61787/05_2025/9jsz_61787.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.06, per 1000 atoms: 0.62 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: 6.73 Conformation dependent library (CDL) restraints added in 3.1 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: 10.14 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: 10.62 Time building geometry restraints manager: 7.97 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=" C LEU N 169 " pdb=" O LEU N 169 " ideal model delta sigma weight residual 1.249 1.230 0.019 8.50e-03 1.38e+04 4.81e+00 bond pdb=" C3' DT L 18 " pdb=" O3' DT L 18 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB GLU E 132 " pdb=" CG GLU E 132 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CA ASP A 414 " pdb=" C ASP A 414 " ideal model delta sigma weight residual 1.525 1.506 0.019 1.13e-02 7.83e+03 2.83e+00 bond pdb=" O5' A C 3 " pdb=" C5' A C 3 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.76e+00 ... (remaining 31779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 42614 2.21 - 4.41: 884 4.41 - 6.62: 119 6.62 - 8.82: 32 8.82 - 11.03: 11 Bond angle restraints: 43660 Sorted by residual: angle pdb=" CA GLU J 247 " pdb=" CB GLU J 247 " pdb=" CG GLU J 247 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA MET E 403 " pdb=" CB MET E 403 " pdb=" CG MET E 403 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" C GLU A 115 " pdb=" N PRO A 116 " pdb=" CA PRO A 116 " ideal model delta sigma weight residual 119.84 115.11 4.73 1.25e+00 6.40e-01 1.43e+01 angle pdb=" CA GLN N 374 " pdb=" CB GLN N 374 " pdb=" CG GLN N 374 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CA MET J 47 " pdb=" CB MET J 47 " pdb=" CG MET J 47 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.38e+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: 3621 0.050 - 0.100: 881 0.100 - 0.150: 231 0.150 - 0.200: 22 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: 8.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 70.020 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 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= 0.180 Angle : 0.768 11.028 43660 Z= 0.412 Chirality : 0.047 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 : 7.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.051 0.002 TRP J 212 HIS 0.006 0.001 HIS F 106 PHE 0.070 0.002 PHE F 323 TYR 0.030 0.002 TYR F 79 ARG 0.011 0.000 ARG N 102 Details of bonding type rmsd hydrogen bonds : bond 0.15630 ( 995) hydrogen bonds : angle 7.28914 ( 2691) covalent geometry : bond 0.00373 (31784) covalent geometry : angle 0.76768 (43660) *********************** 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 : 3.755 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: 0.5922 (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: 0.4271 time to fit residues: 226.6003 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 : 2.983 ------------------------------------------------------------------------------- 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 293 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 140 optimal weight: 0.0570 chunk 272 optimal weight: 0.0070 chunk 105 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 316 optimal weight: 10.0000 overall best weight: 1.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN F 103 GLN I 181 ASN I 280 GLN J 215 HIS J 321 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.088515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073642 restraints weight = 137749.479| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 4.43 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31784 Z= 0.141 Angle : 0.582 8.825 43660 Z= 0.308 Chirality : 0.040 0.174 4764 Planarity : 0.005 0.084 5124 Dihedral : 16.099 162.576 5740 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 4.59 % Allowed : 34.22 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 3425 helix: 0.37 (0.17), residues: 926 sheet: -1.20 (0.20), residues: 664 loop : -2.56 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 212 HIS 0.005 0.001 HIS F 106 PHE 0.014 0.001 PHE F 289 TYR 0.015 0.001 TYR E 413 ARG 0.006 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 995) hydrogen bonds : angle 5.32668 ( 2691) covalent geometry : bond 0.00309 (31784) covalent geometry : angle 0.58217 (43660) *********************** 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 385 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 250 time to evaluate : 3.217 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: 0.8815 (OUTLIER) cc_final: 0.8280 (tp) REVERT: A 30 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: A 157 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7218 (mmt180) REVERT: A 306 TYR cc_start: 0.5761 (p90) cc_final: 0.5287 (p90) REVERT: B 13 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: B 133 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: B 184 TYR cc_start: 0.7622 (m-80) cc_final: 0.7387 (m-80) REVERT: B 194 LEU cc_start: 0.8775 (mt) cc_final: 0.8234 (pp) REVERT: M 356 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: N 334 TRP cc_start: 0.7910 (m100) cc_final: 0.7698 (m100) REVERT: E 185 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6491 (ppp) REVERT: E 195 PHE cc_start: 0.8483 (p90) cc_final: 0.8144 (p90) REVERT: F 62 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6305 (mmmt) REVERT: F 249 ASN cc_start: 0.5931 (OUTLIER) cc_final: 0.5672 (t0) REVERT: J 211 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7250 (p90) outliers start: 135 outliers final: 78 residues processed: 366 average time/residue: 0.3752 time to fit residues: 228.7862 Evaluate side-chains 315 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 228 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 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 47 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 222 CYS 