Starting phenix.real_space_refine on Wed Feb 14 08:26:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4o_30080/02_2024/6m4o_30080_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4o_30080/02_2024/6m4o_30080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4o_30080/02_2024/6m4o_30080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4o_30080/02_2024/6m4o_30080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4o_30080/02_2024/6m4o_30080_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4o_30080/02_2024/6m4o_30080_updated.pdb" } resolution = 3.4 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 50 5.16 5 C 5746 2.51 5 N 1507 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ARG 116": "NH1" <-> "NH2" Residue "S ARG 151": "NH1" <-> "NH2" Residue "S ARG 181": "NH1" <-> "NH2" Residue "S ARG 189": "NH1" <-> "NH2" Residue "S ARG 236": "NH1" <-> "NH2" Residue "S ARG 239": "NH1" <-> "NH2" Residue "S ARG 270": "NH1" <-> "NH2" Residue "S ARG 287": "NH1" <-> "NH2" Residue "S ARG 321": "NH1" <-> "NH2" Residue "S ARG 329": "NH1" <-> "NH2" Residue "S ARG 405": "NH1" <-> "NH2" Residue "S ARG 422": "NH1" <-> "NH2" Residue "S ARG 459": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 129": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "T TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 225": "NH1" <-> "NH2" Residue "T ARG 271": "NH1" <-> "NH2" Residue "T ARG 278": "NH1" <-> "NH2" Residue "T ARG 302": "NH1" <-> "NH2" Residue "T ARG 326": "NH1" <-> "NH2" Residue "T TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 447": "NH1" <-> "NH2" Residue "T ARG 450": "NH1" <-> "NH2" Residue "T ARG 451": "NH1" <-> "NH2" Residue "T ARG 489": "NH1" <-> "NH2" Residue "T ARG 507": "NH1" <-> "NH2" Residue "T ARG 509": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3258 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 398} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3887 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "E" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 240 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "T" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C2 PLP T 601 " occ=0.80 ... (13 atoms not shown) pdb=" P PLP T 601 " occ=0.80 Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8918 At special positions: 0 Unit cell: (90.234, 83.55, 119.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 1 15.00 O 1614 8.00 N 1507 7.00 C 5746 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 36.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'S' and resid 57 through 60 No H-bonds generated for 'chain 'S' and resid 57 through 60' Processing helix chain 'S' and resid 115 through 122 Processing helix chain 'S' and resid 125 through 128 No H-bonds generated for 'chain 'S' and resid 125 through 128' Processing helix chain 'S' and resid 144 through 155 removed outlier: 3.999A pdb=" N GLU S 149 " --> pdb=" O HIS S 145 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS S 154 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 170 No H-bonds generated for 'chain 'S' and resid 168 through 170' Processing helix chain 'S' and resid 193 through 201 removed outlier: 3.770A pdb=" N GLY S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN S 200 " --> pdb=" O GLN S 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 228 removed outlier: 3.591A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU S 227 " --> pdb=" O GLU S 223 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 236 No H-bonds generated for 'chain 'S' and resid 234 through 236' Processing helix chain 'S' and resid 258 through 267 removed outlier: 3.567A pdb=" N LYS S 262 " --> pdb=" O PRO S 258 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU S 263 " --> pdb=" O GLU S 259 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR S 265 " --> pdb=" O VAL S 261 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS S 266 " --> pdb=" O LYS S 262 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR S 267 " --> pdb=" O LEU S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 289 through 292 No H-bonds generated for 'chain 'S' and resid 289 through 292' Processing helix chain 'S' and resid 297 through 299 No