Starting phenix.real_space_refine on Thu Mar 14 19:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/03_2024/6xwn_10632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/03_2024/6xwn_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_10632/03_2024/6xwn_10632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/03_2024/6xwn_10632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/03_2024/6xwn_10632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwn_10632/03_2024/6xwn_10632_updated.pdb" } resolution = 3.47 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= 0.002 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.11, per 1000 atoms: 0.54 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: 3.62 Conformation dependent library (CDL) restraints added in 1.8 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: 1.79 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: 2.63 Time building geometry restraints manager: 3.92 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: 4910 16.69 - 33.39: 640 33.39 - 50.08: 154 50.08 - 66.77: 32 66.77 - 83.46: 6 Dihedral angle restraints: 5742 sinusoidal: 2145 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 5739 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 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: 0.700 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: 0.000 Extract box with map and model: 3.980 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.790 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 15.889 83.463 3460 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 % Allowed : 18.10 % Favored : 73.90 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 16 HIS 0.004 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.010 0.001 TYR A 9 ARG 0.002 0.000 ARG B 179 *********************** 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 : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6773 (m-10) REVERT: A 365 MET cc_start: 0.6575 (ttm) cc_final: 0.6191 (ttm) REVERT: B 109 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6539 (m-10) outliers start: 80 outliers final: 44 residues processed: 193 average time/residue: 0.1583 time to fit residues: 45.9743 Evaluate side-chains 130 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 84 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 413 THR 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: 10.0000 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1484 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= 0.177 Angle : 0.561 9.057 13234 Z= 0.280 Chirality : 0.039 0.159 1647 Planarity : 0.005 0.058 1626 Dihedral : 7.998 59.920 1459 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.30 % Allowed : 22.70 % Favored : 74.00 % 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: -0.68 (0.23), residues: 1270 helix: 0.17 (0.16), residues: 987 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.011 0.001 PHE B 275 TYR 0.010 0.001 TYR A 238 ARG 0.003 0.000 ARG C 179 *********************** 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 121 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6636 (m-10) REVERT: A 365 MET cc_start: 0.6580 (ttm) cc_final: 0.6232 (ttm) REVERT: B 109 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6440 (m-10) outliers start: 33 outliers final: 17 residues processed: 117 average time/residue: 0.1719 time to fit residues: 31.0241 Evaluate side-chains 96 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 378 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1908 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= 0.165 Angle : 0.540 8.494 13234 Z= 0.267 Chirality : 0.039 0.149 1647 Planarity : 0.004 0.057 1626 Dihedral : 6.865 57.960 1406 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.50 % Allowed : 23.50 % Favored : 73.00 % 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: 0.23 (0.24), residues: 1270 helix: 0.81 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 16 HIS 0.004 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.009 0.001 TYR A 90 ARG 0.002 0.000 ARG C 401 *********************** 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 123 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6538 (m-10) REVERT: A 321 GLN cc_start: 0.6817 (mt0) cc_final: 0.6571 (mt0) REVERT: B 109 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6533 (m-10) REVERT: C 295 MET cc_start: 0.6487 (mmm) cc_final: 0.6096 (mmm) outliers start: 35 outliers final: 21 residues processed: 119 average time/residue: 0.1547 time to fit residues: 29.0872 Evaluate side-chains 102 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 424 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0470 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2321 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= 0.152 Angle : 0.539 8.536 13234 Z= 0.266 Chirality : 0.039 0.151 1647 Planarity : 0.004 0.055 1626 Dihedral : 6.447 57.970 1404 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.20 % Allowed : 24.30 % Favored : 72.50 % 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: 0.67 (0.24), residues: 1270 helix: 1.13 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -1.97 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.013 0.001 PHE A 100 TYR 0.009 0.001 TYR A 90 ARG 0.001 0.000 ARG C 401 *********************** 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 118 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6423 (m-10) REVERT: B 109 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6562 (m-10) REVERT: C 295 MET cc_start: 0.6437 (mmm) cc_final: 0.6012 (mmm) REVERT: C 365 MET cc_start: 0.7765 (mmm) cc_final: 0.7284 (mmt) outliers start: 32 outliers final: 19 residues processed: 114 average time/residue: 0.1576 time to fit residues: 28.3005 Evaluate side-chains 100 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9724 Z= 0.251 Angle : 0.569 8.049 13234 Z= 0.284 Chirality : 0.040 0.151 1647 Planarity : 0.004 0.055 1626 Dihedral : 6.424 57.738 1403 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.50 % Allowed : 23.50 % Favored : 73.00 % 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: 0.93 (0.24), residues: 1270 helix: 1.25 (0.17), residues: 997 sheet: None (None), residues: 0 loop : -1.68 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 20 HIS 0.003 0.001 HIS A 334 PHE 0.012 0.001 PHE B 302 TYR 0.010 0.001 TYR A 238 ARG 0.001 0.000 ARG C 401 *********************** 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 116 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6651 (m-10) REVERT: B 109 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6568 (m-10) REVERT: C 365 MET cc_start: 0.7690 (mmm) cc_final: 0.7311 (mmt) outliers start: 35 outliers final: 23 residues processed: 111 average time/residue: 