Starting phenix.real_space_refine on Thu Mar 14 14:51:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze5_14684/03_2024/7ze5_14684_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze5_14684/03_2024/7ze5_14684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze5_14684/03_2024/7ze5_14684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze5_14684/03_2024/7ze5_14684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze5_14684/03_2024/7ze5_14684_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze5_14684/03_2024/7ze5_14684_neut_updated.pdb" } resolution = 2.94 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= 0.005 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 30 5.16 5 C 5796 2.51 5 N 1598 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 461": "OD1" <-> "OD2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 546": "OD1" <-> "OD2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D GLU 521": "OE1" <-> "OE2" Residue "D ARG 523": "NH1" <-> "NH2" Residue "D ASP 558": "OD1" <-> "OD2" 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9077 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4421 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "D" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4592 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.01, per 1000 atoms: 0.55 Number of scatterers: 9077 At special positions: 0 Unit cell: (117.18, 97.929, 102.951, 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 30 16.00 P 6 15.00 Mg 2 11.99 O 1645 8.00 N 1598 7.00 C 5796 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 4 sheets defined 62.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'C' and resid 2 through 49 removed outlier: 3.583A pdb=" N LEU C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Proline residue: C 6 - end of helix removed outlier: 4.063A pdb=" N ALA C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 15 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TRP C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 20 " --> pdb=" O MET C 17 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 21 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 24 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 34 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 38 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 39 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C 43 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 45 " --> pdb=" O PHE C 42 " (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 102 removed outlier: 3.532A pdb=" N ALA C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 126 through 135 removed outlier: 3.566A pdb=" N LEU C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N HIS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 removed outlier: 3.650A pdb=" N ILE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 186 through 208 removed outlier: 3.526A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.727A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 266 Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.817A pdb=" N VAL C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 288 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 290 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N PHE C 291 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 292 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.826A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 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 412 No H-bonds generated for 'chain 'C' and resid 409 through 412' 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 459 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 removed outlier: 3.567A pdb=" N ARG C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'D' and resid 3 through 53 removed outlier: 3.866A pdb=" N SER D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER D 20 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 109 Processing helix chain 'D' and resid 111 through 116 removed outlier: 4.209A pdb=" N GLY D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.825A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 removed outlier: 4.690A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix removed outlier: 3.564A pdb=" N ALA D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 185 Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 187 through 210 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 221 through 273 removed outlier: 3.631A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.675A pdb=" N ALA D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.757A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.743A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 418 through 424 removed outlier: 3.990A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 4.258A 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 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' 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 removed outlier: 3.565A pdb=" N ALA D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.877A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 571 Processing helix chain 'D' and resid 575 through 583 removed outlier: 3.593A pdb=" N HIS D 583 " --> pdb=" O THR D 579 " (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 549 through 554 removed outlier: 6.794A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 526 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE C 371 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET C 528 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.793A 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 Processing sheet with id= D, first strand: chain 'D' and resid 560 through 563 removed outlier: 6.644A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 552 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR D 537 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 381 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N MET D 539 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY D 383 " --> pdb=" O MET D 539 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1383 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: 2.85 Time building geometry restraints manager: 3.70 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: 2143 1.33 - 1.45: 1811 1.45 - 1.57: 5235 1.57 - 1.69: 10 1.69 - 1.81: 58 Bond restraints: 9257 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C5 ATP C 602 " pdb=" C6 ATP C 602 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.82e+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 2.68e+01 bond pdb=" C5 ATP C 602 " pdb=" N7 ATP C 602 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.93e+01 ... (remaining 9252 not shown) Histogram of bond angle deviations from ideal: 100.04 - 107.25: 320 107.25 - 114.47: 5457 114.47 - 121.68: 4882 121.68 - 128.90: 1850 128.90 - 136.12: 79 Bond angle restraints: 12588 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 139.87 119.44 20.43 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 121.12 15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 118.78 8.02 1.00e+00 1.00e+00 6.44e+01 angle pdb=" N3 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N9 ATP C 602 " ideal model delta sigma weight residual 127.04 135.02 -7.98 1.15e+00 7.59e-01 4.83e+01 angle pdb=" N1 ATP C 602 " pdb=" C2 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 128.69 123.67 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 12583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.76: 5090 19.76 - 39.51: 372 39.51 - 59.27: 67 59.27 - 79.02: 26 79.02 - 98.78: 5 Dihedral angle restraints: 5560 sinusoidal: 2233 harmonic: 3327 Sorted by residual: dihedral pdb=" CA LEU D 425 " pdb=" C LEU D 425 " pdb=" N SER D 426 " pdb=" CA SER D 426 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU C 106 " pdb=" C LEU C 106 " pdb=" N SER C 107 " pdb=" CA SER C 107 " ideal model delta harmonic sigma weight residual 180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA THR C 530 " pdb=" C THR C 530 " pdb=" N HIS C 531 " pdb=" CA HIS C 531 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1206 0.054 - 0.107: 215 0.107 - 0.161: 32 0.161 - 0.215: 3 0.215 - 0.269: 3 Chirality restraints: 1459 Sorted by residual: chirality pdb=" CB THR C 530 " pdb=" CA THR C 530 " pdb=" OG1 THR C 530 " pdb=" CG2 THR C 530 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 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 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE C 397 " pdb=" N ILE C 397 " pdb=" C ILE C 397 " pdb=" CB ILE C 397 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1456 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 114 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C TYR C 114 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR C 114 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 115 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 177 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 178 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 527 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C LEU C 527 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU C 527 " 0.010 2.00e-02 2.50e+03 pdb=" N MET C 528 " 0.009 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 46 2.50 - 3.10: 6455 3.10 - 3.70: 14221 3.70 - 4.30: 21409 4.30 - 4.90: 35450 Nonbonded interactions: 77581 Sorted by model distance: nonbonded pdb=" OE1 GLN D 430 " pdb="MG MG D 601 " model vdw 1.901 2.170 nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.903 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3G ANP D 602 " model vdw 1.907 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ANP D 602 " model vdw 1.929 2.170 nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 1.970 2.170 ... (remaining 77576 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: 0.990 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: 5.280 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.930 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 0.144 9257 Z= 0.350 Angle : 0.738 20.427 12588 Z= 0.476 Chirality : 0.044 0.269 1459 Planarity : 0.003 0.042 1602 Dihedral : 14.944 98.778 3414 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -0.78 (0.24), residues: 1155 helix: -0.45 (0.19), residues: 685 sheet: -0.45 (0.64), residues: 62 loop : -0.33 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 427 HIS 0.006 0.001 HIS D 542 PHE 0.016 0.001 PHE C 539 TYR 0.016 0.001 TYR D 88 ARG 0.005 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8500 (tttm) cc_final: 0.8137 (ttmt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.5112 time to fit residues: 182.1530 Evaluate side-chains 95 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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: 3.