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 B residue 378 TRP 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 259 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE 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 476 VAL Chi-restraints excluded: chain E residue 477 ILE 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 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 412 ASP Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 429 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 36 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 70 THR 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 215 HIS 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 39 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 292 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN J 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.088672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.073780 restraints weight = 138489.143| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.45 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31784 Z= 0.117 Angle : 0.557 9.129 43660 Z= 0.291 Chirality : 0.040 0.218 4764 Planarity : 0.004 0.062 5124 Dihedral : 15.952 163.859 5732 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 4.55 % Allowed : 33.13 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3425 helix: 0.82 (0.18), residues: 927 sheet: -1.10 (0.20), residues: 665 loop : -2.49 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 212 HIS 0.006 0.001 HIS F 106 PHE 0.014 0.001 PHE N 211 TYR 0.018 0.001 TYR E 413 ARG 0.004 0.000 ARG M 453 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 995) hydrogen bonds : angle 5.01897 ( 2691) covalent geometry : bond 0.00260 (31784) covalent geometry : angle 0.55728 (43660) *********************** 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 378 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 244 time to evaluate : 3.503 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 157 ARG cc_start: 0.7844 (mtp180) cc_final: 0.7272 (mmt180) REVERT: A 306 TYR cc_start: 0.5808 (p90) cc_final: 0.5488 (p90) REVERT: A 403 MET cc_start: 0.8113 (mmt) cc_final: 0.7715 (mmm) REVERT: B 20 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8481 (tpt170) REVERT: B 133 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 194 LEU cc_start: 0.8810 (mt) cc_final: 0.8269 (pp) REVERT: B 222 CYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8077 (p) REVERT: B 270 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5355 (m-30) REVERT: M 153 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (tppt) REVERT: N 334 TRP cc_start: 0.7929 (m100) cc_final: 0.7598 (m100) REVERT: E 195 PHE cc_start: 0.8553 (p90) cc_final: 0.8258 (p90) REVERT: F 249 ASN cc_start: 0.6013 (OUTLIER) cc_final: 0.5743 (t0) REVERT: F 320 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6504 (m90) REVERT: J 211 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7321 (p90) outliers start: 134 outliers final: 84 residues processed: 355 average time/residue: 0.3808 time to fit residues: 223.8597 Evaluate side-chains 316 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 224 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 233 LEU 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 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 20 ARG Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 222 CYS 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 320 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain M residue 9 ASP 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 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 437 ILE 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 336 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG 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 476 VAL Chi-restraints excluded: chain F residue 16 GLU 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 93 ASN Chi-restraints excluded: chain F residue 129 VAL 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 249 ASN Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 320 HIS 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 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 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 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 329 LEU Chi-restraints excluded: chain J residue 345 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 317 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 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 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS F 103 GLN F 379 HIS I 21 HIS J 17 ASN J 215 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.083177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068258 restraints weight = 141831.235| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.37 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 31784 Z= 0.338 Angle : 0.749 9.490 43660 Z= 0.395 Chirality : 0.046 0.205 4764 Planarity : 0.005 0.069 5124 Dihedral : 16.178 166.321 5729 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.80 % Favored : 88.18 % Rotamer: Outliers : 6.80 % Allowed : 31.94 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3425 helix: 0.58 (0.17), residues: 937 sheet: -1.45 (0.20), residues: 625 loop : -2.60 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 204 HIS 0.007 0.001 HIS A 118 PHE 0.024 0.002 PHE E 289 TYR 0.023 0.002 TYR E 266 ARG 0.009 0.001 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.05850 ( 995) hydrogen bonds : angle 5.46741 ( 2691) covalent geometry : bond 0.00742 (31784) covalent geometry : angle 0.74869 (43660) *********************** 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 416 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 216 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: A 255 GLU cc_start: 0.8369 (pt0) cc_final: 0.8137 (pt0) REVERT: A 306 TYR cc_start: 