Starting phenix.real_space_refine on Tue Nov 14 16:14:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdt_14669/11_2023/7zdt_14669_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdt_14669/11_2023/7zdt_14669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdt_14669/11_2023/7zdt_14669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdt_14669/11_2023/7zdt_14669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdt_14669/11_2023/7zdt_14669_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdt_14669/11_2023/7zdt_14669_neut_updated.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 5761 2.51 5 N 1584 2.21 5 O 1624 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 GLU 80": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 73": "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 159": "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 ASP 234": "OD1" <-> "OD2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D GLU 452": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ARG 523": "NH1" <-> "NH2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D GLU 569": "OE1" <-> "OE2" Residue "D PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9003 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4425 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "D" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4546 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 27, 'TRANS': 555} 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} Time building chain proxies: 5.23, per 1000 atoms: 0.58 Number of scatterers: 9003 At special positions: 0 Unit cell: (137.268, 77.841, 100.44, 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 3 15.00 Mg 1 11.99 O 1624 8.00 N 1584 7.00 C 5761 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: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 63.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'C' and resid 2 through 11 Proline residue: C 6 - end of helix removed outlier: 3.696A pdb=" N ALA C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 49 removed outlier: 3.654A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 102 removed outlier: 3.585A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.750A 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 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 116 through 135 removed outlier: 4.687A pdb=" N VAL C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N HIS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 removed outlier: 3.768A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 208 Proline residue: C 178 - end of helix removed outlier: 4.649A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.782A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 268 removed outlier: 3.596A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.772A pdb=" N VAL C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 288 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C 290 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE C 291 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 318 removed outlier: 4.570A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (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 413 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 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 18 removed outlier: 3.825A pdb=" N SER D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 54 Processing helix chain 'D' and resid 64 through 116 removed outlier: 3.702A pdb=" N GLY D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Proline residue: D 111 - end of helix removed outlier: 4.109A 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: 3.819A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 removed outlier: 4.767A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 3.837A 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 Proline residue: D 174 - end of helix Proline residue: D 177 - end of helix removed outlier: 5.428A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 221 through 273 removed outlier: 3.652A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 327 Proline residue: D 298 - end of helix removed outlier: 3.625A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.703A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 removed outlier: 3.695A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) 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: 3.625A pdb=" N LYS D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.587A pdb=" N LEU D 445 " --> pdb=" O ASP D 441 " (cutoff:3.500A) 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 499 Processing helix chain 'D' and resid 518 through 532 removed outlier: 3.546A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 572 removed outlier: 3.997A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 582 Processing sheet with id= A, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.656A 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: 6.998A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL C 526 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE C 371 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET C 528 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.656A 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: 6.772A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.624A 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: 7.630A pdb=" N LEU D 381 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET D 539 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLY D 383 " --> pdb=" O MET D 539 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1536 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: 2.74 Time building geometry restraints manager: 3.99 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: 1923 1.33 - 1.45: 1980 1.45 - 1.57: 5217 1.57 - 1.69: 5 1.69 - 1.81: 57 Bond restraints: 9182 Sorted by residual: bond pdb=" N GLN C 500 " pdb=" CA GLN C 500 