H-bonds generated for 'chain 'S' and resid 297 through 299' Processing helix chain 'S' and resid 322 through 328 removed outlier: 3.935A pdb=" N ASP S 326 " --> pdb=" O SER S 322 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS S 327 " --> pdb=" O PHE S 323 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 322 through 328' Processing helix chain 'S' and resid 343 through 358 Processing helix chain 'S' and resid 362 through 373 removed outlier: 3.787A pdb=" N LYS S 367 " --> pdb=" O PHE S 363 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS S 369 " --> pdb=" O VAL S 365 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN S 372 " --> pdb=" O GLU S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 422 removed outlier: 3.588A pdb=" N GLU S 414 " --> pdb=" O ARG S 410 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL S 416 " --> pdb=" O LEU S 412 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN S 421 " --> pdb=" O ASP S 417 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG S 422 " --> pdb=" O GLN S 418 " (cutoff:3.500A) Processing helix chain 'S' and resid 454 through 456 No H-bonds generated for 'chain 'S' and resid 454 through 456' Processing helix chain 'S' and resid 458 through 469 removed outlier: 3.505A pdb=" N ILE S 464 " --> pdb=" O ALA S 460 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 467 " --> pdb=" O THR S 463 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA S 468 " --> pdb=" O ILE S 464 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN S 469 " --> pdb=" O LYS S 465 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 90 removed outlier: 3.615A pdb=" N LEU T 73 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL T 76 " --> pdb=" O VAL T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 120 No H-bonds generated for 'chain 'T' and resid 118 through 120' Processing helix chain 'T' and resid 122 through 125 No H-bonds generated for 'chain 'T' and resid 122 through 125' Processing helix chain 'T' and resid 190 through 196 removed outlier: 3.747A pdb=" N LYS T 194 " --> pdb=" O GLU T 190 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL T 195 " --> pdb=" O ALA T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 227 removed outlier: 3.568A pdb=" N ALA T 224 " --> pdb=" O GLU T 220 " (cutoff:3.500A) Processing helix chain 'T' and resid 239 through 242 No H-bonds generated for 'chain 'T' and resid 239 through 242' Processing helix chain 'T' and resid 246 through 249 No H-bonds generated for 'chain 'T' and resid 246 through 249' Processing helix chain 'T' and resid 264 through 272 removed outlier: 3.567A pdb=" N ALA T 270 " --> pdb=" O LEU T 266 " (cutoff:3.500A) Processing helix chain 'T' and resid 285 through 296 removed outlier: 3.580A pdb=" N LEU T 291 " --> pdb=" O SER T 287 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE T 296 " --> pdb=" O LEU T 292 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 334 removed outlier: 4.450A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 398 removed outlier: 3.855A pdb=" N TYR T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 427 removed outlier: 3.698A pdb=" N GLU T 417 " --> pdb=" O PRO T 413 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS T 425 " --> pdb=" O THR T 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE T 426 " --> pdb=" O SER T 422 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET T 427 " --> pdb=" O MET T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 439 through 455 removed outlier: 3.676A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG T 450 " --> pdb=" O THR T 446 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG T 451 " --> pdb=" O ARG T 447 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 488 removed outlier: 3.843A pdb=" N GLY T 480 " --> pdb=" O PRO T 476 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 534 removed outlier: 3.619A pdb=" N ALA T 524 " --> pdb=" O ILE T 520 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL T 531 " --> pdb=" O GLU T 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 38 removed outlier: 3.514A pdb=" N LEU A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 51 through 62 removed outlier: 3.613A pdb=" N