0.5769 (p90) cc_final: 0.5453 (p90) REVERT: A 397 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8285 (tp) REVERT: A 403 MET cc_start: 0.8149 (mmt) cc_final: 0.7724 (mmm) REVERT: B 133 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: B 222 CYS cc_start: 0.8454 (m) cc_final: 0.8171 (p) REVERT: B 328 GLU cc_start: 0.7981 (tt0) cc_final: 0.7710 (tp30) REVERT: M 153 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8401 (tppt) REVERT: N 37 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: N 296 LYS cc_start: 0.7463 (tppt) cc_final: 0.7099 (tppt) REVERT: N 334 TRP cc_start: 0.8207 (m100) cc_final: 0.7815 (m100) REVERT: N 379 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8335 (m-70) REVERT: E 185 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6725 (ppp) REVERT: E 195 PHE cc_start: 0.8697 (p90) cc_final: 0.8410 (p90) REVERT: E 475 GLU cc_start: 0.8213 (tt0) cc_final: 0.7848 (tt0) REVERT: E 480 ASP cc_start: 0.8751 (p0) cc_final: 0.8228 (p0) REVERT: F 47 MET cc_start: 0.7646 (tmm) cc_final: 0.7376 (tpp) REVERT: F 232 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8421 (tm-30) REVERT: F 253 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7107 (t-90) REVERT: F 261 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: F 306 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7805 (t80) REVERT: F 320 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6421 (m-70) REVERT: J 187 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5541 (mpt90) REVERT: J 211 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7086 (p90) REVERT: J 330 MET cc_start: 0.8735 (ptt) cc_final: 0.8496 (ptt) outliers start: 200 outliers final: 129 residues processed: 383 average time/residue: 0.3770 time to fit residues: 240.4663 Evaluate side-chains 353 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 211 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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 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 209 VAL Chi-restraints excluded: chain A residue 233 LEU 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 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 PHE 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 76 SER 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 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 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 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 307 MET 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 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 169 LEU 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 336 LEU 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 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 384 LEU 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 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 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 249 ASN Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 261 TYR 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 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 I residue 9 ASP 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 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 307 MET 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 11 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 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 212 TRP Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 345 THR 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 61 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 334 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 316 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 HIS ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN J 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.084452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.069541 restraints weight = 139701.193| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.37 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31784 Z= 0.189 Angle : 0.627 9.541 43660 Z= 0.329 Chirality : 0.042 0.242 4764 Planarity : 0.005 0.061 5124 Dihedral : 16.090 163.294 5729 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.25 % Favored : 89.72 % Rotamer: Outliers : 5.91 % Allowed : 32.86 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3425 helix: 0.77 (0.17), residues: 936 sheet: -1.44 (0.20), residues: 637 loop : -2.55 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 204 HIS 0.010 0.001 HIS J 215 PHE 0.021 0.002 PHE E 275 TYR 0.026 0.002 TYR E 398 ARG 0.005 0.000 ARG M 453 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 995) hydrogen bonds : angle 5.18235 ( 2691) covalent geometry : bond 0.00417 (31784) covalent geometry : angle 0.62658 (43660) *********************** 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 397 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 223 time to evaluate : 3.193 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 30 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: A 124 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7716 (ptp) REVERT: A 255 GLU cc_start: 0.8390 (pt0) cc_final: 0.8172 (pt0) REVERT: A 306 TYR cc_start: 0.5622 (p90) cc_final: 0.5387 (p90) REVERT: A 397 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8300 (tp) REVERT: A 403 MET cc_start: 0.8107 (mmt) cc_final: 0.7707 (mmm) REVERT: B 133 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: B 141 LEU cc_start: 0.7481 (tt) cc_final: 0.7205 (tt) REVERT: B 222 CYS cc_start: 0.8522 (m) cc_final: 0.8205 (p) REVERT: B 328 GLU cc_start: 0.7904 (tt0) cc_final: 0.7611 (tp30) REVERT: B 421 VAL cc_start: 0.2985 (OUTLIER) cc_final: 0.2771 (t) REVERT: M 153 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8332 (tppt) REVERT: M 304 HIS cc_start: 0.7926 (m170) cc_final: 0.7680 (m170) REVERT: N 37 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: N 246 