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.10e-03 1.21e+04 1.17e+01 bond pdb=" N GLN D 302 " pdb=" CA GLN D 302 " ideal model delta sigma weight residual 1.462 1.486 -0.024 7.70e-03 1.69e+04 9.48e+00 bond pdb=" N PHE D 159 " pdb=" CA PHE D 159 " ideal model delta sigma weight residual 1.461 1.488 -0.026 9.20e-03 1.18e+04 8.26e+00 bond pdb=" N GLU C 460 " pdb=" CA GLU C 460 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.34e-02 5.57e+03 7.62e+00 bond pdb=" N GLN C 351 " pdb=" CA GLN C 351 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 6.96e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.53: 253 106.53 - 113.46: 5112 113.46 - 120.40: 3628 120.40 - 127.33: 3380 127.33 - 134.26: 107 Bond angle restraints: 12480 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 139.87 133.93 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 132.97 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA GLN C 500 " pdb=" C GLN C 500 " pdb=" O GLN C 500 " ideal model delta sigma weight residual 120.47 117.97 2.50 6.90e-01 2.10e+00 1.31e+01 angle pdb=" CA THR C 502 " pdb=" C THR C 502 " pdb=" O THR C 502 " ideal model delta sigma weight residual 122.63 117.97 4.66 1.29e+00 6.01e-01 1.31e+01 angle pdb=" CA ASP C 461 " pdb=" C ASP C 461 " pdb=" N ALA C 462 " ideal model delta sigma weight residual 119.98 117.02 2.96 8.50e-01 1.38e+00 1.21e+01 ... (remaining 12475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 4885 16.15 - 32.29: 456 32.29 - 48.43: 102 48.43 - 64.58: 16 64.58 - 80.72: 8 Dihedral angle restraints: 5467 sinusoidal: 2154 harmonic: 3313 Sorted by residual: dihedral pdb=" CA ARG C 473 " pdb=" C ARG C 473 " pdb=" N GLN C 474 " pdb=" CA GLN C 474 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+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 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ARG C 136 " pdb=" C ARG C 136 " pdb=" N VAL C 137 " pdb=" CA VAL C 137 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1098 0.044 - 0.087: 255 0.087 - 0.131: 76 0.131 - 0.175: 17 0.175 - 0.218: 3 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CA PHE C 181 " pdb=" N PHE C 181 " pdb=" C PHE C 181 " pdb=" CB PHE C 181 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG C 534 " pdb=" N ARG C 534 " pdb=" C ARG C 534 " pdb=" CB ARG C 534 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG C 538 " pdb=" N ARG C 538 " pdb=" C ARG C 538 " pdb=" CB ARG C 538 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1446 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 61 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO C 62 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 158 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C ILE D 158 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE D 158 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE D 159 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 159 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C PHE D 159 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE D 159 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO D 160 " 0.011 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 49 2.54 - 3.13: 6755 3.13 - 3.72: 14425 3.72 - 4.31: 20938 4.31 - 4.90: 34934 Nonbonded interactions: 77101 Sorted by model distance: nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 1.945 2.170 nonbonded pdb=" N GLU D 545 " pdb=" OE1 GLU D 545 " model vdw 2.204 2.520 nonbonded pdb="MG MG C 601 " pdb=" O1B ATP C 602 " model vdw 2.215 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.228 2.170 nonbonded pdb=" NH2 ARG D 337 " pdb=" OE1 GLU D 419 " model vdw 2.257 2.520 ... (remaining 77096 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.250 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.160 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 0.047 9182 Z= 0.318 Angle : 0.662 7.561 12480 Z= 0.416 Chirality : 0.044 0.218 1449 Planarity : 0.004 0.052 1593 Dihedral : 13.487 80.724 3331 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -0.81 (0.23), residues: 1151 helix: -0.62 (0.18), residues: 712 sheet: 0.22 (0.67), residues: 63 loop : -0.10 (0.30), residues: 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.924 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.5469 time to fit residues: 205.9352 Evaluate side-chains 97 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 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 210 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9182 Z= 0.210 Angle : 0.530 6.161 12480 Z= 0.279 Chirality : 0.040 0.152 1449 Planarity : 0.004 0.050 1593 Dihedral : 5.027 85.083 1261 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.07 % Allowed : 8.00 % Favored : 90.93 % 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: 1.21 (0.24), residues: 1151 helix: 1.27 (0.19), residues: 719 sheet: 0.26 (0.63), residues: 63 loop : 0.15 (0.31), residues: 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.076 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 107 average time/residue: 1.4366 time to fit residues: 163.4590 Evaluate side-chains 90 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1253 time to fit residues: 1.9070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9182 Z= 0.190 Angle : 0.494 7.765 12480 Z= 0.256 Chirality : 0.038 0.145 1449 Planarity : 0.004 0.047 1593 Dihedral : 4.809 79.269 1261 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.13 % Allowed : 8.96 % Favored : 88.90 % 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: 1.94 (0.24), residues: 1151 helix: 2.00 (0.19), residues: 712 sheet: 0.20 (0.62), residues: 63 loop : 0.19 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.079 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 106 average time/residue: 1.5591 time to fit residues: 175.1553 Evaluate side-chains 97 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1343 time to fit residues: 2.0587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9182 Z= 