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.0030 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 208 GLN C 228 ASN ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 433 GLN ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9257 Z= 0.199 Angle : 0.553 6.680 12588 Z= 0.284 Chirality : 0.040 0.154 1459 Planarity : 0.004 0.038 1602 Dihedral : 9.594 85.802 1329 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.70 % Allowed : 8.60 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1155 helix: 0.97 (0.20), residues: 699 sheet: -0.16 (0.66), residues: 62 loop : -0.18 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 163 HIS 0.003 0.001 HIS D 204 PHE 0.015 0.001 PHE C 89 TYR 0.022 0.001 TYR D 88 ARG 0.004 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8455 (tttm) cc_final: 0.8115 (ttmt) REVERT: C 521 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8174 (mtp) REVERT: D 115 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: D 226 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7173 (tm-30) outliers start: 16 outliers final: 4 residues processed: 104 average time/residue: 1.5711 time to fit residues: 172.4900 Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9257 Z= 0.253 Angle : 0.528 6.514 12588 Z= 0.268 Chirality : 0.040 0.145 1459 Planarity : 0.004 0.041 1602 Dihedral : 8.651 85.375 1329 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 11.04 % Favored : 86.73 % 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: 1155 helix: 1.34 (0.20), residues: 715 sheet: -0.09 (0.64), residues: 62 loop : 0.02 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.017 0.001 PHE C 89 TYR 0.022 0.001 TYR D 88 ARG 0.005 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 171 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 186 LYS cc_start: 0.8427 (tttm) cc_final: 0.8161 (ttpt) REVERT: C 521 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: D 47 ARG cc_start: 0.7343 (mtp85) cc_final: 0.7087 (mtm180) REVERT: D 115 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: D 226 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: D 339 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: D 523 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7732 (mmt90) outliers start: 21 outliers final: 4 residues processed: 115 average time/residue: 1.3993 time to fit residues: 171.1344 Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 92 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9257 Z= 0.184 Angle : 0.491 6.559 12588 Z= 0.250 Chirality : 0.039 0.154 1459 Planarity : 0.004 0.042 1602 Dihedral : 7.755 81.135 1329 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.55 % Allowed : 11.68 % Favored : 85.77 % 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: 1.58 (0.25), residues: 1155 helix: 1.76 (0.20), residues: 701 sheet: 0.03 (0.65), residues: 62 loop : 0.02 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.003 0.001 HIS D 312 PHE 0.017 0.001 PHE C 89 TYR 0.022 0.001 TYR D 88 ARG 0.008 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 171 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 521 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8087 (mtp) REVERT: D 47 ARG cc_start: 0.7380 (mtp85) cc_final: 0.7111 (mmm160) REVERT: D 115 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: D 226 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: D 339 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7128 (mp0) outliers start: 24 outliers final: 5 residues processed: 108 average time/residue: 1.5396 time to fit residues: 176.2426 Evaluate side-chains 101 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 94 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9257 Z= 0.228 Angle : 0.511 7.721 12588 Z= 0.257 Chirality : 0.039 0.153 1459 Planarity : 0.004 0.050 1602 Dihedral : 7.440 77.516 1329 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.34 % Allowed : 12.42 % Favored : 85.24 % 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: 1.66 (0.25), residues: 1155 helix: 1.77 (0.20), residues: 713 sheet: 0.04 (0.65), residues: 62 loop : 0.12 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 PHE 0.017 0.001 PHE C 89 TYR 0.020 0.001 TYR D 88 ARG 0.010 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 521 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: D 47 ARG cc_start: 0.7378 (mtp85) cc_final: 0.7096 (mmm160) REVERT: D 115 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: D 226 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: D 336 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: D 339 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 523 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7739 (mmt90) outliers start: 22 outliers final: 7 residues processed: 104 average time/residue: 1.5479 time to fit residues: 170.1828 Evaluate side-chains 103 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 549 ASP 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: 2.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 111 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9257 Z= 0.177 Angle : 0.489 7.279 12588 Z= 0.247 Chirality : 0.038 0.139 1459 Planarity : 0.004 0.053 1602 Dihedral : 7.095 77.050 1329 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.65 % Allowed : 13.38 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1155 helix: 1.91 (0.20), residues: 708 sheet: 0.12 (0.65), residues: 62 loop : 0.11 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 PHE 0.017 0.001 PHE C 89 TYR 0.019 0.001 TYR D 88 ARG 0.011 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: C 521 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8122 (mtp) REVERT: D 47 ARG cc_start: 0.7388 (mtp85) cc_final: 0.7113 (mmm160) REVERT: D 226 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: D 339 