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8562 (m-30) REVERT: N 267 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6708 (pp) REVERT: N 296 LYS cc_start: 0.7519 (tppt) cc_final: 0.7072 (tppt) REVERT: N 334 TRP cc_start: 0.8161 (m100) cc_final: 0.7852 (m100) REVERT: N 379 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.8273 (m-70) REVERT: E 183 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6506 (ttp80) REVERT: E 185 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6573 (ppp) REVERT: E 191 MET cc_start: 0.7894 (mpp) cc_final: 0.7639 (mpp) REVERT: E 195 PHE cc_start: 0.8574 (p90) cc_final: 0.8225 (p90) REVERT: F 204 TRP cc_start: 0.6335 (p90) cc_final: 0.5937 (p90) REVERT: F 232 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8494 (tm-30) REVERT: F 261 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: F 306 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7781 (t80) REVERT: F 320 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6806 (m90) REVERT: J 187 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5554 (mpt90) REVERT: J 211 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6978 (p90) REVERT: J 330 MET cc_start: 0.8747 (ptt) cc_final: 0.8528 (ptt) outliers start: 174 outliers final: 117 residues processed: 371 average time/residue: 0.3804 time to fit residues: 234.4942 Evaluate side-chains 352 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 218 time to evaluate : 3.096 ------------------------------------------------------------------------------- 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 124 MET 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 204 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 233 LEU 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 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 76 SER 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 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 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 421 VAL 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 276 THR 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 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU 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 338 ILE Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 379 HIS Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 136 MET 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 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 383 VAL Chi-restraints excluded: chain E residue 384 LEU 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 19 VAL Chi-restraints excluded: chain F residue 46 VAL 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 254 LEU Chi-restraints excluded: chain F residue 261 TYR 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 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 211 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 83 THR 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 168 MET Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 212 TRP Chi-restraints excluded: chain J residue 215 HIS Chi-restraints excluded: chain J residue 245 ILE 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 205 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 273 HIS M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.083766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.068886 restraints weight = 141076.660| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 4.36 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.005 0.044 31784 Z= 0.220 Angle : 0.647 12.295 43660 Z= 0.339 Chirality : 0.042 0.184 4764 Planarity : 0.005 0.061 5124 Dihedral : 16.081 164.773 5729 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.45 % Favored : 88.53 % Rotamer: Outliers : 6.90 % Allowed : 32.01 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3425 helix: 0.78 (0.17), residues: 940 sheet: -1.49 (0.20), residues: 636 loop : -2.59 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 204 HIS 0.025 0.001 HIS J 215 PHE 0.024 0.002 PHE E 59 TYR 0.032 0.002 TYR E 398 ARG 0.005 0.000 ARG E 374 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 995) hydrogen bonds : angle 5.20864 ( 2691) covalent geometry : bond 0.00484 (31784) covalent geometry : angle 0.64700 (43660) *********************** 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 421 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 218 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: A 112 ILE cc_start: 0.7415 (mm) cc_final: 0.7202 (mm) REVERT: A 255 GLU cc_start: 0.8397 (pt0) cc_final: 0.8147 (pt0) REVERT: A 281 MET cc_start: 0.8166 (pmm) cc_final: 0.7937 (pmm) REVERT: A 306 TYR cc_start: 0.5762 (p90) cc_final: 0.5500 (p90) REVERT: A 397 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 403 MET cc_start: 0.8071 (mmt) cc_final: 0.7671 (mmm) REVERT: B 222 CYS cc_start: 0.8514 (m) cc_final: 0.8200 (p) REVERT: B 328 GLU cc_start: 0.7961 (tt0) cc_final: 0.7652 (tp30) REVERT: M 64 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8840 (p) REVERT: M 153 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8360 (tppt) REVERT: M 304 HIS cc_start: 0.7965 (m170) cc_final: 0.7731 (m170) REVERT: N 168 MET cc_start: 0.8166 (mmm) cc_final: 0.6468 (mmm) REVERT: N 246 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8622 (m-30) REVERT: N 296 LYS cc_start: 0.7554 (tppt) cc_final: 0.7118 (tppt) REVERT: N 334 TRP cc_start: 0.8194 (m100) cc_final: 0.7846 (m100) REVERT: N 379 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8261 (m-70) REVERT: E 183 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6446 (ttp80) REVERT: E 185 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6791 (ppp) REVERT: E 195 PHE cc_start: 0.8552 (p90) cc_final: 0.8225 (p90) REVERT: E 281 MET cc_start: 0.8210 (pmm) cc_final: 0.7973 (pmm) REVERT: E 307 MET cc_start: 0.7938 (mmm) cc_final: 0.7725 (mmm) REVERT: F 204 TRP cc_start: 0.6237 (p90) cc_final: 0.5905 (p90) REVERT: F 232 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 249 ASN cc_start: 0.5746 (OUTLIER) cc_final: 0.5406 (t0) REVERT: F 253 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: F 261 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: F 306 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7843 (t80) REVERT: F 320 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6731 (m90) REVERT: J 53 MET cc_start: 0.8805 (pmm) cc_final: 0.8150 (pmm) REVERT: J 211 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7085 (p90) REVERT: J 330 MET cc_start: 0.8743 (ptt) cc_final: 0.8505 (ptt) REVERT: J 354 PHE cc_start: 0.8892 (m-80) cc_final: 0.8625 (m-80) outliers start: 203 outliers final: 146 residues processed: 393 average time/residue: 0.3733 time to fit residues: 245.2215 Evaluate side-chains 372 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 212 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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 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 204 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 233 LEU 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 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 A residue 485 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 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 76 SER 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 242 HIS 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 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 252 LEU Chi-restraints excluded: chain M residue 276 THR 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 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 245 ILE Chi-restraints excluded: chain N residue 246 ASP Chi-restraints excluded: chain N residue 259 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 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 46 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 136 MET 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 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 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 384 LEU 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 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 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 249 ASN Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain F residue 285 VAL 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 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 211 ILE Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 252 LEU 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 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 56 MET Chi-restraints excluded: chain J residue 83 THR 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 211 PHE Chi-restraints excluded: chain J residue 212 TRP Chi-restraints excluded: chain J residue 215 HIS 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 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 294 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** J 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.086307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071469 restraints weight = 138873.446| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.38 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31784 Z= 0.114 Angle : 0.590 11.347 43660 Z= 0.304 Chirality : 0.040 0.175 4764 Planarity : 0.004 0.062 5124 Dihedral : 15.928 162.758 5725 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.67 % Favored : 91.30 % Rotamer: Outliers : 4.83 % Allowed : 34.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3425 helix: 0.99 (0.18), residues: 942 sheet: -1.25 (0.20), residues: 648 loop : -2.45 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 420 HIS 0.038 0.001 HIS J 215 PHE 0.024 0.001 PHE E 59 TYR 0.024 0.001 TYR E 398 ARG 0.005 0.000 ARG M 453 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 995) hydrogen bonds : angle 4.90920 ( 2691) covalent geometry : bond 0.00257 (31784) covalent geometry : angle 0.58994 (43660) *********************** 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 375 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 233 time to evaluate : 3.063 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: 0.8712 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: A 157 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7384 (mtt-85) REVERT: A 185 MET cc_start: 0.7903 (pmm) cc_final: 0.7236 (pmm) REVERT: A 255 GLU cc_start: 0.8340 (pt0) cc_final: 0.8079 (pt0) REVERT: A 306 TYR cc_start: 0.5910 (p90) cc_final: 0.5483 (p90) REVERT: A 403 MET cc_start: 0.8061 (mmt) cc_final: 0.7710 (mmm) REVERT: B 194 LEU cc_start: 0.8935 (mt) cc_final: 0.8628 (mt) REVERT: B 222 CYS cc_start: 0.8491 (m) cc_final: 0.8163 (p) REVERT: B 270 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5700 (m-30) REVERT: B 328 GLU cc_start: 0.7982 (tt0) cc_final: 0.7740 (tp30) REVERT: M 64 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8679 (p) REVERT: M 153 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8301 (tppt) REVERT: M 304 HIS cc_start: 0.7906 (m170) cc_final: 0.7682 (m170) REVERT: N 168 MET cc_start: 0.8105 (mmm) cc_final: 0.6647 (mmm) REVERT: N 296 LYS cc_start: 0.7617 (tppt) cc_final: 0.7234 (tppt) REVERT: N 334 TRP cc_start: 0.8112 (m100) cc_final: 0.7851 (m100) REVERT: E 195 PHE cc_start: 0.8483 (p90) cc_final: 0.8197 (p90) REVERT: F 204 TRP cc_start: 0.6171 (p90) cc_final: 0.5911 (p90) REVERT: F 232 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8581 (tm-30) REVERT: F 306 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7838 (t80) REVERT: F 307 LYS cc_start: 0.7612 (tppt) cc_final: 0.7245 (mmmm) REVERT: F 320 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6667 (m90) REVERT: F 414 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.2299 (ptp-170) REVERT: I 114 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6829 (mmtt) REVERT: I 216 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7450 (pttp) REVERT: J 53 MET cc_start: 0.8769 (pmm) cc_final: 0.8167 (pmm) REVERT: J 211 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6840 (p90) REVERT: J 354 PHE cc_start: 0.8838 (m-80) cc_final: 0.8559 (m-80) outliers start: 142 outliers final: 105 residues processed: 353 average time/residue: 0.3736 time to fit residues: 217.7605 Evaluate side-chains 330 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 215 time to evaluate : 3.069 ------------------------------------------------------------------------------- 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 145 VAL 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 485 ILE Chi-restraints excluded: chain B residue 14 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 76 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 245 ILE 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 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 M residue 9 ASP Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS 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 276 THR 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 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 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 324 SER Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 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 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 449 GLN Chi-restraints excluded: chain E residue 470 TYR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 VAL 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 254 LEU 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 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 191 MET 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 475 GLU 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 83 THR Chi-restraints excluded: chain J residue 107 SER 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 345 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 163 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.083473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.068648 restraints weight = 141743.688| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.33 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31784 Z= 0.232 Angle : 0.670 10.351 43660 Z= 0.347 Chirality : 0.043 0.186 4764 Planarity : 0.005 0.058 5124 Dihedral : 16.000 168.889 5725 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.47 % Favored : 88.50 % Rotamer: Outliers : 5.30 % Allowed : 33.81 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.14), residues: 3425 helix: 0.88 (0.17), residues: 944 sheet: -1.42 (0.20), residues: 634 loop : -2.49 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 378 HIS 0.006 0.001 HIS B 242 PHE 0.021 0.002 PHE E 275 TYR 0.026 0.002 TYR E 398 ARG 0.007 0.000 ARG E 377 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 995) hydrogen bonds : angle 5.14828 ( 2691) covalent geometry : bond 0.00514 (31784) covalent geometry : angle 0.66977 (43660) *********************** 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 368 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 212 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: A 157 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7420 (mtt-85) REVERT: A 185 MET cc_start: 0.7965 (pmm) cc_final: 0.7416 (pmm) REVERT: A 255 GLU cc_start: 0.8400 (pt0) cc_final: 0.7961 (pt0) REVERT: A 306 TYR cc_start: 0.5777 (p90) cc_final: 0.5482 (p90) REVERT: A 397 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 403 MET cc_start: 0.8084 (mmt) cc_final: 0.7704 (mmm) REVERT: B 222 CYS cc_start: 0.8548 (m) cc_final: 0.8159 (p) REVERT: B 328 GLU cc_start: 0.7999 (tt0) cc_final: 0.7689 (tp30) REVERT: B 349 TYR cc_start: 0.7981 (m-80) cc_final: 0.7487 (m-80) REVERT: M 304 HIS cc_start: 0.8000 (m170) cc_final: 0.7772 (m170) REVERT: N 168 MET cc_start: 0.8172 (mmm) cc_final: 0.6698 (mmm) REVERT: N 296 LYS cc_start: 0.7631 (tppt) cc_final: 0.7307 (tppt) REVERT: N 334 TRP cc_start: 0.8241 (m100) cc_final: 0.7870 (m100) REVERT: E 195 PHE cc_start: 0.8591 (p90) cc_final: 0.8285 (p90) REVERT: E 307 MET cc_start: 0.7879 (mmm) cc_final: 0.7676 (mmm) REVERT: E 446 ASN cc_start: 0.6436 (OUTLIER) cc_final: 0.5929 (t0) REVERT: F 16 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6319 (pt0) REVERT: F 204 TRP cc_start: 0.6192 (p90) cc_final: 0.5915 (p90) REVERT: F 232 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8517 (tm-30) REVERT: F 253 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: F 306 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7834 (t80) REVERT: F 320 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6583 (m90) REVERT: F 414 ARG cc_start: 0.3915 (OUTLIER) cc_final: 0.2440 (ptp-170) REVERT: I 114 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6774 (mmtt) REVERT: I 216 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7482 (pttp) REVERT: J 211 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6996 (p90) REVERT: J 354 PHE cc_start: 0.8844 (m-80) cc_final: 0.8562 (m-80) outliers start: 156 outliers final: 124 residues processed: 346 average time/residue: 0.3850 time to fit residues: 220.8653 Evaluate side-chains 340 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 205 time to evaluate : 3.152 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 233 LEU 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 420 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 23 PHE 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 76 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LEU 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 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 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 67 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 209 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 