Starting phenix.real_space_refine on Thu Mar 14 14:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdr_14667/03_2024/7zdr_14667_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdr_14667/03_2024/7zdr_14667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdr_14667/03_2024/7zdr_14667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdr_14667/03_2024/7zdr_14667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdr_14667/03_2024/7zdr_14667_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdr_14667/03_2024/7zdr_14667_neut_updated.pdb" } resolution = 3.05 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= 0.006 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 3 5.49 5 Mg 1 5.21 5 S 29 5.16 5 C 5770 2.51 5 N 1584 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C ASP 391": "OD1" <-> "OD2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ASP 461": "OD1" <-> "OD2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ASP 506": "OD1" <-> "OD2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ASP 517": "OD1" <-> "OD2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ARG 566": "NH1" <-> "NH2" Residue "D TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 4415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4415 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 554} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4599 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'peptide': 585, 'undetermined': 2} Link IDs: {'PTRANS': 27, 'TRANS': 557, None: 2} Not linked: pdbres="ILE D 588 " pdbres=" MG D 601 " Not linked: pdbres=" MG D 601 " pdbres="ANP D 602 " Time building chain proxies: 5.25, per 1000 atoms: 0.58 Number of scatterers: 9014 At special positions: 0 Unit cell: (120.528, 77.841, 112.995, 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 29 16.00 P 3 15.00 Mg 1 11.99 O 1627 8.00 N 1584 7.00 C 5770 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=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 6 sheets defined 60.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'C' and resid 2 through 11 Proline residue: C 6 - end of helix removed outlier: 4.012A pdb=" N ALA C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 49 removed outlier: 3.523A pdb=" N ILE C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 59 through 103 removed outlier: 3.579A pdb=" N TYR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 removed outlier: 3.684A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 125 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 157 removed outlier: 3.896A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.760A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 186 through 208 Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.510A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 268 removed outlier: 3.608A pdb=" N MET C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.526A pdb=" N LEU C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 288 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 290 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE C 291 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 292 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.840A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 409 through 415 removed outlier: 3.741A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 453 removed outlier: 3.532A pdb=" N SER C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 481 through 491 Processing helix chain 'C' and resid 507 through 519 removed outlier: 3.686A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 565 through 571 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.605A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 63 through 108 removed outlier: 3.520A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 removed outlier: 4.319A pdb=" N GLY D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.577A pdb=" N THR D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 138 removed outlier: 4.424A pdb=" N ASP D 135 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 138 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 removed outlier: 3.702A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.623A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'D' and resid 195 through 218 removed outlier: 4.172A pdb=" N GLY D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS D 204 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLU D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 272 removed outlier: 4.085A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 329 Proline residue: D 298 - end of helix removed outlier: 3.931A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 4.810A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 314 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 397 removed outlier: 3.849A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 424 removed outlier: 3.962A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 488 through 499 Processing helix chain 'D' and resid 518 through 529 Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.502A pdb=" N ARG D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 339 through 342 Processing sheet with id= B, first strand: chain 'C' and resid 369 through 372 removed outlier: 6.375A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 542 through 546 removed outlier: 3.767A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 371 through 373 removed outlier: 3.526A pdb=" N PHE D 371 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.599A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 560 through 565 removed outlier: 3.594A pdb=" N ARG D 560 " --> pdb=" O GLN D 557 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 557 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN D 564 " --> pdb=" O ILE D 553 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 553 " --> pdb=" O GLN D 564 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1407 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: 2.48 Time building geometry restraints manager: 3.82 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: 2897 1.33 - 1.45: 1107 1.45 - 1.57: 5127 1.57 - 1.69: 5 1.69 - 1.81: 56 Bond restraints: 9192 Sorted by residual: bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O5' ANP D 602 " pdb=" PA ANP D 602 " ideal model delta sigma weight residual 1.655 1.580 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N GLN D 377 " pdb=" CA GLN D 377 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.10e+00 bond pdb=" N GLU C 350 " pdb=" CA GLU C 350 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.88e+00 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.72: 188 105.72 - 112.80: 4968 112.80 - 119.89: 3035 119.89 - 126.98: 4183 126.98 - 134.06: 122 Bond angle restraints: 12496 Sorted by residual: angle pdb=" PB ANP D 602 " pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 126.95 109.72 17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" N ASN C 121 " pdb=" CA ASN C 121 " pdb=" C ASN C 121 " ideal model delta sigma weight residual 112.89 108.02 4.87 1.24e+00 6.50e-01 1.54e+01 angle pdb=" O1B ANP D 602 " pdb=" PB ANP D 602 " pdb=" O2B ANP D 602 " ideal model delta sigma weight residual 120.08 109.62 10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N GLN C 248 " pdb=" CA GLN C 248 " pdb=" C GLN C 248 " ideal model delta sigma weight residual 113.41 109.30 4.11 1.22e+00 6.72e-01 1.14e+01 angle pdb=" CA GLU C 350 " pdb=" C GLU C 350 " pdb=" O GLU C 350 " ideal model delta sigma weight residual 121.81 118.07 3.74 1.18e+00 7.18e-01 1.01e+01 ... (remaining 12491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.64: 4989 19.64 - 39.29: 433 39.29 - 58.93: 51 58.93 - 78.58: 24 78.58 - 98.22: 5 Dihedral angle restraints: 5502 sinusoidal: 2180 harmonic: 3322 Sorted by residual: dihedral pdb=" CA LYS C 12 " pdb=" C LYS C 12 " pdb=" N ARG C 13 " pdb=" CA ARG C 13 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA MET D 556 " pdb=" C MET D 556 " pdb=" N GLN D 557 " pdb=" CA GLN D 557 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" O1B ANP D 602 " pdb=" N3B ANP D 602 " pdb=" PB ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sinusoidal sigma weight residual 35.15 -63.07 98.22 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 5499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1177 0.054 - 0.108: 247 0.108 - 0.162: 26 0.162 - 0.215: 3 0.215 - 0.269: 1 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR C 348 " pdb=" N TYR C 348 " pdb=" C TYR C 348 " pdb=" CB TYR C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLN C 232 " pdb=" N GLN C 232 " pdb=" C GLN C 232 " pdb=" CB GLN C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 1451 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 347 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C THR C 347 " -0.055 2.00e-02 2.50e+03 pdb=" O THR C 347 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR C 348 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 179 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 552 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C GLU C 552 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU C 552 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN C 553 " -0.008 2.00e-02 2.50e+03 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 64 2.61 - 3.18: 7711 3.18 - 3.75: 13938 3.75 - 4.33: 19727 4.33 - 4.90: 32822 Nonbonded interactions: 74262 Sorted by model distance: nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 2.031 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1G ANP D 602 " model vdw 2.056 2.170 nonbonded pdb=" OE1 GLN D 129 " pdb=" OG SER D 323 " model vdw 2.196 2.440 nonbonded pdb=" NH2 ARG D 5 " pdb=" OD1 ASP D 322 " model vdw 2.203 2.520 nonbonded pdb=" OG SER C 438 " pdb=" OG SER C 441 " model vdw 2.213 2.440 ... (remaining 74257 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=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: 1.080 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: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.380 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 9192 Z= 0.399 Angle : 0.708 17.228 12496 Z= 0.378 Chirality : 0.044 0.269 1454 Planarity : 0.004 0.039 1595 Dihedral : 15.073 98.223 3360 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -2.22 (0.22), residues: 1154 helix: -1.59 (0.18), residues: 687 sheet: 0.34 (0.70), residues: 52 loop : -1.17 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 427 HIS 0.005 0.001 HIS C 368 PHE 0.010 0.001 PHE D 73 TYR 0.015 0.001 TYR D 311 ARG 0.020 0.001 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.025 Fit side-chains REVERT: C 343 ASP cc_start: 0.7857 (t0) cc_final: 0.7495 (t0) REVERT: C 541 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7819 (tp40) REVERT: D 311 TYR cc_start: 0.7620 (t80) cc_final: 0.7407 (t80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2572 time to fit residues: 37.4350 Evaluate side-chains 92 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS C 531 HIS C 553 GLN C 563 GLN D 15 GLN D 143 GLN D 433 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9192 Z= 0.217 Angle : 0.584 8.250 12496 Z= 0.296 Chirality : 0.040 0.150 1454 Planarity : 0.005 0.045 1595 Dihedral : 7.430 90.580 1294 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.75 % Allowed : 6.84 % Favored : 92.41 % 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: -0.50 (0.23), residues: 1154 helix: 0.10 (0.19), residues: 707 sheet: 0.34 (0.76), residues: 47 loop : -1.01 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS D 93 PHE 0.015 0.001 PHE C 164 TYR 0.018 0.002 TYR D 88 ARG 0.008 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.079 Fit side-chains REVERT: C 343 ASP cc_start: 0.7844 (t0) cc_final: 0.7238 (t0) REVERT: C 541 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7618 (tp-100) REVERT: D 94 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8836 (mp) REVERT: D 154 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8018 (mp) outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 0.2415 time to fit residues: 35.2981 Evaluate side-chains 96 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 0.0010 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN C 394 GLN C 549 GLN D 394 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9192 Z= 0.215 Angle : 0.539 8.072 12496 Z= 0.270 Chirality : 0.040 0.149 1454 Planarity : 0.004 0.043 1595 Dihedral : 6.230 88.371 1294 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.18 % Allowed : 10.59 % Favored : 88.24 % 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: 0.31 (0.24), residues: 1154 helix: 0.84 (0.19), residues: 707 sheet: 0.82 (0.75), residues: 52 loop : -0.95 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.003 0.001 HIS C 368 PHE 0.017 0.001 PHE C 346 TYR 0.020 0.001 TYR D 88 ARG 0.010 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.047 Fit side-chains REVERT: C 343 ASP cc_start: 0.7817 (t0) cc_final: 0.7203 (t0) REVERT: C 394 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: C 541 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7585 (tp-100) REVERT: D 94 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8893 (mp) REVERT: D 154 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8262 (mt) REVERT: D 234 ASP cc_start: 0.7707 (t0) cc_final: 0.7502 (t0) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.2526 time to fit residues: 38.2222 Evaluate side-chains 102 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 394 GLN Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 92 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN C 394 GLN C 549 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9192 Z= 0.148 Angle : 0.490 7.703 12496 Z= 0.248 Chirality : 0.038 0.147 1454 Planarity : 0.004 0.043 1595 Dihedral : 5.667 87.121 1294 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.82 % Allowed : 12.09 % Favored : 86.10 % 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: 0.88 (0.25), residues: 1154 helix: 1.36 (0.20), residues: 706 sheet: 0.78 (0.76), residues: 52 loop : -0.83 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.002 0.000 HIS D 93 PHE 0.016 0.001 PHE C 346 TYR 0.019 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.115 Fit side-chains REVERT: C 118 GLU cc_start: 0.6927 (pp20) cc_final: 0.6721 (pp20) REVERT: C 343 ASP cc_start: 0.7867 (t0) cc_final: 0.7266 (t0) REVERT: C 541 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7568 (tp-100) REVERT: D 94 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8887 (mp) REVERT: D 154 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8337 (mt) REVERT: D 566 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7101 (mtt90) outliers start: 17 outliers final: 8 residues processed: 119 average time/residue: 0.2504 time to fit residues: 39.9877 Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN C 549 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9192 Z= 0.386 Angle : 0.617 9.059 12496 Z= 0.303 Chirality : 0.045 0.301 1454 Planarity : 0.004 0.051 1595 Dihedral : 5.845 82.752 1294 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.82 % Allowed : 13.58 % Favored : 84.60 % 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: 0.57 (0.24), residues: 1154 helix: 1.11 (0.20), residues: 698 sheet: 0.47 (0.74), residues: 52 loop : -0.87 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 81 HIS 0.006 0.001 HIS C 368 PHE 0.020 0.002 PHE C 346 TYR 0.018 0.002 TYR D 88 ARG 0.010 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.054 Fit side-chains REVERT: C 343 ASP cc_start: 0.7888 (t0) cc_final: 0.7321 (t0) REVERT: C 541 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7577 (tp-100) REVERT: D 94 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8908 (mp) REVERT: D 154 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8372 (mt) REVERT: D 566 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7216 (mtt90) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.2360 time to fit residues: 33.7703 Evaluate side-chains 104 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9192 Z= 0.237 Angle : 0.537 7.127 12496 Z= 0.269 Chirality : 0.041 0.250 1454 Planarity : 0.004 0.049 1595 Dihedral : 5.666 81.107 1294 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.60 % Allowed : 14.33 % Favored : 84.06 % 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: 0.77 (0.25), residues: 1154 helix: 1.30 (0.20), residues: 701 sheet: 0.42 (0.73), residues: 52 loop : -0.85 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS C 368 PHE 0.020 0.001 PHE C 346 TYR 0.018 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.018 Fit side-chains REVERT: C 343 ASP cc_start: 0.7867 (t0) cc_final: 0.7272 (t0) REVERT: C 541 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7519 (tp-100) REVERT: D 94 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8918 (mp) REVERT: D 154 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8390 (mt) REVERT: D 460 ASP cc_start: 0.7816 (m-30) cc_final: 0.7563 (m-30) REVERT: D 566 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7207 (mtt90) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.2467 time to fit residues: 37.1093 Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9192 Z= 0.218 Angle : 0.523 6.659 12496 Z= 0.263 Chirality : 0.040 0.230 1454 Planarity : 0.004 0.046 1595 Dihedral : 5.550 78.821 1294 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.82 % Allowed : 14.12 % Favored : 84.06 % 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: 0.91 (0.25), residues: 1154 helix: 1.46 (0.20), residues: 700 sheet: 0.37 (0.74), residues: 52 loop : -0.88 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.003 0.001 HIS C 368 PHE 0.021 0.001 PHE C 346 TYR 0.018 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.040 Fit side-chains REVERT: C 343 ASP cc_start: 0.7865 (t0) cc_final: 0.7180 (t0) REVERT: C 541 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7425 (tp-100) REVERT: D 94 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8930 (mp) REVERT: D 154 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8400 (mt) REVERT: D 342 LEU cc_start: 0.8995 (tp) cc_final: 0.8715 (tp) REVERT: D 460 ASP cc_start: 0.7768 (m-30) cc_final: 0.7540 (m-30) REVERT: D 566 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7231 (mtt180) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.2346 time to fit residues: 35.5749 Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9192 Z= 0.191 Angle : 0.514 7.513 12496 Z= 0.256 Chirality : 0.039 0.206 1454 Planarity : 0.004 0.040 1595 Dihedral : 5.454 76.296 1294 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.03 % Allowed : 14.33 % Favored : 83.64 % 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: 1.02 (0.25), residues: 1154 helix: 1.55 (0.20), residues: 706 sheet: 0.48 (0.76), residues: 52 loop : -0.87 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.003 0.001 HIS D 93 PHE 0.024 0.001 PHE C 346 TYR 0.019 0.001 TYR D 88 ARG 0.009 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.890 Fit side-chains REVERT: C 343 ASP cc_start: 0.7833 (t0) cc_final: 0.7167 (t0) REVERT: C 541 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7394 (tp-100) REVERT: D 94 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8927 (mp) REVERT: D 154 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8397 (mt) REVERT: D 342 LEU cc_start: 0.8938 (tp) cc_final: 0.8722 (tp) REVERT: D 455 LEU cc_start: 0.8329 (tp) cc_final: 0.7902 (tp) REVERT: D 566 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7242 (mtt180) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 0.2340 time to fit residues: 35.1834 Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 97 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9192 Z= 0.175 Angle : 0.498 6.534 12496 Z= 0.249 Chirality : 0.039 0.193 1454 Planarity : 0.004 0.040 1595 Dihedral : 5.326 73.230 1294 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 15.08 % Favored : 83.42 % 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: 1.18 (0.25), residues: 1154 helix: 1.69 (0.20), residues: 701 sheet: 0.54 (0.76), residues: 52 loop : -0.81 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.002 0.000 HIS D 93 PHE 0.029 0.001 PHE C 346 TYR 0.019 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.945 Fit side-chains REVERT: C 343 ASP cc_start: 0.7835 (t0) cc_final: 0.7187 (t0) REVERT: C 541 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7388 (tp-100) REVERT: D 94 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8904 (mp) REVERT: D 154 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8425 (mt) REVERT: D 342 LEU cc_start: 0.8860 (tp) cc_final: 0.8643 (tp) REVERT: D 566 ARG cc_start: 0.7576 (mtp85) cc_final: 0.7192 (mtt180) outliers start: 14 outliers final: 10 residues processed: 110 average time/residue: 0.2344 time to fit residues: 34.9638 Evaluate side-chains 105 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 520 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 549 GLN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9192 Z= 0.178 Angle : 0.506 8.288 12496 Z= 0.252 Chirality : 0.039 0.193 1454 Planarity : 0.004 0.036 1595 Dihedral : 5.296 71.450 1294 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.39 % Allowed : 15.61 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1154 helix: 1.74 (0.20), residues: 695 sheet: 0.56 (0.76), residues: 52 loop : -0.77 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 390 HIS 0.003 0.000 HIS D 204 PHE 0.037 0.001 PHE C 346 TYR 0.019 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.028 Fit side-chains REVERT: C 343 ASP cc_start: 0.7839 (t0) cc_final: 0.7194 (t0) REVERT: C 541 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7390 (tp-100) REVERT: D 94 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8919 (mp) REVERT: D 154 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8429 (mt) REVERT: D 342 LEU cc_start: 0.8848 (tp) cc_final: 0.8605 (tp) REVERT: D 566 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7202 (mtt90) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.2288 time to fit residues: 34.3139 Evaluate side-chains 107 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 520 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.0770 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107504 restraints weight = 10511.265| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.67 r_work: 0.3046 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9192 Z= 0.172 Angle : 0.501 7.074 12496 Z= 0.250 Chirality : 0.038 0.182 1454 Planarity : 0.004 0.033 1595 Dihedral : 5.228 69.361 1294 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.39 % Allowed : 15.83 % Favored : 82.78 % 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: 1.29 (0.25), residues: 1154 helix: 1.81 (0.20), residues: 687 sheet: 0.60 (0.77), residues: 52 loop : -0.74 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 390 HIS 0.002 0.000 HIS D 204 PHE 0.038 0.001 PHE C 346 TYR 0.019 0.001 TYR D 88 ARG 0.008 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.58 seconds wall clock time: 37 minutes 1.01 seconds (2221.01 seconds total)