Starting phenix.real_space_refine on Thu Jun 26 11:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsz_61787/06_2025/9jsz_61787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsz_61787/06_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_61787/06_2025/9jsz_61787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsz_61787/06_2025/9jsz_61787.map" model { file = "/net/cci-nas-00/data/ceres_data/9jsz_61787/06_2025/9jsz_61787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsz_61787/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 22.31, per 1000 atoms: 0.73 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: 8.35 Conformation dependent library (CDL) restraints added in 3.8 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: 12.09 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: 12.29 Time building geometry restraints manager: 9.91 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: 7.320 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: 0.030 Extract box with map and model: 1.480 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 83.460 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.510 ------------------------------------------------------------------------------- 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 : 3.315 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: 0.4419 time to fit residues: 237.4744 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 : 4.536 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073656 restraints weight = 137749.543| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 4.42 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 : 8.840 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: 0.8281 (tp) REVERT: A 30 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: A 157 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7215 (mmt180) REVERT: A 306 TYR cc_start: 0.5758 (p90) cc_final: 0.5284 (p90) REVERT: B 13 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: B 133 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: B 184 TYR cc_start: 0.7614 (m-80) cc_final: 0.7380 (m-80) REVERT: B 194 LEU cc_start: 0.8783 (mt) cc_final: 0.8243 (pp) REVERT: M 356 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: N 334 TRP cc_start: 0.7906 (m100) cc_final: 0.7695 (m100) REVERT: E 185 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6494 (ppp) REVERT: E 195 PHE cc_start: 0.8481 (p90) cc_final: 0.8140 (p90) REVERT: F 62 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6308 (mmmt) REVERT: F 249 ASN cc_start: 0.5934 (OUTLIER) cc_final: 0.5674 (t0) REVERT: J 211 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7258 (p90) outliers start: 135 outliers final: 78 residues processed: 366 average time/residue: 0.5509 time to fit residues: 345.5386 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 : 4.292 ------------------------------------------------------------------------------- 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: 1.9990 chunk 110 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 292 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 78 HIS E 224 GLN J 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.087696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.072803 restraints weight = 138323.299| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 4.44 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31784 Z= 0.143 Angle : 0.573 8.956 43660 Z= 0.301 Chirality : 0.040 0.229 4764 Planarity : 0.004 0.065 5124 Dihedral : 15.977 164.344 5732 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 5.33 % Allowed : 32.31 % Favored : 62.35 % 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: -1.87 (0.14), residues: 3425 helix: 0.84 (0.18), residues: 927 sheet: -1.15 (0.20), residues: 657 loop : -2.50 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 212 HIS 0.006 0.001 HIS F 106 PHE 0.015 0.001 PHE N 211 TYR 0.018 0.001 TYR E 413 ARG 0.005 0.000 ARG M 453 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 995) hydrogen bonds : angle 5.05687 ( 2691) covalent geometry : bond 0.00316 (31784) covalent geometry : angle 0.57289 (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 391 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 234 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7252 (mmt180) REVERT: A 306 TYR cc_start: 0.5807 (p90) cc_final: 0.5492 (p90) REVERT: A 403 MET cc_start: 0.8144 (mmt) cc_final: 0.7748 (mmm) REVERT: B 20 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8448 (tpt170) REVERT: B 133 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: B 184 TYR cc_start: 0.7785 (m-80) cc_final: 0.7558 (m-80) REVERT: B 194 LEU cc_start: 0.8813 (mt) cc_final: 0.8261 (pp) REVERT: B 222 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8092 (p) REVERT: B 270 ASP cc_start: 0.5895 (OUTLIER) cc_final: 0.5354 (m-30) REVERT: M 153 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8353 (tppt) REVERT: N 334 TRP cc_start: 0.7980 (m100) cc_final: 0.7577 (m100) REVERT: E 195 PHE cc_start: 0.8546 (p90) cc_final: 0.8267 (p90) REVERT: F 249 ASN cc_start: 0.5953 (OUTLIER) cc_final: 0.5683 (t0) REVERT: F 320 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6560 (m90) REVERT: J 187 