HIS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.673A pdb=" N GLY A 92 " --> pdb=" O MET A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.862A pdb=" N ILE A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR A 105 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.880A pdb=" N LEU A 109 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 111 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 113 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR A 116 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A 117 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 118 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 removed outlier: 3.676A pdb=" N VAL A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'E' and resid 8 through 25 removed outlier: 3.583A pdb=" N MET E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE E 16 " --> pdb=" O GLN E 12 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N THR E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 45 removed outlier: 3.692A pdb=" N ILE E 44 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 3.503A pdb=" N GLY E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 39 removed outlier: 3.597A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= B, first strand: chain 'S' and resid 160 through 164 removed outlier: 3.512A pdb=" N ILE S 162 " --> pdb=" O CYS S 318 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS S 318 " --> pdb=" O ILE S 162 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 205 through 208 removed outlier: 3.576A pdb=" N VAL S 185 " --> pdb=" O ASP S 205 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL S 187 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE S 241 " --> pdb=" O PHE S 186 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL S 244 " --> pdb=" O PHE S 272 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 231 through 235 removed outlier: 3.588A pdb=" N GLY T 386 " --> pdb=" O TYR T 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY T 389 " --> pdb=" O MET T 373 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL T 372 " --> pdb=" O LEU T 341 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU T 255 " --> pdb=" O LEU T 311 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU T 313 " --> pdb=" O LEU T 255 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU T 257 " --> pdb=" O LEU T 313 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR T 276 " --> pdb=" O ILE T 256 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER T 258 " --> pdb=" O THR T 276 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG T 278 " --> pdb=" O SER T 258 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 468 through 471 193 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2619 1.33 - 1.45: 1432 1.45 - 1.57: 4977 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 9112 Sorted by residual: bond pdb=" CA LEU T 261 " pdb=" CB LEU T 261 " ideal model delta sigma weight residual 1.527 1.589 -0.062 1.75e-02 3.27e+03 1.27e+01 bond pdb=" CG1 ILE S 162 " pdb=" CD1 ILE S 162 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.26e+00 bond pdb=" N SER T 540 " pdb=" CA SER T 540 " ideal model delta sigma weight residual 1.453 1.475 -0.022 1.31e-02 5.83e+03 2.70e+00 bond pdb=" C GLU E 30 " pdb=" N PRO E 31 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.65e+00 bond pdb=" CA ILE T 246 " pdb=" C ILE T 246 " ideal model delta sigma weight residual 1.520 1.533 -0.013 8.80e-03 1.29e+04 2.33e+00 ... (remaining 9107 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.33: 187 105.33 - 112.53: 4484 112.53 - 119.74: 3327 119.74 - 126.94: 4219 126.94 - 134.14: 111 Bond angle restraints: 12328 Sorted by residual: angle pdb=" C TYR A 116 " pdb=" N THR A 117 " pdb=" CA THR A 117 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C THR S 453 " pdb=" N GLU S 454 " pdb=" CA GLU S 454 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N VAL S 73 " pdb=" CA VAL S 73 " pdb=" C VAL S 73 " ideal model delta sigma weight residual 108.88 118.22 -9.34 2.16e+00 2.14e-01 1.87e+01 angle pdb=" C LYS T 109 " pdb=" N ASP T 110 " pdb=" CA ASP T 110 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA ARG S 239 " pdb=" CB ARG S 239 " pdb=" CG ARG S 239 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 ... (remaining 12323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 5039 15.46 - 30.92: 309 30.92 - 46.38: 85 46.38 - 61.85: 6 61.85 - 77.31: 8 Dihedral angle restraints: 5447 sinusoidal: 2189 harmonic: 3258 Sorted by residual: dihedral pdb=" CA VAL T 48 " pdb=" C VAL T 48 " pdb=" N THR T 49 " pdb=" CA THR T 49 " ideal model delta harmonic sigma weight residual -180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA VAL S 281 " pdb=" C VAL S 281 " pdb=" N LEU S 282 " pdb=" CA LEU S 282 " ideal model delta harmonic sigma weight residual 180.00 148.93 31.07 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA PHE S 394 " pdb=" C PHE S 394 " pdb=" N HIS S 395 " pdb=" CA HIS S 395 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 930 0.057 - 0.113: 355 0.113 - 0.170: 81 0.170 - 0.226: 10 0.226 - 0.283: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE T 459 " pdb=" CA ILE T 459 " pdb=" CG1 ILE T 459 " pdb=" CG2 ILE T 459 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE T 171 " pdb=" CA ILE T 171 " pdb=" CG1 ILE T 171 " pdb=" CG2 ILE T 171 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL S 237 " pdb=" CA VAL S 237 " pdb=" CG1 VAL S 237 " pdb=" CG2 VAL S 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1377 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR T 501 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO T 502 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO T 502 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO T 502 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER T 402 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C SER T 402 " 0.044 2.00e-02 2.50e+03 pdb=" O SER T 402 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS T 403 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR T 103 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C THR T 103 " -0.041 2.00e-02 2.50e+03 pdb=" O THR T 103 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU T 104 " 0.014 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1016 2.74 - 3.28: 8249 3.28 - 3.82: 14235 3.82 - 4.36: 17265 4.36 - 4.90: 29553 Nonbonded interactions: 70318 Sorted by model distance: nonbonded pdb=" OD2 ASP S 188 " pdb=" OH TYR S 248 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR S 178 " pdb=" O VAL S 324 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR S 427 " pdb=" OE1 GLU T 209 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR A 110 " pdb=" OG1 THR A 128 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR T 448 " pdb=" OD1 ASP T 522 " model vdw 2.323 2.440 ... (remaining 70313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 7.320 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.410 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.007 0.073 9112 Z= 0.489 Angle : 1.144 12.740 12328 Z= 0.613 Chirality : 0.062 0.283 1380 Planarity : 0.008 0.077 1562 Dihedral : 11.527 77.308 3361 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.41 % Favored : 88.41 % Rotamer: Outliers : 1.15 % Allowed : 7.23 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.81 (0.17), residues: 1113 helix: -4.55 (0.10), residues: 459 sheet: -3.66 (0.42), residues: 101 loop : -3.22 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP T 134 HIS 0.010 0.002 HIS T 347 PHE 0.030 0.003 PHE S 209 TYR 0.034 0.003 TYR S 166 ARG 0.011 0.002 ARG S 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 268 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: S 95 VAL cc_start: 0.9104 (t) cc_final: 0.8815 (p) REVERT: S 107 ASN cc_start: 0.8117 (p0) cc_final: 0.7890 (p0) REVERT: S 146 LEU cc_start: 0.8843 (mm) cc_final: 0.8335 (mm) REVERT: S 345 LEU cc_start: 0.8823 (mm) cc_final: 0.8433 (mt) REVERT: T 82 THR cc_start: 0.9049 (t) cc_final: 0.8631 (p) REVERT: T 86 TYR cc_start: 0.8506 (m-80) cc_final: 0.7581 (m-80) REVERT: T 155 ASP cc_start: 0.7079 (t0) cc_final: 0.6842 (t70) REVERT: T 177 ASN cc_start: 0.8167 (t0) cc_final: 0.7582 (t0) REVERT: T 304 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7012 (ttp-170) REVERT: T 537 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 116 TYR cc_start: 