Starting phenix.real_space_refine (version: dev) on Tue Apr 5 00:29:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt9_0506/04_2022/6nt9_0506.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt9_0506/04_2022/6nt9_0506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt9_0506/04_2022/6nt9_0506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt9_0506/04_2022/6nt9_0506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt9_0506/04_2022/6nt9_0506.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt9_0506/04_2022/6nt9_0506.pdb" } resolution = 3.3 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= 0.001 sd= 0.009 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 27": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" 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: 9906 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4881 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 585} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "B" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4881 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 585} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Time building chain proxies: 5.96, per 1000 atoms: 0.60 Number of scatterers: 9906 At special positions: 0 Unit cell: (80.25, 114.49, 144.45, 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 1852 8.00 N 1692 7.00 C 6314 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: 3.80 Conformation dependent library (CDL) restraints added in 1.6 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 55.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 50 through 61 removed outlier: 3.751A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.524A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 108 through 130 removed outlier: 3.684A pdb=" N ASN A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.731A pdb=" N GLY A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.943A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.836A pdb=" N PHE A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 removed outlier: 3.597A pdb=" N PHE A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.776A pdb=" N PHE A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 483 removed outlier: 3.802A pdb=" N SER A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 527 removed outlier: 3.882A pdb=" N LYS A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 removed outlier: 3.857A pdb=" N HIS A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 572 removed outlier: 3.751A pdb=" N LEU A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 605 removed outlier: 3.808A pdb=" N TYR A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 658 removed outlier: 4.057A pdb=" N GLU A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 removed outlier: 3.751A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 removed outlier: 3.525A pdb=" N VAL B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 108 through 130 removed outlier: 3.683A pdb=" N ASN B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.731A pdb=" N GLY B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.943A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.835A pdb=" N PHE B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 344 removed outlier: 3.598A pdb=" N PHE B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.775A pdb=" N PHE B 370 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 483 removed outlier: 3.803A pdb=" N SER B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 527 removed outlier: 3.883A pdb=" N LYS B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 539 removed outlier: 3.857A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 572 removed outlier: 3.750A pdb=" N LEU B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 605 removed outlier: 3.808A pdb=" N TYR B 591 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 658 removed outlier: 4.057A pdb=" N GLU B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.548A pdb=" N ARG A 25 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 14 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3 removed outlier: 5.055A pdb=" N LYS A 82 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 72 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.593A pdb=" N SER A 247 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 326 removed outlier: 9.695A pdb=" N ILE A 379 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N HIS A 312 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 381 " --> pdb=" O HIS A 312 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 314 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 352 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.548A pdb=" N ARG B 25 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 14 " --> pdb=" O ARG B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 3 removed outlier: 5.055A pdb=" N LYS B 82 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 72 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 145 Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.593A pdb=" N SER B 247 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 320 through 326 removed outlier: 9.695A pdb=" N ILE B 379 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS B 312 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL B 381 " --> pdb=" O HIS B 312 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE B 314 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B 352 " --> pdb=" O LEU B 359 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1728 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: 3.08 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2878 1.33 - 1.45: 1642 1.45 - 1.57: 5508 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 10104 Sorted by residual: bond pdb=" CB VAL B 381 " pdb=" CG2 VAL B 381 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.82e+00 bond pdb=" CB VAL A 381 " pdb=" CG2 VAL A 381 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 bond pdb=" CB ILE B 418 " pdb=" CG2 ILE B 418 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CB ILE A 418 " pdb=" CG2 