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5634 (mpt90) REVERT: J 211 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7297 (p90) outliers start: 157 outliers final: 99 residues processed: 363 average time/residue: 0.4216 time to fit residues: 257.4406 Evaluate side-chains 329 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 221 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 145 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 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 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 76 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 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 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 365 LEU Chi-restraints excluded: chain E residue 94 PHE 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 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 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain F residue 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 94 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 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 Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 317 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 333 GLN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 HIS I 21 HIS J 17 ASN J 215 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.084842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.069892 restraints weight = 140012.917| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.38 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31784 Z= 0.232 Angle : 0.645 9.599 43660 Z= 0.339 Chirality : 0.042 0.187 4764 Planarity : 0.005 0.061 5124 Dihedral : 16.054 165.571 5732 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.92 % Favored : 89.05 % Rotamer: Outliers : 6.08 % Allowed : 32.18 % Favored : 61.74 % 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: -1.95 (0.14), residues: 3425 helix: 0.84 (0.18), residues: 937 sheet: -1.31 (0.20), residues: 637 loop : -2.55 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 204 HIS 0.005 0.001 HIS F 106 PHE 0.017 0.002 PHE N 211 TYR 0.016 0.002 TYR E 413 ARG 0.006 0.001 ARG E 229 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 995) hydrogen bonds : angle 5.18424 ( 2691) covalent geometry : bond 0.00508 (31784) covalent geometry : angle 0.64513 (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 405 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 226 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: A 124 MET cc_start: 0.8042 (ptt) cc_final: 0.7482 (ptp) REVERT: A 157 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7138 (mtt-85) REVERT: A 255 GLU cc_start: 0.8342 (pt0) cc_final: 0.8098 (pt0) REVERT: A 306 TYR cc_start: 0.5826 (p90) cc_final: 0.5585 (p90) REVERT: A 397 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 403 MET cc_start: 0.8137 (mmt) cc_final: 0.7709 (mmm) REVERT: B 133 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 194 LEU cc_start: 0.8902 (mt) cc_final: 0.8346 (pp) REVERT: B 222 CYS cc_start: 0.8525 (m) cc_final: 0.8216 (p) REVERT: M 64 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8721 (p) REVERT: M 153 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8366 (tppt) REVERT: N 334 TRP cc_start: 0.8154 (m100) cc_final: 0.7627 (m100) REVERT: N 379 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8283 (m-70) REVERT: E 185 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6587 (ppp) REVERT: E 191 MET cc_start: 0.7755 (mpp) cc_final: 0.7466 (mpp) REVERT: E 195 PHE cc_start: 0.8647 (p90) cc_final: 0.8334 (p90) REVERT: F 47 MET cc_start: 0.7683 (tmm) cc_final: 0.7466 (tpp) REVERT: F 204 TRP cc_start: 0.6426 (p90) cc_final: 0.6048 (p90) REVERT: F 232 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8331 (tm-30) REVERT: F 249 ASN cc_start: 0.5748 (OUTLIER) cc_final: 0.5458 (t0) REVERT: F 253 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7095 (t-90) REVERT: F 261 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: F 306 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7780 (t80) REVERT: F 320 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.6682 (m90) REVERT: J 187 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5479 (mpt90) REVERT: J 211 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7164 (p90) outliers start: 179 outliers final: 112 residues processed: 378 average time/residue: 0.4180 time to fit residues: 261.9490 Evaluate side-chains 341 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 215 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 425 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 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 M residue 9 ASP Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 437 ILE Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 318 VAL Chi-restraints excluded: chain N residue 320 HIS 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 136 MET 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 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 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 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 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 