0.7117 (m-80) cc_final: 0.6867 (m-80) REVERT: E 13 MET cc_start: 0.8130 (tpt) cc_final: 0.7665 (tpt) outliers start: 11 outliers final: 2 residues processed: 275 average time/residue: 0.2589 time to fit residues: 93.0115 Evaluate side-chains 142 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 537 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 81 ASN S 114 ASN S 231 ASN S 428 GLN T 47 HIS T 116 GLN T 212 ASN T 216 HIS T 242 ASN T 284 ASN T 490 ASN T 516 HIS T 536 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9112 Z= 0.266 Angle : 0.703 8.989 12328 Z= 0.360 Chirality : 0.047 0.226 1380 Planarity : 0.006 0.085 1562 Dihedral : 6.686 52.388 1238 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 4.08 % Allowed : 12.98 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.45 (0.20), residues: 1113 helix: -3.00 (0.18), residues: 458 sheet: -3.25 (0.44), residues: 106 loop : -2.80 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 134 HIS 0.006 0.001 HIS S 395 PHE 0.019 0.002 PHE T 449 TYR 0.018 0.002 TYR S 166 ARG 0.007 0.001 ARG S 422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8028 (p0) cc_final: 0.7781 (p0) REVERT: S 114 ASN cc_start: 0.8070 (t0) cc_final: 0.7863 (t0) REVERT: S 428 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8124 (tm130) REVERT: T 86 TYR cc_start: 0.8582 (m-80) cc_final: 0.7629 (m-80) REVERT: T 126 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8672 (tt) REVERT: T 155 ASP cc_start: 0.6890 (t0) cc_final: 0.6627 (t70) REVERT: T 177 ASN cc_start: 0.8143 (t0) cc_final: 0.7466 (t0) REVERT: T 304 ARG cc_start: 0.8009 (mmt90) cc_final: 0.7280 (ttp-110) REVERT: E 13 MET cc_start: 0.8234 (tpt) cc_final: 0.7555 (tpt) outliers start: 39 outliers final: 27 residues processed: 188 average time/residue: 0.2227 time to fit residues: 57.2334 Evaluate side-chains 166 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 210 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 368 GLU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 533 ASP Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 30 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9112 Z= 0.281 Angle : 0.677 8.742 12328 Z= 0.342 Chirality : 0.047 0.184 1380 Planarity : 0.005 0.072 1562 Dihedral : 6.170 37.889 1236 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.24 % Allowed : 14.14 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.65 (0.22), residues: 1113 helix: -2.08 (0.22), residues: 451 sheet: -3.24 (0.44), residues: 108 loop : -2.51 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 134 HIS 0.005 0.001 HIS S 395 PHE 0.014 0.002 PHE A 124 TYR 0.016 0.002 TYR T 362 ARG 0.007 0.001 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8198 (p0) cc_final: 0.7979 (p0) REVERT: S 213 ASP cc_start: 0.7808 (t70) cc_final: 0.7521 (t0) REVERT: S 274 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8221 (tm-30) REVERT: S 428 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8174 (tp-100) REVERT: S 465 LYS cc_start: 0.8386 (tmtt) cc_final: 0.7880 (tttm) REVERT: T 86 TYR cc_start: 0.8513 (m-80) cc_final: 0.7552 (m-80) REVERT: T 126 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8686 (tt) REVERT: T 155 ASP cc_start: 0.6976 (t0) cc_final: 0.6713 (t0) REVERT: T 177 ASN cc_start: 0.8175 (t0) cc_final: 0.7781 (t0) REVERT: T 304 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7043 (ttp-170) REVERT: T 317 ILE cc_start: 0.8743 (mp) cc_final: 0.8483 (mt) REVERT: T 437 GLU cc_start: 0.5799 (pm20) cc_final: 0.5539 (pm20) REVERT: T 533 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8136 (t0) REVERT: T 537 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8330 (pp) REVERT: A 81 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8131 (mtp85) REVERT: E 13 MET cc_start: 0.8214 (tpt) cc_final: 0.7549 (tpt) REVERT: E 26 LEU cc_start: 0.8980 (mm) cc_final: 0.8673 (mm) outliers start: 50 outliers final: 24 residues processed: 185 average time/residue: 0.2170 time to fit residues: 55.4740 Evaluate side-chains 166 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 427 THR Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 520 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain T residue 533 