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 78 THR Chi-restraints excluded: chain N residue 245 ILE 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 338 ILE Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 197 ILE 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 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 402 SER 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 470 TYR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 VAL 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 226 VAL 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 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 191 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 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 83 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 216 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 233 optimal weight: 0.0170 chunk 258 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.084795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.069990 restraints weight = 139711.592| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.35 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31784 Z= 0.146 Angle : 0.615 13.987 43660 Z= 0.317 Chirality : 0.041 0.286 4764 Planarity : 0.004 0.059 5124 Dihedral : 15.942 166.852 5725 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.40 % Favored : 90.57 % Rotamer: Outliers : 4.89 % Allowed : 34.22 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3425 helix: 0.95 (0.18), residues: 946 sheet: -1.32 (0.20), residues: 645 loop : -2.45 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 212 HIS 0.005 0.001 HIS F 106 PHE 0.016 0.001 PHE N 211 TYR 0.021 0.001 TYR E 398 ARG 0.005 0.000 ARG E 157 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 995) hydrogen bonds : angle 4.99133 ( 2691) covalent geometry : bond 0.00328 (31784) covalent geometry : angle 0.61512 (43660) *********************** 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 354 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 210 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: A 157 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7420 (mtt-85) REVERT: A 185 MET cc_start: 0.7871 (pmm) cc_final: 0.7363 (pmm) REVERT: A 255 GLU cc_start: 0.8379 (pt0) cc_final: 0.7960 (pt0) REVERT: A 306 TYR cc_start: 0.5754 (p90) cc_final: 0.5395 (p90) REVERT: A 403 MET cc_start: 0.8123 (mmt) cc_final: 0.7781 (mmm) REVERT: B 222 CYS cc_start: 0.8578 (m) cc_final: 0.8173 (p) REVERT: B 328 GLU cc_start: 0.7972 (tt0) cc_final: 0.7718 (tp30) REVERT: B 349 TYR cc_start: 0.7967 (m-80) cc_final: 0.7498 (m-80) REVERT: M 304 HIS cc_start: 0.7921 (m170) cc_final: 0.7711 (m170) REVERT: N 168 MET cc_start: 0.8137 (mmm) cc_final: 0.6701 (mmm) REVERT: N 296 LYS cc_start: 0.7611 (tppt) cc_final: 0.7209 (tppt) REVERT: N 334 TRP cc_start: 0.8212 (m100) cc_final: 0.7892 (m100) REVERT: E 183 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6585 (ttp80) REVERT: E 195 PHE cc_start: 0.8505 (p90) cc_final: 0.8208 (p90) REVERT: F 16 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6275 (pt0) REVERT: F 204 TRP cc_start: 0.6163 (p90) cc_final: 0.5834 (p90) REVERT: F 232 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8486 (tm-30) REVERT: F 306 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7871 (t80) REVERT: F 320 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6662 (m90) REVERT: F 414 ARG cc_start: 0.3738 (OUTLIER) cc_final: 0.2294 (ptp-170) REVERT: I 114 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6910 (mmtt) REVERT: I 216 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7427 (pttp) REVERT: J 211 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6971 (p90) REVERT: J 354 PHE cc_start: 0.8820 (m-80) cc_final: 0.8543 (m-80) outliers start: 144 outliers final: 119 residues processed: 334 average time/residue: 0.3737 time to fit residues: 207.3604 Evaluate side-chains 335 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 207 time to evaluate : 3.117 ------------------------------------------------------------------------------- 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 145 VAL Chi-restraints excluded: chain A residue 204 VAL 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 485 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 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 76 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 HIS 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 345 THR 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 67 VAL Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 105 THR 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 78 THR 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 324 SER 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 354 PHE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 197 ILE 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 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 398 TYR Chi-restraints excluded: chain E residue 402 SER 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 470 TYR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 46 VAL 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 194 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL 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 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 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 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 83 THR 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 211 PHE Chi-restraints excluded: chain J residue 297 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 194 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 236 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.085605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.070779 restraints weight = 140093.152| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.39 