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 130 ILE Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain I residue 444 ASN Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 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 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: 9.9990 chunk 105 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 301 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 HIS M 380 ASN M 416 ASN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 320 HIS J 215 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.082196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.067321 restraints weight = 142088.389| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.33 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 31784 Z= 0.324 Angle : 0.750 10.761 43660 Z= 0.393 Chirality : 0.046 0.224 4764 Planarity : 0.005 0.067 5124 Dihedral : 16.235 165.476 5731 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 7.41 % Allowed : 31.40 % 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: -2.28 (0.14), residues: 3425 helix: 0.53 (0.17), residues: 933 sheet: -1.64 (0.20), residues: 627 loop : -2.67 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 204 HIS 0.051 0.002 HIS J 215 PHE 0.028 0.002 PHE E 275 TYR 0.019 0.002 TYR A 266 ARG 0.007 0.001 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.05779 ( 995) hydrogen bonds : angle 5.52809 ( 2691) covalent geometry : bond 0.00708 (31784) covalent geometry : angle 0.74980 (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 429 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 211 time to evaluate : 3.646 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: 0.8639 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: A 124 MET cc_start: 0.8148 (ptt) cc_final: 0.7694 (ptp) REVERT: A 157 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7681 (mmt90) REVERT: A 255 GLU cc_start: 0.8436 (pt0) cc_final: 0.8205 (pt0) REVERT: A 281 MET cc_start: 0.8200 (pmm) cc_final: 0.7960 (pmm) REVERT: A 306 TYR cc_start: 0.5731 (p90) cc_final: 0.5509 (p90) REVERT: A 397 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 403 MET cc_start: 0.8155 (mmt) cc_final: 0.7745 (mmm) REVERT: B 222 CYS cc_start: 0.8560 (m) cc_final: 0.8172 (p) REVERT: B 283 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6863 (mtm-85) REVERT: M 64 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8935 (p) REVERT: M 153 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8408 (tppt) REVERT: N 246 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8600 (m-30) REVERT: N 296 LYS cc_start: 0.7228 (tppt) cc_final: 0.6931 (tppt) REVERT: N 334 TRP cc_start: 0.8242 (m100) cc_final: 0.7869 (m100) REVERT: N 378 TRP cc_start: 0.8652 (t60) cc_final: 0.8385 (t60) REVERT: E 185 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6693 (ppp) REVERT: E 191 MET cc_start: 0.7779 (mpp) cc_final: 0.7495 (mpp) REVERT: E 195 PHE cc_start: 0.8638 (p90) cc_final: 0.8317 (p90) REVERT: E 480 ASP cc_start: 0.8843 (p0) cc_final: 0.8335 (p0) REVERT: F 232 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8529 (tm-30) REVERT: F 253 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7132 (t-90) REVERT: F 306 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7821 (t80) REVERT: F 320 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6853 (m90) REVERT: F 414 ARG cc_start: 0.4132 (OUTLIER) cc_final: 0.2558 (ptp-170) REVERT: I 216 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7509 (pttp) REVERT: I 268 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: J 211 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.6982 (p90) REVERT: J 354 PHE cc_start: 0.8972 (m-80) cc_final: 0.8693 (m-80) outliers start: 218 outliers final: 146 residues processed: 399 average time/residue: 0.5293 time to fit residues: 360.5728 Evaluate side-chains 363 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 203 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 LYS 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 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 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 245 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 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 466 GLU 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 245 ILE Chi-restraints excluded: chain N residue 246 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 336 LEU Chi-restraints excluded: chain N residue 338 ILE Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 249 ARG Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 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 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 366 ASP 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 185 MET Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 268 GLU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 444 ASN 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 116 ASP Chi-restraints excluded: chain J residue 129 VAL 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 245 ILE Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 352 HIS Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 323 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 312 