ILE A 418 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CG LEU C 374 " pdb=" CD2 LEU C 374 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 ... (remaining 10099 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.80: 140 104.80 - 112.11: 4966 112.11 - 119.42: 3606 119.42 - 126.73: 4792 126.73 - 134.04: 138 Bond angle restraints: 13642 Sorted by residual: angle pdb=" C GLY A 175 " pdb=" N THR A 176 " pdb=" CA THR A 176 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C GLY B 175 " pdb=" N THR B 176 " pdb=" CA THR B 176 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C PRO D 371 " pdb=" N GLN D 372 " pdb=" CA GLN D 372 " ideal model delta sigma weight residual 122.15 133.45 -11.30 3.47e+00 8.31e-02 1.06e+01 angle pdb=" C PRO C 371 " pdb=" N GLN C 372 " pdb=" CA GLN C 372 " ideal model delta sigma weight residual 122.15 133.41 -11.26 3.47e+00 8.31e-02 1.05e+01 angle pdb=" C GLY B 294 " pdb=" N PHE B 295 " pdb=" CA PHE B 295 " ideal model delta sigma weight residual 122.09 116.95 5.14 1.79e+00 3.12e-01 8.23e+00 ... (remaining 13637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 5778 14.55 - 29.10: 232 29.10 - 43.64: 76 43.64 - 58.19: 6 58.19 - 72.74: 6 Dihedral angle restraints: 6098 sinusoidal: 2516 harmonic: 3582 Sorted by residual: dihedral pdb=" CA TRP A 293 " pdb=" C TRP A 293 " pdb=" N GLY A 294 " pdb=" CA GLY A 294 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TRP B 293 " pdb=" C TRP B 293 " pdb=" N GLY B 294 " pdb=" CA GLY B 294 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG B 308 " pdb=" C ARG B 308 " pdb=" N MET B 309 " pdb=" CA MET B 309 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1015 0.051 - 0.103: 424 0.103 - 0.154: 81 0.154 - 0.205: 8 0.205 - 0.257: 4 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE B 73 " pdb=" CA ILE B 73 " pdb=" CG1 ILE B 73 " pdb=" CG2 ILE B 73 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1529 not shown) Planarity restraints: 1732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 137 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 138 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 137 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 138 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 325 " -0.019 2.00e-02 2.50e+03 1.86e-02 6.94e+00 pdb=" CG TYR A 325 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 325 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 325 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 325 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 325 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 325 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 325 " -0.002 2.00e-02 2.50e+03 ... (remaining 1729 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2114 2.78 - 3.31: 8637 3.31 - 3.84: 15360 3.84 - 4.37: 17261 4.37 - 4.90: 31485 Nonbonded interactions: 74857 Sorted by model distance: nonbonded pdb=" OE2 GLU B 111 " pdb=" OH TYR B 153 " model vdw 2.250 2.440 nonbonded pdb=" OE2 GLU A 111 " pdb=" OH TYR A 153 " model vdw 2.251 2.440 nonbonded pdb=" NH2 ARG A 357 " pdb=" OD2 ASP B 452 " model vdw 2.274 2.520 nonbonded pdb=" O ASP A 523 " pdb=" OG SER A 527 " model vdw 2.342 2.440 nonbonded pdb=" O ASP B 523 " pdb=" OG SER B 527 " model vdw 2.342 2.440 ... (remaining 74852 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 6314 2.51 5 N 1692 2.21 5 O 1852 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: 0.390 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: 3.120 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 : 0.010 0.074 10104 Z= 0.660 Angle : 0.894 11.305 13642 Z= 0.489 Chirality : 0.056 0.257 1532 Planarity : 0.007 0.066 1732 Dihedral : 9.659 72.738 3778 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1200 helix: -0.77 (0.17), residues: 628 sheet: -1.48 (0.39), residues: 146 loop : -1.98 (0.25), residues: 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.268 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.2372 time to fit residues: 64.1348 Evaluate side-chains 104 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.0570 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 312 HIS A 369 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 655 GLN B 81 HIS B 312 HIS B 369 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 GLN B 655 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 10104 Z= 0.153 Angle : 0.475 6.767 13642 Z= 0.251 Chirality : 0.039 0.127 1532 Planarity : 0.004 0.050 1732 Dihedral : 3.845 16.368 1318 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.64 % 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: 0.66 (0.24), residues: 1200 helix: 1.95 (0.20), residues: 628 sheet: -1.44 (0.39), residues: 136 loop : -1.20 (0.28), residues: 436 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.257 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 145 average time/residue: 0.2099 time to fit residues: 43.9210 Evaluate side-chains 110 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0899 time to fit residues: 2.2175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS A 317 GLN A 565 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.059 10104 Z= 0.560 Angle : 0.672 6.153 13642 Z= 0.354 Chirality : 0.049 0.153 1532 Planarity : 0.005 0.048 1732 Dihedral : 4.149 14.778 1318 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.09 % 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: 1200 helix: 2.02 (0.20), residues: 628 sheet: -1.48 (0.39), residues: 132 loop : -1.16 (0.27), residues: 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.198 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 111 average time/residue: 0.2147 time to fit residues: 34.4215 Evaluate side-chains 103 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0962 time to fit residues: 3.4587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 10104 Z= 0.152 Angle : 0.457 6.546 13642 Z= 0.242 Chirality : 0.040 0.134 1532 Planarity : 0.004 0.055 1732 Dihedral : 3.527 14.001 1318 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 1.09 % 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: 1.67 (0.25), residues: 