Starting phenix.real_space_refine (version: dev) on Mon Apr 4 22:59:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/04_2022/6xwn_10632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/04_2022/6xwn_10632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/04_2022/6xwn_10632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/04_2022/6xwn_10632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/04_2022/6xwn_10632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/04_2022/6xwn_10632_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.018 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C GLU 422": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9547 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3184 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3151 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TB1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'TB1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.72, per 1000 atoms: 0.60 Number of scatterers: 9547 At special positions: 0 Unit cell: (82.984, 107.272, 108.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1662 8.00 N 1539 7.00 C 6298 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: 3.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 0 sheets defined 70.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 No H-bonds generated for 'chain 'A' and resid 6 through 9' Processing helix chain 'A' and resid 14 through 34 Processing helix chain 'A' and resid 38 through 41 No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.710A pdb=" N MET A 61 " --> pdb=" O MET A 58 " (cutoff:3.500A) Proline residue: A 62 - end of helix removed outlier: 4.084A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER A 67 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 68 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 109 removed outlier: 3.950A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 177 through 221 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 260 through 277 removed outlier: 5.415A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 299 through 311 removed outlier: 4.084A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 316 through 332 removed outlier: 4.253A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.695A pdb=" N VAL A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 394 through 418 removed outlier: 4.401A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'B' and resid 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 15 through 32 removed outlier: 4.497A pdb=" N LEU B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP B 20 " --> pdb=" O TRP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.268A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N MET B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix Processing helix chain 'B' and resid 77 through 109 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 176 through 221 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 229 through 255 removed outlier: 4.153A pdb=" N TYR B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 removed outlier: 5.396A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 302 through 309 Proline residue: B 307 - end of helix Processing helix chain 'B' and resid 315 through 331 removed outlier: 3.750A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.744A pdb=" N ILE B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 382 through 420 removed outlier: 3.874A pdb=" N ILE B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 34 removed outlier: 3.643A pdb=" N LEU C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 46 through 72 removed outlier: 4.378A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N MET C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 77 through 109 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.508A pdb=" N LYS C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 172 removed outlier: 3.940A pdb=" N ASN C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 203 Processing helix chain 'C' and resid 207 through 221 Processing helix chain 'C' and resid 228 through 255 removed outlier: 3.991A pdb=" N LYS C 232 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 233 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 234 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 239 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 242 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 245 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 247 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 248 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR C 249 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 250 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'C' and resid 338 through 355 Processing helix chain 'C' and resid 365 through 373 removed outlier: 4.249A pdb=" N VAL C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.779A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 420 removed outlier: 4.714A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1746 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: 2.52 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2963 1.34 - 1.46: 1423 1.46 - 1.57: 5242 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 9724 Sorted by residual: bond pdb=" C10 TB1 C 501 " pdb=" C7 TB1 C 501 " ideal model delta sigma weight residual 1.548 1.523 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C1 TB1 B 501 " pdb=" C4 TB1 B 501 " ideal model delta sigma weight residual 1.503 1.526 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C10 TB1 B 501 " pdb=" C7 TB1 B 501 " ideal model delta sigma weight residual 1.548 1.525 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C11 TB1 C 501 " pdb=" C9 TB1 C 501 " ideal model delta sigma weight residual 1.545 1.524 0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C1 TB1 C 501 " pdb=" C4 TB1 C 501 " ideal model delta