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** B 257 GLN M 20 HIS F 60 GLN F 253 HIS F 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.069090 restraints weight = 140725.827| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.35 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31784 Z= 0.172 Angle : 0.628 10.082 43660 Z= 0.328 Chirality : 0.042 0.185 4764 Planarity : 0.004 0.062 5124 Dihedral : 16.109 162.856 5727 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.45 % Favored : 89.52 % Rotamer: Outliers : 5.78 % Allowed : 33.13 % 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: 0.79 (0.17), residues: 937 sheet: -1.52 (0.20), residues: 654 loop : -2.59 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 204 HIS 0.007 0.001 HIS B 242 PHE 0.025 0.002 PHE E 59 TYR 0.029 0.001 TYR E 398 ARG 0.004 0.000 ARG M 297 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 995) hydrogen bonds : angle 5.20269 ( 2691) covalent geometry : bond 0.00383 (31784) covalent geometry : angle 0.62790 (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 388 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 218 time to evaluate : 4.510 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: 0.8687 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: A 124 MET cc_start: 0.8045 (ptt) cc_final: 0.7633 (ptp) REVERT: A 132 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8734 (tm-30) REVERT: A 249 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8406 (ptt-90) REVERT: A 255 GLU cc_start: 0.8399 (pt0) cc_final: 0.8173 (pt0) REVERT: A 281 MET cc_start: 0.8167 (pmm) cc_final: 0.7949 (pmm) REVERT: A 306 TYR cc_start: 0.5752 (p90) cc_final: 0.5448 (p90) REVERT: A 397 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8345 (tp) REVERT: A 403 MET cc_start: 0.8064 (mmt) cc_final: 0.7683 (mmm) REVERT: B 222 CYS cc_start: 0.8587 (m) cc_final: 0.8180 (p) REVERT: B 283 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6754 (mtm-85) REVERT: B 349 TYR cc_start: 0.7933 (m-80) cc_final: 0.7429 (m-80) REVERT: M 64 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.8882 (p) REVERT: M 153 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8337 (tppt) REVERT: M 304 HIS cc_start: 0.7975 (m170) cc_final: 0.7744 (m170) REVERT: N 168 MET cc_start: 0.8144 (mmm) cc_final: 0.6568 (mmm) REVERT: N 169 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7833 (tt) REVERT: N 246 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8563 (m-30) REVERT: N 296 LYS cc_start: 0.7348 (tppt) cc_final: 0.7104 (tppt) REVERT: N 334 TRP cc_start: 0.8175 (m100) cc_final: 0.7834 (m100) REVERT: N 379 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7623 (t-90) REVERT: E 185 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6810 (ppp) REVERT: E 195 PHE cc_start: 0.8507 (p90) cc_final: 0.8208 (p90) REVERT: E 284 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7465 (tm-30) REVERT: E 470 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.7038 (p90) REVERT: F 204 TRP cc_start: 0.6268 (p90) cc_final: 0.5780 (p90) REVERT: F 232 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8503 (tm-30) REVERT: F 253 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7330 (t70) REVERT: F 306 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7883 (t80) REVERT: F 307 LYS cc_start: 0.7829 (tppt) cc_final: 0.7615 (tppt) REVERT: F 414 ARG cc_start: 0.3899 (OUTLIER) cc_final: 0.2412 (ptp-170) REVERT: I 114 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6748 (mmtt) REVERT: I 216 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7485 (pttp) REVERT: J 211 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6998 (p90) REVERT: J 354 PHE cc_start: 0.8875 (m-80) cc_final: 0.8579 (m-80) outliers start: 170 outliers final: 123 residues processed: 363 average time/residue: 0.5069 time to fit residues: 310.9510 Evaluate side-chains 348 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 208 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 LYS 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 249 ARG 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 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 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 283 ARG 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 382 LEU Chi-restraints excluded: chain B residue 408 SER 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 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 346 GLU Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 425 THR Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 169 LEU 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 320 HIS 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 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 376 LEU 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 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 253 HIS Chi-restraints excluded: chain F residue 254 LEU 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 336 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 412 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain I residue 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 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 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 