ASP Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 30 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 536 GLN A 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9112 Z= 0.171 Angle : 0.619 7.667 12328 Z= 0.307 Chirality : 0.044 0.234 1380 Planarity : 0.005 0.059 1562 Dihedral : 5.667 36.305 1236 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 4.29 % Allowed : 15.71 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.02 (0.24), residues: 1113 helix: -1.44 (0.24), residues: 446 sheet: -3.02 (0.47), residues: 104 loop : -2.24 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 134 HIS 0.002 0.001 HIS T 347 PHE 0.012 0.001 PHE A 124 TYR 0.018 0.001 TYR E 18 ARG 0.009 0.000 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8143 (p0) cc_final: 0.7919 (p0) REVERT: S 274 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8117 (tm-30) REVERT: T 68 MET cc_start: 0.8574 (tpt) cc_final: 0.8246 (tpt) REVERT: T 86 TYR cc_start: 0.8418 (m-80) cc_final: 0.7525 (m-80) REVERT: T 126 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8650 (tt) REVERT: T 155 ASP cc_start: 0.6874 (t0) cc_final: 0.6607 (t70) REVERT: T 177 ASN cc_start: 0.8141 (t0) cc_final: 0.7441 (t0) REVERT: T 304 ARG cc_start: 0.8031 (mmt90) cc_final: 0.6972 (ttp-170) REVERT: T 317 ILE cc_start: 0.8642 (mp) cc_final: 0.8392 (mt) REVERT: T 533 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8076 (t0) REVERT: T 537 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8301 (pp) REVERT: A 150 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6451 (tt) REVERT: E 13 MET cc_start: 0.8195 (tpt) cc_final: 0.7552 (tpt) REVERT: E 26 LEU cc_start: 0.8909 (mm) cc_final: 0.8532 (mm) REVERT: B 45 LYS cc_start: 0.8264 (pptt) cc_final: 0.7941 (pptt) outliers start: 41 outliers final: 25 residues processed: 184 average time/residue: 0.1989 time to fit residues: 51.1961 Evaluate side-chains 170 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 368 GLU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 427 THR Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain T residue 533 ASP Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9112 Z= 0.281 Angle : 0.656 8.814 12328 Z= 0.325 Chirality : 0.046 0.167 1380 Planarity : 0.005 0.058 1562 Dihedral : 5.750 41.282 1236 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 5.76 % Allowed : 15.92 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.76 (0.25), residues: 1113 helix: -1.28 (0.24), residues: 464 sheet: -2.80 (0.47), residues: 107 loop : -2.07 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 134 HIS 0.003 0.001 HIS T 101 PHE 0.019 0.001 PHE B 40 TYR 0.013 0.001 TYR B 23 ARG 0.007 0.001 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 137 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8357 (p0) cc_final: 0.8139 (p0) REVERT: S 274 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8121 (tm-30) REVERT: T 86 TYR cc_start: 0.8516 (m-80) cc_final: 0.7442 (m-80) REVERT: T 126 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8668 (tt) REVERT: T 177 ASN cc_start: 0.8148 (t0) cc_final: 0.7702 (t0) REVERT: T 317 ILE cc_start: 0.8784 (mp) cc_final: 0.8525 (mt) REVERT: T 537 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 150 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6530 (tt) REVERT: E 13 MET cc_start: 0.8211 (tpt) cc_final: 0.7514 (tpt) outliers start: 55 outliers final: 38 residues processed: 174 average time/residue: 0.2031 time to fit residues: 49.7376 Evaluate side-chains 171 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 210 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 331 ILE Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 520 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 GLN T 135 ASN T 242 ASN ** T 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9112 Z= 0.177 Angle : 0.619 8.289 12328 Z= 0.305 Chirality : 0.044 0.161 1380 Planarity : 0.004 0.055 1562 Dihedral : 5.432 38.027 1236 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 4.19 % Allowed : 17.59 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.48 (0.25), residues: 1113 helix: -0.93 (0.25), residues: 456 sheet: -2.83 (0.48), residues: 104 loop : -1.99 