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: D 523 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (mmt90) outliers start: 25 outliers final: 9 residues processed: 108 average time/residue: 1.4868 time to fit residues: 169.9514 Evaluate side-chains 105 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 339 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 0.0050 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 GLN D 115 GLN D 316 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9257 Z= 0.158 Angle : 0.479 7.206 12588 Z= 0.242 Chirality : 0.038 0.137 1459 Planarity : 0.004 0.056 1602 Dihedral : 6.869 79.615 1329 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 14.12 % Favored : 83.65 % 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 (0.25), residues: 1155 helix: 2.07 (0.20), residues: 708 sheet: 0.15 (0.64), residues: 62 loop : 0.11 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.016 0.001 TYR D 88 ARG 0.013 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.049 Fit side-chains REVERT: C 500 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: C 521 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8154 (mtp) REVERT: D 47 ARG cc_start: 0.7380 (mtp85) cc_final: 0.7092 (mmm160) REVERT: D 226 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6932 (tm-30) outliers start: 21 outliers final: 7 residues processed: 106 average time/residue: 1.5464 time to fit residues: 173.1720 Evaluate side-chains 99 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9257 Z= 0.182 Angle : 0.495 8.171 12588 Z= 0.249 Chirality : 0.038 0.133 1459 Planarity : 0.004 0.062 1602 Dihedral : 6.850 81.515 1329 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.12 % Allowed : 15.50 % Favored : 82.38 % 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: 1.99 (0.25), residues: 1155 helix: 2.10 (0.20), residues: 707 sheet: 0.19 (0.63), residues: 62 loop : 0.12 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 427 HIS 0.004 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.016 0.001 TYR D 88 ARG 0.014 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.063 Fit side-chains REVERT: C 521 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: D 47 ARG cc_start: 0.7397 (mtp85) cc_final: 0.7104 (mmm160) REVERT: D 336 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7392 (tm-30) outliers start: 20 outliers final: 6 residues processed: 100 average time/residue: 1.5713 time to fit residues: 166.2246 Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9257 Z= 0.201 Angle : 0.505 8.492 12588 Z= 0.253 Chirality : 0.038 0.134 1459 Planarity : 0.004 0.068 1602 Dihedral : 6.903 83.613 1329 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.12 % Allowed : 15.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1155 helix: 2.08 (0.20), residues: 708 sheet: 0.15 (0.62), residues: 62 loop : 0.13 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 427 HIS 0.005 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.015 0.001 TYR D 88 ARG 0.014 0.000 ARG D 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.989 Fit side-chains REVERT: C 519 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8142 (tp30) REVERT: C 521 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: D 47 ARG cc_start: 0.7410 (mtp85) cc_final: 0.7117 (mmm160) outliers start: 20 outliers final: 8 residues processed: 102 average time/residue: 1.4841 time to fit residues: 160.2148 Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 0.0060 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 0.039 9257 Z= 0.187 Angle : 0.509 8.901 12588 Z= 0.254 Chirality : 0.038 0.133 1459 Planarity : 0.004 0.068 1602 Dihedral : 6.803 87.473 1329 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.17 % Allowed : 16.24 % Favored : 82.59 % 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 (0.25), residues: 1155 helix: 2.13 (0.20), residues: 708 sheet: 0.18 (0.62), residues: 62 loop : 0.16 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 427 HIS 0.004 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.016 0.001 TYR D 88 ARG 0.015 0.000 ARG D 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.096 Fit side-chains REVERT: C 394 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6843 (pp30) REVERT: C 500 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: C 521 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8260 (mtp) REVERT: D 47 ARG cc_start: 0.7410 (mtp85) cc_final: 0.7121 (mmm160) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 1.5726 time to fit residues: 164.5041 Evaluate side-chains 100 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 549 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 93 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099042 restraints weight = 11828.710| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.61 r_work: 0.3020 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9257 Z= 0.171 Angle : 0.502 8.831 12588 Z= 0.250 Chirality : 0.038 0.134 1459 Planarity : 0.004 0.068 1602 Dihedral : 6.602 87.620 1329 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.27 % Allowed : 16.45 % Favored : 82.27 % 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: 2.08 (0.25), residues: 1155 helix: 2.17 (0.20), residues: 708 sheet: 0.23 (0.62), residues: 62 loop : 0.15 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 PHE 0.016 0.001 PHE C 89 TYR 0.015 0.001 TYR D 88 ARG 0.015 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3410.70 seconds wall clock time: 60 minutes 52.21 seconds (3652.21 seconds total)