0.284 Angle : 0.532 6.337 12480 Z= 0.275 Chirality : 0.041 0.151 1449 Planarity : 0.004 0.046 1593 Dihedral : 4.851 76.536 1261 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.45 % Allowed : 9.61 % Favored : 87.94 % 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: 1.99 (0.24), residues: 1151 helix: 2.07 (0.19), residues: 712 sheet: 0.14 (0.61), residues: 63 loop : 0.16 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.182 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 105 average time/residue: 1.5448 time to fit residues: 171.8048 Evaluate side-chains 102 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1272 time to fit residues: 2.4019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 GLN D 557 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9182 Z= 0.174 Angle : 0.468 6.197 12480 Z= 0.244 Chirality : 0.038 0.140 1449 Planarity : 0.003 0.043 1593 Dihedral : 4.677 75.058 1261 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.92 % Allowed : 10.78 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1151 helix: 2.34 (0.19), residues: 711 sheet: 0.00 (0.61), residues: 63 loop : 0.28 (0.31), residues: 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.949 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 1.5263 time to fit residues: 174.4842 Evaluate side-chains 99 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1225 time to fit residues: 2.4141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 ASN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9182 Z= 0.366 Angle : 0.563 7.275 12480 Z= 0.289 Chirality : 0.043 0.150 1449 Planarity : 0.004 0.043 1593 Dihedral : 4.889 75.193 1261 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.13 % Allowed : 11.85 % Favored : 86.02 % 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: 2.01 (0.24), residues: 1151 helix: 2.11 (0.19), residues: 706 sheet: 0.01 (0.61), residues: 63 loop : 0.15 (0.31), residues: 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.921 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 1.6875 time to fit residues: 174.5685 Evaluate side-chains 100 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 0.1413 time to fit residues: 2.9000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9182 Z= 0.195 Angle : 0.479 6.242 12480 Z= 0.249 Chirality : 0.038 0.139 1449 Planarity : 0.004 0.041 1593 Dihedral : 4.717 74.026 1261 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.17 % Allowed : 12.81 % Favored : 86.02 % 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: 2.28 (0.25), residues: 1151 helix: 2.33 (0.19), residues: 712 sheet: -0.04 (0.60), residues: 63 loop : 0.26 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.086 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 1.5432 time to fit residues: 161.9515 Evaluate side-chains 97 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1675 time to fit residues: 2.0184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9182 Z= 0.162 Angle : 0.456 6.305 12480 Z= 0.238 Chirality : 0.037 0.137 1449 Planarity : 0.004 0.041 1593 Dihedral : 4.590 72.691 1261 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.39 % Allowed : 12.59 % Favored : 86.02 % 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: 2.49 (0.25), residues: 1151 helix: 2.52 (0.19), residues: 712 sheet: -0.11 (0.59), residues: 63 loop : 0.32 (0.32), residues: 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.063 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 1.5146 time to fit residues: 168.7041 Evaluate side-chains 101 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0818 time to fit residues: 1.5040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 GLN D 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9182 Z= 0.238 Angle : 0.503 7.358 12480 Z= 0.259 Chirality : 0.039 0.140 1449 Planarity : 0.004 0.041 1593 Dihedral : 4.685 73.111 1261 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.39 % Allowed : 13.23 % Favored : 85.38 % 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: 2.35 (0.25), residues: 1151 helix: 2.40 (0.19), residues: 712 sheet: 0.03 (0.64), residues: 58 loop : 0.23 (0.31), residues: 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.997 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 1.4836 time to fit residues: 157.4900 Evaluate side-chains 101 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.4086 time to fit residues: 3.3263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9182 Z= 0.329 Angle : 0.549 8.395 12480 Z= 0.282 Chirality : 0.042 0.146 1449 Planarity : 0.004 0.041 1593 Dihedral : 4.856 74.165 1261 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.85 % Allowed : 13.66 % Favored : 85.49 % 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: 2.11 (0.25), residues: 1151 helix: 2.20 (0.19), residues: 712 sheet: -0.01 (0.65), residues: 58 loop : 0.16 (0.31), residues: 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.065 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 1.5778 time to fit residues: 160.2409 Evaluate side-chains 97 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1308 time to fit residues: 1.4675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.096768 restraints weight = 11128.683| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.53 r_work: 0.2955 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 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 : 0.004 0.054 9182 Z= 0.265 Angle : 0.517 7.844 12480 Z= 0.268 Chirality : 0.040 0.143 1449 Planarity : 0.004 0.042 1593 Dihedral : 4.804 73.576 1261 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.17 % Allowed : 13.45 % Favored : 85.38 % 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: 2.15 (0.25), residues: 1151 helix: 2.25 (0.19), residues: 713 sheet: -0.06 (0.64), residues: 58 loop : 0.14 (0.31), residues: 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3462.72 seconds wall clock time: 62 minutes 26.65 seconds (3746.65 seconds total)