Starting phenix.real_space_refine on Wed Feb 14 09:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdu_14670/02_2024/7zdu_14670_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdu_14670/02_2024/7zdu_14670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdu_14670/02_2024/7zdu_14670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdu_14670/02_2024/7zdu_14670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdu_14670/02_2024/7zdu_14670_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdu_14670/02_2024/7zdu_14670_neut_updated.pdb" } resolution = 2.98 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 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 6 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 5729 2.51 5 N 1580 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 2": "NH1" <-> "NH2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "C TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C ASP 335": "OD1" <-> "OD2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 510": "OD1" <-> "OD2" Residue "D GLU 521": "OE1" <-> "OE2" Residue "D ARG 523": "NH1" <-> "NH2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ASP 546": "OD1" <-> "OD2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "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: 8975 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4344 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain: "D" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4567 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 27, 'TRANS': 557} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.86, per 1000 atoms: 0.65 Number of scatterers: 8975 At special positions: 0 Unit cell: (100.44, 73.656, 138.105, 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 6 15.00 Mg 2 11.99 O 1629 8.00 N 1580 7.00 C 5729 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: 3.48 Conformation dependent library (CDL) restraints added in 2.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 4 sheets defined 62.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'C' and resid 2 through 49 Proline residue: C 6 - end of helix removed outlier: 3.729A pdb=" N ALA C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 14 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TRP C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 17 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 19 " --> pdb=" O TRP C 16 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 21 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU C 24 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 33 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 38 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 40 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 43 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 61 through 105 removed outlier: 3.537A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Proline residue: C 105 - end of helix Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 116 through 137 removed outlier: 4.311A pdb=" N VAL C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 157 removed outlier: 3.783A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 208 Proline residue: C 178 - end of helix removed outlier: 4.875A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.552A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 268 removed outlier: 3.719A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 293 removed outlier: 3.707A pdb=" N ILE C 280 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS C 286 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA C 290 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 291 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 318 removed outlier: 3.674A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.568A pdb=" N GLN C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) 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: 3.920A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 443 through 453 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 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 477 through 491 Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 556 through 562 removed outlier: 3.510A pdb=" N ALA C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 removed outlier: 3.853A pdb=" N SER D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 Processing helix chain 'D' and resid 64 through 109 removed outlier: 3.560A pdb=" N ARG D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.618A pdb=" N THR D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.942A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 removed outlier: 4.612A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 3.782A 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 210 removed outlier: 3.718A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix removed outlier: 3.511A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 221 through 273 removed outlier: 3.517A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 329 Proline residue: D 298 - end of helix removed outlier: 3.773A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.655A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 removed outlier: 3.520A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 424 removed outlier: 3.579A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.945A 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 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 488 through 501 removed outlier: 3.599A pdb=" N ALA D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.843A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 570 No H-bonds generated for 'chain 'D' and resid 567 through 