171 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 212 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 293 SER 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 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 294 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 242 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** F 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.084924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.070071 restraints weight = 139481.330| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.36 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2527 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= 0.139 Angle : 0.596 9.151 43660 Z= 0.310 Chirality : 0.041 0.165 4764 Planarity : 0.004 0.066 5124 Dihedral : 16.004 163.237 5727 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.16 % Favored : 89.81 % Rotamer: Outliers : 5.16 % Allowed : 33.50 % Favored : 61.33 % 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: -1.87 (0.14), residues: 3425 helix: 0.96 (0.18), residues: 938 sheet: -1.38 (0.20), residues: 654 loop : -2.49 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 204 HIS 0.020 0.001 HIS F 253 PHE 0.018 0.001 PHE E 275 TYR 0.030 0.001 TYR E 398 ARG 0.004 0.000 ARG E 183 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 995) hydrogen bonds : angle 5.02320 ( 2691) covalent geometry : bond 0.00310 (31784) covalent geometry : angle 0.59573 (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 376 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 224 time to evaluate : 3.134 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: 0.8691 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: A 124 MET cc_start: 0.7915 (ptt) cc_final: 0.7537 (ptp) REVERT: A 185 MET cc_start: 0.7961 (pmm) cc_final: 0.7316 (pmm) REVERT: A 255 GLU cc_start: 0.8383 (pt0) cc_final: 0.8112 (pt0) REVERT: A 306 TYR cc_start: 0.5754 (p90) cc_final: 0.5488 (p90) REVERT: A 397 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8347 (tp) REVERT: A 403 MET cc_start: 0.8080 (mmt) cc_final: 0.7732 (mmm) REVERT: B 222 CYS cc_start: 0.8569 (m) cc_final: 0.8160 (p) REVERT: B 270 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.5971 (m-30) REVERT: B 283 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6607 (mtm-85) REVERT: B 349 TYR cc_start: 0.7975 (m-80) cc_final: 0.7515 (m-80) REVERT: M 64 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8764 (p) REVERT: M 153 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8302 (tppt) REVERT: M 304 HIS cc_start: 0.7937 (m170) cc_final: 0.7713 (m170) REVERT: N 168 MET cc_start: 0.8116 (mmm) cc_final: 0.6629 (mmm) REVERT: N 296 LYS cc_start: 0.7377 (tppt) cc_final: 0.7059 (tppt) REVERT: N 334 TRP cc_start: 0.8182 (m100) cc_final: 0.7860 (m100) REVERT: E 195 PHE cc_start: 0.8480 (p90) cc_final: 0.8144 (p90) REVERT: E 284 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7352 (tm-30) REVERT: E 475 GLU cc_start: 0.8186 (tt0) cc_final: 0.7721 (tt0) REVERT: F 16 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6284 (pt0) REVERT: F 204 TRP cc_start: 0.6094 (p90) cc_final: 0.5801 (p90) REVERT: F 232 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8471 (tm-30) REVERT: F 249 ASN cc_start: 0.5648 (OUTLIER) cc_final: 0.5314 (t0) REVERT: F 306 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7869 (t80) REVERT: F 414 ARG cc_start: 0.3922 (OUTLIER) cc_final: 0.2422 (ptp-170) REVERT: I 114 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6775 (mmtt) REVERT: I 216 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7445 (pttp) REVERT: J 211 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6869 (p90) REVERT: J 354 PHE cc_start: 0.8839 (m-80) cc_final: 0.8568 (m-80) outliers start: 152 outliers final: 114 residues processed: 355 average time/residue: 0.3848 time to fit residues: 227.0046 Evaluate side-chains 335 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 208 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 283 ARG 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 64 SER 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 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 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 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 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 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 420 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE 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 207 ASN Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 254 LEU 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 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 137 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 372 THR 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 96 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 212 TRP Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 297 LYS Chi-restraints excluded: chain J residue 329 LEU 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: 0.9990 chunk 253 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3844 r_free = 0.3844 target = 0.084274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.069470 restraints weight = 