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31784 Z= 0.128 Angle : 0.602 13.550 43660 Z= 0.307 Chirality : 0.041 0.268 4764 Planarity : 0.004 0.058 5124 Dihedral : 15.861 168.150 5725 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.07 % Favored : 89.90 % Rotamer: Outliers : 4.45 % Allowed : 34.45 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3425 helix: 1.06 (0.18), residues: 943 sheet: -1.19 (0.20), residues: 646 loop : -2.39 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 212 HIS 0.005 0.001 HIS F 106 PHE 0.016 0.001 PHE N 211 TYR 0.018 0.001 TYR E 398 ARG 0.007 0.000 ARG E 229 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 995) hydrogen bonds : angle 4.87393 ( 2691) covalent geometry : bond 0.00288 (31784) covalent geometry : angle 0.60238 (43660) ********************** 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 352 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 221 time to evaluate : 3.468 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: 0.8697 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: A 157 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7490 (mtt-85) REVERT: A 185 MET cc_start: 0.7860 (pmm) cc_final: 0.7547 (pmm) REVERT: A 255 GLU cc_start: 0.8338 (pt0) cc_final: 0.8063 (pt0) REVERT: A 306 TYR cc_start: 0.5729 (p90) cc_final: 0.5300 (p90) REVERT: A 403 MET cc_start: 0.8119 (mmt) cc_final: 0.7843 (mmm) REVERT: B 222 CYS cc_start: 0.8559 (m) cc_final: 0.8167 (p) REVERT: B 270 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.5900 (m-30) REVERT: B 349 TYR cc_start: 0.7990 (m-80) cc_final: 0.7538 (m-80) REVERT: M 304 HIS cc_start: 0.7941 (m170) cc_final: 0.7734 (m170) REVERT: N 168 MET cc_start: 0.8030 (mmm) cc_final: 0.6837 (mmm) REVERT: N 296 LYS cc_start: 0.7640 (tppt) cc_final: 0.7355 (tppt) REVERT: N 334 TRP cc_start: 0.8169 (m100) cc_final: 0.7886 (m100) REVERT: E 195 PHE cc_start: 0.8463 (p90) cc_final: 0.8169 (p90) REVERT: F 187 ARG cc_start: 0.4991 (mmt180) cc_final: 0.3322 (mtt180) REVERT: F 232 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8525 (tm-30) REVERT: F 249 ASN cc_start: 0.5967 (OUTLIER) cc_final: 0.5650 (t0) REVERT: F 306 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7896 (t80) REVERT: F 320 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6587 (m90) REVERT: I 114 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6905 (mmtt) REVERT: I 216 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7457 (pttp) REVERT: J 211 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6841 (p90) REVERT: J 354 PHE cc_start: 0.8807 (m-80) cc_final: 0.8528 (m-80) REVERT: J 377 MET cc_start: 0.8599 (tmm) cc_final: 0.8380 (ttt) outliers start: 131 outliers final: 115 residues processed: 331 average time/residue: 0.3850 time to fit residues: 211.4343 Evaluate side-chains 339 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 216 time to evaluate : 3.231 ------------------------------------------------------------------------------- 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 145 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 233 LEU 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 485 ILE Chi-restraints excluded: chain B residue 14 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 76 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 245 ILE 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 298 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 345 THR 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 M residue 9 ASP Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 105 THR 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 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 78 THR 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 324 SER Chi-restraints excluded: chain N residue 338 ILE Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 354 PHE Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 183 ARG Chi-restraints excluded: chain E residue 197 ILE 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 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 398 TYR 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 470 TYR 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 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 194 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 249 ASN 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 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 191 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 252 LEU 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 20 ARG Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 83 THR 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 297 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 100 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3878 r_free = 0.3878 target = 0.086032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.071235 restraints weight = 139466.124| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.39 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31784 Z= 0.121 Angle : 0.598 13.269 43660 Z= 0.305 Chirality : 0.040 0.233 4764 Planarity : 0.004 0.059 5124 Dihedral : 15.809 169.741 5725 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.83 % Rotamer: Outliers : 4.32 % Allowed : 34.83 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3425 helix: 1.06 (0.18), residues: 945 sheet: -1.12 (0.20), residues: 647 loop : -2.35 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP F 204 HIS 0.006 0.001 HIS F 106 PHE 0.015 0.001 PHE N 211 TYR 0.017 0.001 TYR E 398 ARG 0.004 0.000 ARG E 183 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 995) hydrogen bonds : angle 4.83394 ( 2691) covalent geometry : bond 0.00272 (31784) covalent geometry : angle 0.59843 (43660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12829.77 seconds wall clock time: 224 minutes 20.16 seconds (13460.16 seconds total)