sigma weight residual 1.503 1.523 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 9719 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.38: 268 106.38 - 113.30: 5560 113.30 - 120.22: 3718 120.22 - 127.14: 3612 127.14 - 134.05: 76 Bond angle restraints: 13234 Sorted by residual: angle pdb=" N ALA A 124 " pdb=" CA ALA A 124 " pdb=" C ALA A 124 " ideal model delta sigma weight residual 114.56 109.66 4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N VAL C 276 " pdb=" CA VAL C 276 " pdb=" C VAL C 276 " ideal model delta sigma weight residual 113.53 110.25 3.28 9.80e-01 1.04e+00 1.12e+01 angle pdb=" N ALA A 207 " pdb=" CA ALA A 207 " pdb=" C ALA A 207 " ideal model delta sigma weight residual 109.81 116.00 -6.19 2.21e+00 2.05e-01 7.84e+00 angle pdb=" CA LEU B 15 " pdb=" CB LEU B 15 " pdb=" CG LEU B 15 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 angle pdb=" C VAL A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta sigma weight residual 121.54 126.76 -5.22 1.91e+00 2.74e-01 7.47e+00 ... (remaining 13229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4909 16.69 - 33.39: 625 33.39 - 50.08: 141 50.08 - 66.77: 31 66.77 - 83.46: 6 Dihedral angle restraints: 5712 sinusoidal: 2115 harmonic: 3597 Sorted by residual: dihedral pdb=" CA TRP C 16 " pdb=" C TRP C 16 " pdb=" N LYS C 17 " pdb=" CA LYS C 17 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN A 340 " pdb=" C GLN A 340 " pdb=" N GLN A 341 " pdb=" CA GLN A 341 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN B 330 " pdb=" CB ASN B 330 " pdb=" CG ASN B 330 " pdb=" OD1 ASN B 330 " ideal model delta sinusoidal sigma weight residual 120.00 -174.56 -65.44 2 2.00e+01 2.50e-03 9.93e+00 ... (remaining 5709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1153 0.038 - 0.076: 396 0.076 - 0.113: 87 0.113 - 0.151: 9 0.151 - 0.189: 2 Chirality restraints: 1647 Sorted by residual: chirality pdb=" C7 TB1 B 501 " pdb=" N TB1 B 501 " pdb=" C10 TB1 B 501 " pdb=" C11 TB1 B 501 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" C7 TB1 C 501 " pdb=" N TB1 C 501 " pdb=" C10 TB1 C 501 " pdb=" C11 TB1 C 501 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ASN A 116 " pdb=" N ASN A 116 " pdb=" C ASN A 116 " pdb=" CB ASN A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 1644 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 245 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C ILE C 245 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 245 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL C 246 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 46 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 47 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 207 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO B 208 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " -0.029 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 127 2.68 - 3.23: 10011 3.23 - 3.79: 15519 3.79 - 4.34: 20345 4.34 - 4.90: 34005 Nonbonded interactions: 80007 Sorted by model distance: nonbonded pdb=" O LYS C 299 " pdb=" OG SER C 303 " model vdw 2.121 2.440 nonbonded pdb=" OG SER C 67 " pdb=" OH TYR C 197 " model vdw 2.140 2.440 nonbonded pdb=" O MET C 368 " pdb=" OG SER C 372 " model vdw 2.193 2.440 nonbonded pdb=" O THR C 378 " pdb=" OG SER C 381 " model vdw 2.198 2.440 nonbonded pdb=" O ILE B 63 " pdb=" OG SER B 67 " model vdw 2.218 2.440 ... (remaining 80002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 430) selection = (chain 'B' and resid 8 through 430) selection = (chain 'C' and resid 8 through 430) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6298 2.51 5 N 1539 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.850 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: 4.240 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 28.140 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 : 0.004 0.035 9724 Z= 0.269 Angle : 0.614 9.699 13234 Z= 0.332 Chirality : 0.039 0.189 1647 Planarity : 0.005 0.052 1626 Dihedral : 15.635 83.463 3430 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 8.00 % 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: -2.83 (0.20), residues: 1270 helix: -1.39 (0.14), residues: 988 sheet: None (None), residues: 0 loop : -3.05 (0.32), residues: 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 119 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 44 residues processed: 193 average time/residue: 0.1703 time to fit residues: 49.9905 Evaluate side-chains 129 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 85 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1031 time to fit residues: 10.5074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 110 ASN B 128 GLN B 134 GLN B 205 GLN B 244 GLN B 330 ASN B 340 GLN C 321 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9724 Z= 0.186 Angle : 0.567 9.096 13234 Z= 0.284 Chirality : 0.040 0.138 1647 Planarity : 0.005 0.058 1626 Dihedral : 3.895 23.230 1361 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1270 helix: 0.12 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.57 (0.33), residues: 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 113 average time/residue: 0.1805 time to fit residues: 31.1527 Evaluate side-chains 87 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0912 time to fit residues: 3.2062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.9650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 9724 Z= 0.169 Angle : 0.542 8.632 13234 Z= 0.268 Chirality : 0.039 0.149 1647 Planarity : 0.004 0.057 1626 Dihedral : 3.708 20.781 1361 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.90 % 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: 0.17 (0.24), residues: 1270 helix: 0.78 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 102 average time/residue: 0.1695 time to fit residues: 26.9853 Evaluate side-chains 84 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0873 time to fit residues: 2.