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 134 HIS 0.002 0.000 HIS T 347 PHE 0.013 0.001 PHE B 40 TYR 0.021 0.001 TYR E 18 ARG 0.011 0.000 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: S 274 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8095 (tm-30) REVERT: S 465 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7751 (tttm) REVERT: T 86 TYR cc_start: 0.8433 (m-80) cc_final: 0.7436 (m-80) REVERT: T 91 LEU cc_start: 0.8474 (mp) cc_final: 0.8210 (pp) REVERT: T 126 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8620 (tt) REVERT: T 177 ASN cc_start: 0.8073 (t0) cc_final: 0.7378 (t0) REVERT: T 317 ILE cc_start: 0.8666 (mp) cc_final: 0.8417 (mt) REVERT: T 537 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8318 (pp) REVERT: E 13 MET cc_start: 0.8144 (tpt) cc_final: 0.7410 (tpt) outliers start: 40 outliers final: 26 residues processed: 165 average time/residue: 0.2056 time to fit residues: 47.5143 Evaluate side-chains 154 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 427 THR Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN S 452 GLN ** T 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9112 Z= 0.158 Angle : 0.613 9.762 12328 Z= 0.299 Chirality : 0.043 0.176 1380 Planarity : 0.004 0.054 1562 Dihedral : 5.149 37.842 1236 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.56 % Allowed : 18.53 % Favored : 77.91 % 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: -2.20 (0.25), residues: 1113 helix: -0.62 (0.25), residues: 458 sheet: -2.66 (0.50), residues: 104 loop : -1.92 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 134 HIS 0.002 0.000 HIS T 101 PHE 0.013 0.001 PHE B 40 TYR 0.008 0.001 TYR T 342 ARG 0.007 0.000 ARG S 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8138 (p0) cc_final: 0.7928 (p0) REVERT: S 274 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8094 (tm-30) REVERT: T 86 TYR cc_start: 0.8426 (m-80) cc_final: 0.7398 (m-80) REVERT: T 126 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8609 (tt) REVERT: T 177 ASN cc_start: 0.8004 (t0) cc_final: 0.7366 (t0) REVERT: T 537 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8312 (pp) REVERT: A 81 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7814 (mtp85) REVERT: E 13 MET cc_start: 0.8197 (tpt) cc_final: 0.7409 (tpt) REVERT: E 26 LEU cc_start: 0.8882 (mm) cc_final: 0.8571 (mm) REVERT: E 33 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6943 (mt-10) outliers start: 34 outliers final: 24 residues processed: 169 average time/residue: 0.2020 time to fit residues: 47.2892 Evaluate side-chains 155 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN T 282 HIS ** T 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9112 Z= 0.186 Angle : 0.632 9.445 12328 Z= 0.306 Chirality : 0.044 0.153 1380 Planarity : 0.004 0.059 1562 Dihedral : 5.161 38.255 1236 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.08 % Allowed : 18.22 % Favored : 77.70 % 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: -2.04 (0.25), residues: 1113 helix: -0.45 (0.25), residues: 458 sheet: -2.59 (0.50), residues: 104 loop : -1.88 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 134 HIS 0.002 0.001 HIS T 101 PHE 0.013 0.001 PHE B 40 TYR 0.014 0.001 TYR T 461 ARG 0.013 0.000 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.231 Fit side-chains REVERT: S 107 ASN cc_start: 0.8221 (p0) cc_final: 0.7991 (p0) REVERT: S 274 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8147 (tm-30) REVERT: S 428 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: T 86 TYR cc_start: 0.8494 (m-80) cc_final: 0.7670 (m-80) REVERT: T 126 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8619 (tt) REVERT: T 177 ASN cc_start: 0.8037 (t0) cc_final: 0.7371 (t0) REVERT: T 537 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8276 (pp) REVERT: E 13 MET cc_start: 0.8223 (tpt) cc_final: 0.8009 (tpt) REVERT: E 33 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6921 (mt-10) outliers start: 39 outliers final: 29 residues processed: 165 average time/residue: 0.2089 time to fit residues: 48.0450 Evaluate side-chains 154 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 210 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** T 