0.1630 time to fit residues: 28.4412 Evaluate side-chains 103 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** 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: 0.7818 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9724 Z= 0.157 Angle : 0.549 8.977 13234 Z= 0.270 Chirality : 0.039 0.177 1647 Planarity : 0.004 0.055 1626 Dihedral : 6.294 57.277 1403 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.00 % Allowed : 25.00 % Favored : 72.00 % 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: 1.13 (0.25), residues: 1270 helix: 1.44 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 20 HIS 0.004 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.008 0.001 TYR B 217 ARG 0.002 0.000 ARG C 401 *********************** 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 118 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: C 295 MET cc_start: 0.6437 (mmm) cc_final: 0.5990 (mmm) REVERT: C 365 MET cc_start: 0.7640 (mmm) cc_final: 0.7326 (mmt) outliers start: 30 outliers final: 19 residues processed: 114 average time/residue: 0.1715 time to fit residues: 29.7640 Evaluate side-chains 100 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9724 Z= 0.188 Angle : 0.555 7.761 13234 Z= 0.273 Chirality : 0.040 0.204 1647 Planarity : 0.004 0.055 1626 Dihedral : 6.085 57.677 1399 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.80 % Allowed : 24.20 % Favored : 73.00 % 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: 1.35 (0.25), residues: 1270 helix: 1.58 (0.17), residues: 983 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 20 HIS 0.003 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.009 0.001 TYR A 320 ARG 0.001 0.000 ARG C 401 *********************** 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 108 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6568 (m-10) REVERT: C 295 MET cc_start: 0.6397 (mmm) cc_final: 0.5947 (mmm) REVERT: C 365 MET cc_start: 0.7698 (mmm) cc_final: 0.7360 (mmt) REVERT: C 371 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7303 (tm-30) outliers start: 28 outliers final: 21 residues processed: 102 average time/residue: 0.1631 time to fit residues: 25.9644 Evaluate side-chains 100 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 371 GLN 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: 0.7980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 0.0370 chunk 110 optimal weight: 0.1980 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 0.0770 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9724 Z= 0.146 Angle : 0.560 10.900 13234 Z= 0.276 Chirality : 0.039 0.223 1647 Planarity : 0.004 0.055 1626 Dihedral : 5.881 57.934 1398 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.00 % Allowed : 25.50 % Favored : 72.50 % 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: 1.48 (0.25), residues: 1270 helix: 1.66 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 16 HIS 0.003 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.010 0.001 TYR A 320 ARG 0.002 0.000 ARG A 225 *********************** 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 111 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: C 295 MET cc_start: 0.6341 (mmm) cc_final: 0.5971 (mmm) REVERT: C 365 MET cc_start: 0.7705 (mmm) cc_final: 0.7231 (mmt) REVERT: C 371 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7324 (tm-30) outliers start: 20 outliers final: 16 residues processed: 106 average time/residue: 0.1689 time to fit residues: 27.8907 Evaluate side-chains 106 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 371 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7810 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9724 Z= 0.163 Angle : 0.555 9.305 13234 Z= 0.274 Chirality : 0.039 0.225 1647 Planarity : 0.004 0.055 1626 Dihedral : 5.507 58.612 1394 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.00 % Allowed : 26.60 % Favored : 71.40 % 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: 1.57 (0.25), residues: 1270 helix: 1.74 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.001 PHE B 302 TYR 0.013 0.001 TYR A 320 ARG 0.002 0.000 ARG C 401 *********************** 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 108 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6572 (m-10) REVERT: B 109 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: C 215 ILE cc_start: 0.8812 (tp) cc_final: 0.8536 (tp) REVERT: C 295 MET cc_start: 0.6311 (mmm) cc_final: 0.5920 (mmm) REVERT: C 365 MET cc_start: 0.7737 (mmm) cc_final: 0.7249 (mmt) outliers start: 20 outliers final: 17 residues processed: 104 average time/residue: 0.1642 time to fit residues: 26.6672 Evaluate side-chains 102 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 125 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7809 moved from start: 0.3293 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= 0.167 Angle : 0.581 11.619 13234 Z= 0.287 Chirality : 0.040 0.226 1647 Planarity : 0.004 0.055 1626 Dihedral : 5.509 58.943 1394 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.20 % Allowed : 27.00 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1270 helix: 1.73 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.024 0.001 TYR A 320 ARG 0.002 0.000 ARG C 401 ********************** 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 105 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6653 (m-10) REVERT: B 109 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6588 (m-10) REVERT: C 215 ILE cc_start: 0.8811 (tp) cc_final: 0.8545 (tp) REVERT: C 295 MET cc_start: 0.6323 (mmm) cc_final: 0.5923 (mmm) REVERT: C 365 MET cc_start: 0.7770 (mmm) cc_final: 0.7308 (mmt) REVERT: C 371 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7333 (tm-30) outliers start: 22 outliers final: 17 residues processed: 101 average time/residue: 0.1583 time to fit residues: 25.1460 Evaluate side-chains 104 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3251 r_free = 0.3251 target = 0.061407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051671 restraints weight = 40569.584| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.46 r_work: 0.2878 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9724 Z= 0.156 Angle : 0.573 11.023 13234 Z= 0.280 Chirality : 0.039 0.227 1647 Planarity : 0.004 0.055 1626 Dihedral : 5.481 59.344 1394 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.90 % Allowed : 27.20 % Favored : 70.90 % 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: 1.66 (0.25), residues: 1270 helix: 1.80 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 428 HIS 0.003 0.001 HIS A 334 PHE 0.014 0.001 PHE B 302 TYR 0.020 0.001 TYR A 320 ARG 0.002 0.000 ARG C 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.66 seconds wall clock time: 34 minutes 14.34 seconds (2054.34 seconds total)