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0020 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9724 Z= 0.177 Angle : 0.543 8.593 13234 Z= 0.269 Chirality : 0.039 0.174 1647 Planarity : 0.004 0.056 1626 Dihedral : 3.634 19.205 1361 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1270 helix: 1.16 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -1.92 (0.34), residues: 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 99 average time/residue: 0.1623 time to fit residues: 25.5636 Evaluate side-chains 85 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0952 time to fit residues: 2.1305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9724 Z= 0.286 Angle : 0.595 8.021 13234 Z= 0.297 Chirality : 0.041 0.150 1647 Planarity : 0.004 0.057 1626 Dihedral : 3.682 21.860 1361 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.40 % 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: 0.90 (0.24), residues: 1270 helix: 1.23 (0.17), residues: 997 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 95 average time/residue: 0.1646 time to fit residues: 24.5012 Evaluate side-chains 85 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0923 time to fit residues: 2.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.0040 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9724 Z= 0.159 Angle : 0.553 8.078 13234 Z= 0.271 Chirality : 0.039 0.160 1647 Planarity : 0.004 0.056 1626 Dihedral : 3.598 17.923 1361 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1270 helix: 1.46 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 0.1851 time to fit residues: 26.8326 Evaluate side-chains 81 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0925 time to fit residues: 1.8014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9724 Z= 0.162 Angle : 0.549 8.310 13234 Z= 0.269 Chirality : 0.039 0.201 1647 Planarity : 0.004 0.056 1626 Dihedral : 3.563 17.683 1361 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.90 % 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: 1.34 (0.25), residues: 1270 helix: 1.57 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.1795 time to fit residues: 25.8422 Evaluate side-chains 82 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1063 time to fit residues: 2.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 95 optimal weight: 0.3980 chunk 110 optimal weight: 0.0970 chunk 116 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 222 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9724 Z= 0.145 Angle : 0.554 9.651 13234 Z= 0.272 Chirality : 0.039 0.225 1647 Planarity : 0.004 0.055 1626 Dihedral : 3.553 18.696 1361 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.90 % 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: 1.54 (0.25), residues: 1270 helix: 1.72 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -1.34 (0.36), residues: 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.1818 time to fit residues: 27.1427 Evaluate side-chains 88 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1009 time to fit residues: 2.4173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9724 Z= 0.209 Angle : 0.584 11.145 13234 Z= 0.289 Chirality : 0.040 0.250 1647 Planarity : 0.004 0.055 1626 Dihedral : 3.542 17.869 1361 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.40 % 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: 1.59 (0.25), residues: 1270 helix: 1.72 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.33 (0.36), residues: 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 87 average time/residue: 0.1904 time to fit residues: 25.1840 Evaluate side-chains 84 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1041 time to fit residues: 1.8166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 106 optimal weight: 3.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9724 Z= 0.178 Angle : 0.577 10.025 13234 Z= 0.286 Chirality : 0.040 0.246 1647 Planarity : 0.004 0.055 1626 Dihedral : 3.546 17.993 1361 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.50 % 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: 1.62 (0.25), residues: 1270 helix: 1.75 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -1.33 (0.36), residues: 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 0.1736 time to fit residues: 24.1354 Evaluate side-chains 84 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0948 time to fit residues: 1.7090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.051648 restraints weight = 40760.500| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.53 r_work: 0.2969 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work: 0.2953 rms_B_bonded: 3.30 restraints_weight: 0.1250 r_work: 0.2945 rms_B_bonded: 3.35 restraints_weight: 0.0625 r_work: 0.2937 rms_B_bonded: 3.42 restraints_weight: 0.0312 r_work: 0.2928 rms_B_bonded: 3.51 restraints_weight: 0.0156 r_work: 0.2920 rms_B_bonded: 3.62 restraints_weight: 0.0078 r_work: 0.2911 rms_B_bonded: 3.74 restraints_weight: 0.0039 r_work: 0.2902 rms_B_bonded: 3.88 restraints_weight: 0.0020 r_work: 0.2892 rms_B_bonded: 4.04 restraints_weight: 0.0010 r_work: 0.2883 rms_B_bonded: 4.21 restraints_weight: 0.0005 r_work: 0.2873 rms_B_bonded: 4.40 restraints_weight: 0.0002 r_work: 0.2862 rms_B_bonded: 4.60 restraints_weight: 0.0001 r_work: 0.2852 rms_B_bonded: 4.82 restraints_weight: 0.0001 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9724 Z= 0.162 Angle : 0.596 10.813 13234 Z= 0.292 Chirality : 0.040 0.244 1647 Planarity : 0.004 0.055 1626 Dihedral : 3.539 18.478 1361 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.00 % 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: 1270 helix: 1.74 (0.17), residues: 983 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 287 =============================================================================== Job complete usr+sys time: 1736.99 seconds wall clock time: 32 minutes 32.98 seconds (1952.98 seconds total)