140554.042| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.35 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31784 Z= 0.172 Angle : 0.620 9.119 43660 Z= 0.321 Chirality : 0.041 0.170 4764 Planarity : 0.004 0.063 5124 Dihedral : 15.969 166.096 5727 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.80 % Favored : 89.17 % Rotamer: Outliers : 5.33 % Allowed : 33.57 % 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: -1.87 (0.14), residues: 3425 helix: 0.95 (0.18), residues: 939 sheet: -1.38 (0.20), residues: 654 loop : -2.49 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 378 HIS 0.009 0.001 HIS N 273 PHE 0.019 0.001 PHE E 275 TYR 0.026 0.001 TYR E 398 ARG 0.007 0.000 ARG E 377 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 995) hydrogen bonds : angle 5.02619 ( 2691) covalent geometry : bond 0.00384 (31784) covalent geometry : angle 0.61975 (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 364 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 207 time to evaluate : 3.491 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: 0.8695 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: A 124 MET cc_start: 0.7969 (ptt) cc_final: 0.7538 (ptp) REVERT: A 185 MET cc_start: 0.7925 (pmm) cc_final: 0.7317 (pmm) REVERT: A 255 GLU cc_start: 0.8387 (pt0) cc_final: 0.7972 (pt0) REVERT: A 306 TYR cc_start: 0.5727 (p90) cc_final: 0.5465 (p90) REVERT: A 397 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 403 MET cc_start: 0.8105 (mmt) cc_final: 0.7758 (mmm) REVERT: B 222 CYS cc_start: 0.8603 (m) cc_final: 0.8204 (p) REVERT: B 270 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6066 (m-30) REVERT: B 283 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6619 (mtm-85) REVERT: B 349 TYR cc_start: 0.7965 (m-80) cc_final: 0.7451 (m-80) REVERT: M 64 SER cc_start: 0.9293 (OUTLIER) cc_final: 0.8764 (p) REVERT: M 153 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8332 (tppt) REVERT: M 304 HIS cc_start: 0.7955 (m170) cc_final: 0.7740 (m170) REVERT: N 168 MET cc_start: 0.8148 (mmm) cc_final: 0.6736 (mmm) REVERT: N 296 LYS cc_start: 0.7401 (tppt) cc_final: 0.7072 (tppt) REVERT: N 334 TRP cc_start: 0.8189 (m100) cc_final: 0.7860 (m100) REVERT: E 195 PHE cc_start: 0.8533 (p90) cc_final: 0.8230 (p90) REVERT: E 284 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7356 (tm-30) REVERT: E 475 GLU cc_start: 0.8270 (tt0) cc_final: 0.7899 (tt0) REVERT: F 16 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6249 (pt0) REVERT: F 204 TRP cc_start: 0.6159 (p90) cc_final: 0.5741 (p90) REVERT: F 249 ASN cc_start: 0.5713 (OUTLIER) cc_final: 0.5378 (t0) REVERT: F 306 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7914 (t80) REVERT: I 114 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6867 (mmtt) REVERT: I 216 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7474 (pttp) REVERT: J 211 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6891 (p90) REVERT: J 354 PHE cc_start: 0.8817 (m-80) cc_final: 0.8543 (m-80) outliers start: 157 outliers final: 125 residues processed: 346 average time/residue: 0.4343 time to fit residues: 252.2977 Evaluate side-chains 339 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 202 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 VAL 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 47 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR 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 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 283 ARG 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 408 SER 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 95 GLU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 372 THR Chi-restraints excluded: chain M residue 419 LEU Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 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 354 PHE Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 136 MET 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 376 LEU Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE 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 207 ASN Chi-restraints excluded: chain F residue 215 HIS Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 306 PHE Chi-restraints excluded: chain F residue 317 PHE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 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 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 216 LYS Chi-restraints excluded: chain I residue 225 ASP 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 11 ILE 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 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 293 SER 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: 4.9990 chunk 225 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 206 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 273 HIS ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.083175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.068377 restraints weight = 141032.332| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.32 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31784 Z= 0.221 Angle : 0.665 13.765 43660 Z= 0.344 Chirality : 0.042 0.176 4764 Planarity : 0.005 0.062 5124 Dihedral : 16.047 168.151 5727 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.47 % Favored : 88.50 % Rotamer: Outliers : 5.50 % Allowed : 33.64 % 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: -1.97 (0.14), residues: 3425 helix: 0.88 (0.17), residues: 938 sheet: -1.51 (0.20), residues: 643 loop : -2.52 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 204 HIS 0.009 0.001 HIS N 273 PHE 0.022 0.002 PHE E 275 TYR 0.024 0.002 TYR E 398 ARG 0.005 0.000 ARG E 374 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 995) hydrogen bonds : angle 5.14708 ( 2691) covalent geometry : bond 0.00488 (31784) covalent geometry : angle 0.66503 (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 366 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 204 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: A 124 MET cc_start: 0.8033 (ptt) cc_final: 0.7633 (ptp) REVERT: A 185 MET cc_start: 0.7937 (pmm) cc_final: 0.7393 (pmm) REVERT: A 249 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8425 (ptt-90) REVERT: A 255 GLU cc_start: 0.8403 (pt0) cc_final: 0.7988 (pt0) REVERT: A 306 TYR cc_start: 0.5686 (p90) cc_final: 0.5387 (p90) REVERT: A 397 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 403 MET cc_start: 0.8097 (mmt) cc_final: 0.7756 (mmm) REVERT: B 222 CYS cc_start: 0.8627 (m) cc_final: 0.8224 (p) REVERT: B 283 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6668 (mtm-85) REVERT: B 349 TYR cc_start: 0.8028 (m-80) cc_final: 0.7439 (m-80) REVERT: M 64 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8802 (p) REVERT: M 153 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8366 (tppt) REVERT: M 304 HIS cc_start: 0.8017 (m170) cc_final: 0.7801 (m170) REVERT: N 168 MET cc_start: 0.8136 (mmm) cc_final: 0.6737 (mmm) REVERT: N 296 LYS cc_start: 0.7441 (tppt) cc_final: 0.7106 (tppt) REVERT: N 334 TRP cc_start: 0.8240 (m100) cc_final: 0.7854 (m100) REVERT: N 379 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.7726 (t-90) REVERT: E 108 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7484 (ptpp) REVERT: E 195 PHE cc_start: 0.8595 (p90) cc_final: 0.8282 (p90) REVERT: E 284 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7272 (tm-30) REVERT: E 475 GLU cc_start: 0.8265 (tt0) cc_final: 0.7759 (tt0) REVERT: F 16 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6317 (pt0) REVERT: F 204 TRP cc_start: 0.6107 (p90) cc_final: 0.5750 (p90) REVERT: F 249 ASN cc_start: 0.5516 (OUTLIER) cc_final: 0.5166 (t0) REVERT: F 306 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7884 (t80) REVERT: F 414 ARG cc_start: 0.4034 (OUTLIER) cc_final: 0.2555 (ptp-170) REVERT: I 114 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6837 (mmtt) REVERT: I 216 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7465 (pttp) REVERT: J 211 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.6935 (p90) REVERT: J 354 PHE cc_start: 0.8895 (m-80) cc_final: 0.8609 (m-80) outliers start: 162 outliers final: 131 residues processed: 346 average time/residue: 0.3853 time to fit residues: 220.6816 Evaluate side-chains 345 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 199 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 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 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 283 ARG 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 408 SER 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 95 GLU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 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 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 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 379 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 133 LEU 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 277 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 477 ILE 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 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 254 LEU 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 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 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 216 LYS Chi-restraints excluded: chain I residue 225 ASP 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 11 ILE 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 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 211 PHE Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain J residue 293 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 194 optimal weight: 0.8980 chunk 336 optimal weight: 20.0000 chunk 236 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 153 optimal weight: 0.3980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 416 ASN N 257 GLN F 17 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.085328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070551 restraints weight = 140800.566| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.38 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31784 Z= 0.123 Angle : 0.600 13.307 43660 Z= 0.307 Chirality : 0.040 0.153 4764 Planarity : 0.004 0.059 5124 Dihedral : 15.924 166.207 5727 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.46 % Favored : 90.51 % Rotamer: Outliers : 4.32 % Allowed : 34.49 % 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: -1.80 (0.14), residues: 3425 helix: 1.02 (0.18), residues: 941 sheet: -1.32 (0.20), residues: 657 loop : -2.45 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 204 HIS 0.007 0.001 HIS N 273 PHE 0.016 0.001 PHE E 275 TYR 0.018 0.001 TYR E 398 ARG 0.005 0.000 ARG E 183 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 995) hydrogen bonds : angle 4.90103 ( 2691) covalent geometry : bond 0.00278 (31784) covalent geometry : angle 0.59955 (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 340 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 213 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 30 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: A 124 MET cc_start: 0.7934 (ptt) cc_final: 0.7536 (ptp) REVERT: A 157 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7383 (mtt-85) REVERT: A 185 MET cc_start: 0.7838 (pmm) cc_final: 0.7416 (pmm) REVERT: A 255 GLU cc_start: 0.8360 (pt0) cc_final: 0.8078 (pt0) REVERT: A 403 MET cc_start: 0.8102 (mmt) cc_final: 0.7836 (mmm) REVERT: B 222 CYS cc_start: 0.8630 (m) cc_final: 0.8223 (p) REVERT: B 270 ASP cc_start: 0.6490 (OUTLIER) cc_final: 0.6021 (m-30) REVERT: B 283 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6512 (mtm-85) REVERT: B 349 TYR cc_start: 0.7995 (m-80) cc_final: 0.7437 (m-80) REVERT: M 153 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8299 (tppt) REVERT: N 168 MET cc_start: 0.8112 (mmm) cc_final: 0.6763 (mmm) REVERT: N 296 LYS cc_start: 0.7477 (tppt) cc_final: 0.7152 (tppt) REVERT: N 334 TRP cc_start: 0.8169 (m100) cc_final: 0.7861 (m100) REVERT: N 377 MET cc_start: 0.8560 (ppp) cc_final: 0.8275 (ppp) REVERT: N 379 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.7633 (t-90) REVERT: E 195 PHE cc_start: 0.8481 (p90) cc_final: 0.8185 (p90) REVERT: E 284 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 475 GLU cc_start: 0.8262 (tt0) cc_final: 0.7947 (tt0) REVERT: F 187 ARG cc_start: 0.4997 (mmt180) cc_final: 0.3148 (mtt180) REVERT: F 204 TRP cc_start: 0.6016 (p90) cc_final: 0.5684 (p90) REVERT: F 232 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 249 ASN cc_start: 0.5698 (OUTLIER) cc_final: 0.5338 (t0) REVERT: F 306 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7947 (t80) REVERT: F 307 LYS cc_start: 0.7514 (tppt) cc_final: 0.7245 (tppt) REVERT: J 211 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6907 (p90) REVERT: J 354 PHE cc_start: 0.8838 (m-80) cc_final: 0.8563 (m-80) outliers start: 127 outliers final: 107 residues processed: 325 average time/residue: 0.3993 time to fit residues: 216.8073 Evaluate side-chains 327 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 211 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU 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 145 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 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 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 283 ARG 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 153 LYS Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 291 LEU Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 346 GLU Chi-restraints excluded: chain M residue 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 476 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 276 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 379 HIS 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 290 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 425 THR 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 113 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 254 LEU 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 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 118 HIS 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 372 THR 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 56 MET Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 96 VAL 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 211 PHE Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 352 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 83 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 chunk 308 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.085340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.070577 restraints weight = 140190.089| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.36 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.161 31784 Z= 0.141 Angle : 0.699 59.200 43660 Z= 0.380 Chirality : 0.040 0.167 4764 Planarity : 0.004 0.058 5124 Dihedral : 15.922 166.231 5727 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.61 % Favored : 90.36 % Rotamer: Outliers : 4.18 % Allowed : 34.52 % Favored : 61.30 % 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: -1.80 (0.14), residues: 3425 helix: 1.01 (0.18), residues: 941 sheet: -1.29 (0.20), residues: 657 loop : -2.46 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 204 HIS 0.006 0.001 HIS F 106 PHE 0.016 0.001 PHE E 275 TYR 0.016 0.001 TYR E 413 ARG 0.005 0.000 ARG E 249 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 995) hydrogen bonds : angle 4.89832 ( 2691) covalent geometry : bond 0.00308 (31784) covalent geometry : angle 0.69894 (43660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15149.49 seconds wall clock time: 275 minutes 3.80 seconds (16503.80 seconds total)