570' Processing helix chain 'D' and resid 575 through 583 Processing sheet with id= A, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.585A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 550 through 554 removed outlier: 6.674A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 526 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE C 371 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET C 528 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY C 373 " --> pdb=" O MET C 528 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 371 through 373 removed outlier: 3.684A pdb=" N PHE D 371 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.770A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN D 564 " --> pdb=" O ILE D 553 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE D 553 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 552 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR D 537 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 381 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET D 539 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY D 383 " --> pdb=" O MET D 539 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1374 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: 2.56 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2254 1.33 - 1.45: 1668 1.45 - 1.57: 5165 1.57 - 1.69: 10 1.69 - 1.81: 55 Bond restraints: 9152 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.13e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C5 ATP C 602 " pdb=" C6 ATP C 602 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C5 ATP D 602 " pdb=" C6 ATP D 602 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C8 ATP D 602 " pdb=" N7 ATP D 602 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.26e+01 ... (remaining 9147 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.72: 272 106.72 - 114.12: 5346 114.12 - 121.52: 4864 121.52 - 128.92: 1887 128.92 - 136.32: 80 Bond angle restraints: 12449 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 119.56 20.31 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 120.08 16.75 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP D 602 " pdb=" O3A ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 136.83 120.80 16.03 1.00e+00 1.00e+00 2.57e+02 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 118.40 8.40 1.00e+00 1.00e+00 7.06e+01 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4953 17.62 - 35.23: 433 35.23 - 52.85: 78 52.85 - 70.47: 26 70.47 - 88.08: 10 Dihedral angle restraints: 5500 sinusoidal: 2206 harmonic: 3294 Sorted by residual: dihedral pdb=" C PHE C 291 " pdb=" N PHE C 291 " pdb=" CA PHE C 291 " pdb=" CB PHE C 291 " ideal model delta harmonic sigma weight residual -122.60 -132.82 10.22 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" CA ASP D 277 " pdb=" CB ASP D 277 " pdb=" CG ASP D 277 " pdb=" OD1 ASP D 277 " ideal model delta sinusoidal sigma weight residual -30.00 -88.65 58.65 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASN D 162 " pdb=" CB ASN D 162 " pdb=" CG ASN D 162 " pdb=" OD1 ASN D 162 " ideal model delta sinusoidal sigma weight residual 120.00 -171.11 -68.89 2 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1272 0.060 - 0.120: 154 0.120 - 0.180: 20 0.180 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CA PHE C 291 " pdb=" N PHE C 291 " pdb=" C PHE C 291 " pdb=" CB PHE C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU D 547 " pdb=" CB LEU D 547 " pdb=" CD1 LEU D 547 " pdb=" CD2 LEU D 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG C 522 " pdb=" N ARG C 522 " pdb=" C ARG C 522 " pdb=" CB ARG C 522 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1445 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 555 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C THR C 555 " 0.041 2.00e-02 2.50e+03 pdb=" O THR C 555 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS C 556 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 104 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO C 105 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 177 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 178 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.022 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 69 2.55 - 3.14: 7022 3.14 - 3.73: 14326 3.73 - 4.31: 20511 4.31 - 4.90: 34403 Nonbonded interactions: 76331 Sorted by model distance: nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.966 2.170 nonbonded pdb=" OE1 GLN D 430 " pdb="MG MG D 601 " model vdw 2.011 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3G ATP D 602 " model vdw 2.014 2.170 nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 2.036 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.083 2.170 ... (remaining 76326 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: 1.140 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: 0.000 Extract box with map and model: 5.230 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.050 Find NCS groups from input model: 0.290 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 : 0.005 0.078 9152 Z= 0.309 Angle : 0.753 20.306 12449 Z= 0.533 Chirality : 0.042 0.301 1448 Planarity : 0.004 0.042 1584 Dihedral : 14.467 88.083 3374 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.09 % 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: -0.78 (0.24), residues: 1144 helix: -0.54 (0.19), residues: 694 sheet: 0.16 (0.65), residues: 64 loop : -0.24 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 427 HIS 0.004 0.001 HIS C 94 PHE 0.018 0.001 PHE D 467 TYR 0.012 0.001 TYR C 59 ARG 0.011 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: C 59 TYR cc_start: 0.8155 (p90) cc_final: 0.7929 (p90) REVERT: C 134 TYR cc_start: 0.8465 (t80) cc_final: 0.6621 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.3733 time to fit residues: 170.8498 Evaluate side-chains 96 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9152 Z= 0.223 Angle : 0.563 8.520 12449 Z= 0.291 Chirality : 0.041 0.152 1448 Planarity : 0.005 0.041 1584 Dihedral : 7.275 82.587 1317 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.93 % Allowed : 8.05 % Favored : 90.02 % 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: 0.80 (0.25), residues: 1144 helix: 1.03 (0.20), residues: 694 sheet: 0.25 (0.64), residues: 64 loop : -0.17 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 427 HIS 0.007 0.001 HIS D 280 PHE 0.012 0.001 PHE D 205 TYR 0.012 0.001 TYR D 88 ARG 0.009 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.044 Fit side-chains REVERT: C 134 TYR cc_start: 0.8465 (t80) cc_final: 0.6558 (m-80) REVERT: D 22 ARG cc_start: 0.7509 (ttt180) cc_final: 0.7295 (ptm160) REVERT: D 88 TYR cc_start: 0.8594 (t80) cc_final: 0.8068 (t80) REVERT: D 336 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7908 (pp30) REVERT: D 560 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7235 (ttm110) outliers start: 18 outliers final: 6 residues processed: 118 average time/residue: 1.3544 time to fit residues: 170.2111 Evaluate side-chains 107 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9152 Z= 0.177 Angle : 0.501 6.355 12449 Z= 0.259 Chirality : 0.039 0.148 1448 Planarity : 0.004 0.041 1584 Dihedral : 7.055 79.096 1317 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.04 % Allowed : 11.16 % Favored : 86.80 % 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: 1.33 (0.25), residues: 1144 helix: 1.53 (0.20), residues: 696 sheet: 0.31 (0.64), residues: 58 loop : -0.10 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 12 HIS 0.005 0.001 HIS D 280 PHE 0.011 0.001 PHE D 205 TYR 0.021 0.001 TYR C 59 ARG 0.007 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.209 Fit side-chains REVERT: C 134 TYR cc_start: 0.8464 (t80) cc_final: 0.6548 (m-80) REVERT: D 22 ARG cc_start: 0.7399 (ttt180) cc_final: 0.7178 (ptm160) REVERT: D 88 TYR cc_start: 0.8533 (t80) cc_final: 0.8004 (t80) REVERT: D 336 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7895 (pp30) REVERT: D 557 GLN cc_start: 0.8200 (tt0) cc_final: 0.7956 (tt0) outliers start: 19 outliers final: 4 residues processed: 114 average time/residue: 1.3136 time to fit residues: 160.4001 Evaluate side-chains 104 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN D 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9152 Z= 0.313 Angle : 0.543 6.690 12449 Z= 0.276 Chirality : 0.041 0.144 1448 Planarity : 0.004 0.043 1584 Dihedral : 7.142 85.164 1317 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.47 % Allowed : 12.88 % Favored : 84.66 % 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: 1.39 (0.25), residues: 1144 helix: 1.59 (0.20), residues: 697 sheet: 0.20 (0.64), residues: 61 loop : -0.07 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 12 HIS 0.005 0.001 HIS D 312 PHE 0.016 0.001 PHE D 467 TYR 0.017 0.002 TYR D 88 ARG 0.007 0.000 ARG D 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.070 Fit side-chains REVERT: C 134 TYR cc_start: 0.8503 (t80) cc_final: 0.6567 (m-80) REVERT: D 336 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7937 (pp30) REVERT: D 558 ASP cc_start: 0.7486 (p0) cc_final: 0.7252 (p0) outliers start: 23 outliers final: 9 residues processed: 111 average time/residue: 1.3234 time to fit residues: 156.5054 Evaluate side-chains 105 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 564 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9152 Z= 0.157 Angle : 0.484 6.304 12449 Z= 0.248 Chirality : 0.038 0.134 1448 Planarity : 0.004 0.042 1584 Dihedral : 6.699 85.015 1317 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.25 % Allowed : 14.91 % Favored : 82.83 % 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: 1.74 (0.26), residues: 1144 helix: 1.93 (0.20), residues: 698 sheet: 0.30 (0.64), residues: 58 loop : -0.07 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 12 HIS 0.004 0.001 HIS D 280 PHE 0.012 0.001 PHE D 205 TYR 0.011 0.001 TYR D 88 ARG 0.007 0.000 ARG D 566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.941 Fit side-chains REVERT: C 134 TYR cc_start: 0.8432 (t80) cc_final: 0.6522 (m-80) REVERT: D 88 TYR cc_start: 0.8362 (t80) cc_final: 0.7708 (t80) REVERT: D 159 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: D 336 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7912 (pp30) outliers start: 21 outliers final: 6 residues processed: 117 average time/residue: 1.2526 time to fit residues: 156.5076 Evaluate side-chains 108 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9152 Z= 0.200 Angle : 0.499 5.952 12449 Z= 0.254 Chirality : 0.039 0.137 1448 Planarity : 0.004 0.041 1584 Dihedral : 6.510 83.550 1317 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.04 % Allowed : 15.45 % Favored : 82.51 % 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: 1.83 (0.26), residues: 1144 helix: 2.02 (0.20), residues: 697 sheet: 0.29 (0.63), residues: 58 loop : -0.07 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 12 HIS 0.004 0.001 HIS D 280 PHE 0.011 0.001 PHE C 181 TYR 0.012 0.001 TYR D 88 ARG 0.009 0.000 ARG D 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.942 Fit side-chains REVERT: C 59 TYR cc_start: 0.8341 (p90) cc_final: 0.8134 (p90) REVERT: C 134 TYR cc_start: 0.8495 (t80) cc_final: 0.6517 (m-80) REVERT: D 88 TYR cc_start: 0.8549 (t80) cc_final: 0.7910 (t80) REVERT: D 159 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: D 336 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7897 (pp30) outliers start: 19 outliers final: 7 residues processed: 110 average time/residue: 1.3093 time to fit residues: 153.6488 Evaluate side-chains 106 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 159 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9152 Z= 0.188 Angle : 0.495 6.395 12449 Z= 0.253 Chirality : 0.039 0.136 1448 Planarity : 0.004 0.046 1584 Dihedral : 6.362 82.295 1317 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.04 % Allowed : 16.63 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1144 helix: 2.11 (0.20), residues: 697 sheet: 0.26 (0.63), residues: 58 loop : -0.06 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 12 HIS 0.004 0.001 HIS D 280 PHE 0.011 0.001 PHE D 205 TYR 0.012 0.001 TYR D 88 ARG 0.010 0.000 ARG D 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.571 Fit side-chains REVERT: C 59 TYR cc_start: 0.8351 (p90) cc_final: 0.8141 (p90) REVERT: C 134 TYR cc_start: 0.8502 (t80) cc_final: 0.6504 (m-80) REVERT: D 88 TYR cc_start: 0.8513 (t80) cc_final: 0.7898 (t80) REVERT: D 336 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7887 (pp30) outliers start: 19 outliers final: 8 residues processed: 113 average time/residue: 1.3003 time to fit residues: 157.1122 Evaluate side-chains 109 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9152 Z= 0.202 Angle : 0.503 6.173 12449 Z= 0.256 Chirality : 0.039 0.137 1448 Planarity : 0.004 0.057 1584 Dihedral : 6.275 82.180 1317 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.61 % Allowed : 17.06 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.25), residues: 1144 helix: 2.11 (0.20), residues: 697 sheet: 0.29 (0.63), residues: 58 loop : -0.08 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 427 HIS 0.004 0.001 HIS D 280 PHE 0.011 0.001 PHE C 181 TYR 0.013 0.001 TYR D 88 ARG 0.012 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.106 Fit side-chains REVERT: C 134 TYR cc_start: 0.8509 (t80) cc_final: 0.6507 (m-80) REVERT: D 22 ARG cc_start: 0.7194 (ptm160) cc_final: 0.6973 (ptm160) REVERT: D 54 MET cc_start: 0.8757 (mmp) cc_final: 0.8436 (mmp) REVERT: D 88 TYR cc_start: 0.8522 (t80) cc_final: 0.7925 (t80) REVERT: D 336 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7890 (pp30) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 1.3734 time to fit residues: 162.3818 Evaluate side-chains 106 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9152 Z= 0.194 Angle : 0.512 6.684 12449 Z= 0.261 Chirality : 0.039 0.166 1448 Planarity : 0.004 0.052 1584 Dihedral : 6.188 81.751 1317 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.50 % Allowed : 17.06 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1144 helix: 2.16 (0.20), residues: 697 sheet: 0.27 (0.63), residues: 58 loop : -0.09 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 12 HIS 0.004 0.001 HIS D 280 PHE 0.011 0.001 PHE D 205 TYR 0.013 0.001 TYR D 88 ARG 0.013 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.042 Fit side-chains REVERT: C 134 TYR cc_start: 0.8487 (t80) cc_final: 0.6457 (m-80) REVERT: D 22 ARG cc_start: 0.7186 (ptm160) cc_final: 0.6962 (ptm160) REVERT: D 88 TYR cc_start: 0.8521 (t80) cc_final: 0.7958 (t80) REVERT: D 162 ASN cc_start: 0.8198 (m110) cc_final: 0.7961 (m-40) REVERT: D 336 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7924 (pp30) outliers start: 14 outliers final: 8 residues processed: 110 average time/residue: 1.3468 time to fit residues: 157.9723 Evaluate side-chains 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9152 Z= 0.167 Angle : 0.505 7.532 12449 Z= 0.257 Chirality : 0.038 0.157 1448 Planarity : 0.004 0.057 1584 Dihedral : 6.039 80.711 1317 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.18 % Allowed : 17.70 % Favored : 81.12 % 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: 2.03 (0.26), residues: 1144 helix: 2.23 (0.20), residues: 696 sheet: 0.28 (0.63), residues: 58 loop : -0.08 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 206 HIS 0.004 0.001 HIS D 280 PHE 0.010 0.001 PHE D 205 TYR 0.012 0.001 TYR D 88 ARG 0.013 0.000 ARG D 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.951 Fit side-chains REVERT: C 59 TYR cc_start: 0.8341 (p90) cc_final: 0.8132 (p90) REVERT: C 134 TYR cc_start: 0.8457 (t80) cc_final: 0.6436 (m-80) REVERT: C 522 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7874 (tpp-160) REVERT: D 22 ARG cc_start: 0.7181 (ptm160) cc_final: 0.6960 (ptm160) REVERT: D 88 TYR cc_start: 0.8459 (t80) cc_final: 0.7922 (t80) REVERT: D 162 ASN cc_start: 0.8169 (m110) cc_final: 0.7964 (m-40) REVERT: D 336 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7970 (pp30) REVERT: D 342 LEU cc_start: 0.7912 (pt) cc_final: 0.7641 (mp) outliers start: 11 outliers final: 7 residues processed: 116 average time/residue: 1.2571 time to fit residues: 155.6025 Evaluate side-chains 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 372 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091961 restraints weight = 12116.436| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.74 r_work: 0.2908 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9152 Z= 0.183 Angle : 0.524 11.582 12449 Z= 0.262 Chirality : 0.040 0.410 1448 Planarity : 0.004 0.057 1584 Dihedral : 6.012 81.074 1317 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.50 % Allowed : 17.27 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 1144 helix: 2.20 (0.20), residues: 696 sheet: 0.33 (0.66), residues: 55 loop : -0.05 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 206 HIS 0.004 0.001 HIS D 280 PHE 0.018 0.001 PHE C 164 TYR 0.013 0.001 TYR D 88 ARG 0.013 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.15 seconds wall clock time: 59 minutes 32.62 seconds (3572.62 seconds total)