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9112 Z= 0.254 Angle : 0.654 9.241 12328 Z= 0.321 Chirality : 0.046 0.159 1380 Planarity : 0.005 0.062 1562 Dihedral : 5.298 36.862 1236 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.98 % Allowed : 19.16 % Favored : 76.86 % 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: -2.04 (0.25), residues: 1113 helix: -0.43 (0.25), residues: 458 sheet: -2.59 (0.49), residues: 105 loop : -1.89 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 134 HIS 0.003 0.001 HIS T 101 PHE 0.014 0.001 PHE B 40 TYR 0.015 0.001 TYR T 461 ARG 0.012 0.001 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 0.941 Fit side-chains REVERT: S 107 ASN cc_start: 0.8278 (p0) cc_final: 0.8040 (p0) REVERT: S 274 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8170 (tm-30) REVERT: S 428 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: T 86 TYR cc_start: 0.8546 (m-80) cc_final: 0.7600 (m-80) REVERT: T 91 LEU cc_start: 0.8514 (mp) cc_final: 0.8165 (pp) REVERT: T 126 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8694 (tt) REVERT: T 177 ASN cc_start: 0.8088 (t0) cc_final: 0.7696 (t0) REVERT: T 261 LEU cc_start: 0.7559 (pt) cc_final: 0.7342 (pp) REVERT: A 81 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7759 (mtp85) outliers start: 38 outliers final: 33 residues processed: 153 average time/residue: 0.1943 time to fit residues: 42.0986 Evaluate side-chains 156 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 210 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 427 THR Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** T 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9112 Z= 0.238 Angle : 0.655 9.138 12328 Z= 0.320 Chirality : 0.046 0.163 1380 Planarity : 0.005 0.061 1562 Dihedral : 5.338 37.664 1236 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.87 % Allowed : 19.37 % Favored : 76.75 % 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 (0.26), residues: 1113 helix: -0.37 (0.25), residues: 456 sheet: -2.57 (0.49), residues: 105 loop : -1.83 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 134 HIS 0.003 0.001 HIS S 327 PHE 0.014 0.001 PHE S 241 TYR 0.024 0.001 TYR E 18 ARG 0.011 0.000 ARG T 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.133 Fit side-chains REVERT: S 107 ASN cc_start: 0.8330 (p0) cc_final: 0.8113 (p0) REVERT: S 274 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8167 (tm-30) REVERT: S 428 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: T 86 TYR cc_start: 0.8556 (m-80) cc_final: 0.7594 (m-80) REVERT: T 91 LEU cc_start: 0.8456 (mp) cc_final: 0.8177 (pp) REVERT: T 126 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8692 (tt) REVERT: T 177 ASN cc_start: 0.8128 (t0) cc_final: 0.7421 (t0) REVERT: T 261 LEU cc_start: 0.7556 (pt) cc_final: 0.7348 (pp) REVERT: A 81 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7758 (mtp85) outliers start: 37 outliers final: 33 residues processed: 155 average time/residue: 0.1955 time to fit residues: 43.1871 Evaluate side-chains 156 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 386 VAL Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 521 LEU Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 135 ASN ** T 418 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 = 0.3658 r_free = 0.3658 target = 0.124970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108719 restraints weight = 15838.340| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.30 r_work: 0.3330 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9112 Z= 0.191 Angle : 0.639 9.155 12328 Z= 0.311 Chirality : 0.044 0.161 1380 Planarity : 0.004 0.061 1562 Dihedral : 5.250 37.451 1236 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.56 % Allowed : 19.58 % Favored : 76.86 % 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: -1.85 (0.26), residues: 1113 helix: -0.25 (0.26), residues: 456 sheet: -2.51 (0.49), residues: 105 loop : -1.79 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 134 HIS 0.002 0.001 HIS T 347 PHE 0.013 0.001 PHE S 241 TYR 0.013 0.001 TYR T 461 ARG 0.011 0.000 ARG T 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.62 seconds wall clock time: 42 minutes 9.73 seconds (2529.73 seconds total)