1200 helix: 2.82 (0.20), residues: 632 sheet: -1.42 (0.41), residues: 138 loop : -0.66 (0.29), residues: 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.284 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 112 average time/residue: 0.2049 time to fit residues: 33.9019 Evaluate side-chains 97 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1019 time to fit residues: 2.9991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10104 Z= 0.209 Angle : 0.475 5.775 13642 Z= 0.251 Chirality : 0.041 0.138 1532 Planarity : 0.004 0.043 1732 Dihedral : 3.420 13.768 1318 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.00 % 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: 1.87 (0.25), residues: 1200 helix: 2.95 (0.20), residues: 632 sheet: -1.40 (0.41), residues: 138 loop : -0.47 (0.30), residues: 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.299 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 111 average time/residue: 0.2005 time to fit residues: 33.2471 Evaluate side-chains 99 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0970 time to fit residues: 2.9300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10104 Z= 0.255 Angle : 0.498 5.506 13642 Z= 0.262 Chirality : 0.042 0.141 1532 Planarity : 0.004 0.054 1732 Dihedral : 3.461 13.537 1318 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.91 % 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: 1.93 (0.25), residues: 1200 helix: 2.97 (0.20), residues: 632 sheet: -1.41 (0.41), residues: 138 loop : -0.37 (0.30), residues: 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.301 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 101 average time/residue: 0.1955 time to fit residues: 29.6986 Evaluate side-chains 99 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1054 time to fit residues: 3.4520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN C 372 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 10104 Z= 0.174 Angle : 0.460 6.843 13642 Z= 0.240 Chirality : 0.040 0.133 1532 Planarity : 0.004 0.046 1732 Dihedral : 3.290 13.606 1318 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.00 % 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: 2.22 (0.25), residues: 1200 helix: 3.20 (0.20), residues: 632 sheet: -1.30 (0.41), residues: 138 loop : -0.23 (0.30), residues: 430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.322 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 108 average time/residue: 0.1978 time to fit residues: 32.0159 Evaluate side-chains 94 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0928 time to fit residues: 2.2756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 69 optimal weight: 0.0030 chunk 34 optimal weight: 0.0050 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 10104 Z= 0.135 Angle : 0.437 6.102 13642 Z= 0.228 Chirality : 0.039 0.139 1532 Planarity : 0.003 0.041 1732 Dihedral : 3.091 12.236 1318 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.18 % 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: 2.56 (0.25), residues: 1200 helix: 3.46 (0.20), residues: 632 sheet: -1.18 (0.42), residues: 138 loop : -0.02 (0.31), residues: 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.244 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 103 average time/residue: 0.1961 time to fit residues: 30.3223 Evaluate side-chains 94 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0881 time to fit residues: 2.0351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.0070 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN B 17 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10104 Z= 0.215 Angle : 0.481 6.640 13642 Z= 0.250 Chirality : 0.041 0.138 1532 Planarity : 0.004 0.040 1732 Dihedral : 3.241 12.265 1318 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.46 % 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: 2.46 (0.25), residues: 1200 helix: 3.34 (0.20), residues: 632 sheet: -1.21 (0.42), residues: 138 loop : -0.00 (0.31), residues: 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.330 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 0.2080 time to fit residues: 30.3086 Evaluate side-chains 91 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0934 time to fit residues: 2.2543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 10104 Z= 0.156 Angle : 0.461 7.378 13642 Z= 0.239 Chirality : 0.040 0.130 1532 Planarity : 0.003 0.039 1732 Dihedral : 3.147 12.118 1318 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.18 % 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: 2.57 (0.25), residues: 1200 helix: 3.40 (0.20), residues: 634 sheet: -1.12 (0.43), residues: 138 loop : 0.06 (0.31), residues: 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.322 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.2228 time to fit residues: 31.3016 Evaluate side-chains 88 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0926 time to fit residues: 1.9312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099571 restraints weight = 14013.128| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.89 r_work: 0.3084 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.3049 rms_B_bonded: 1.77 restraints_weight: 0.1250 r_work: 0.3028 rms_B_bonded: 1.94 restraints_weight: 0.0625 r_work: 0.3004 rms_B_bonded: 2.20 restraints_weight: 0.0312 r_work: 0.2975 rms_B_bonded: 2.56 restraints_weight: 0.0156 r_work: 0.2939 rms_B_bonded: 3.05 restraints_weight: 0.0078 r_work: 0.2895 rms_B_bonded: 3.71 restraints_weight: 0.0039 r_work: 0.2840 rms_B_bonded: 4.62 restraints_weight: 0.0020 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10104 Z= 0.232 Angle : 0.491 6.576 13642 Z= 0.255 Chirality : 0.041 0.139 1532 Planarity : 0.004 0.040 1732 Dihedral : 3.263 12.071 1318 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.36 % 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: 2.41 (0.25), residues: 1200 helix: 3.27 (0.20), residues: 634 sheet: -1.15 (0.42), residues: 138 loop : -0.02 (0.31), residues: 428 =============================================================================== Job complete usr+sys time: 1660.72 seconds wall clock time: 31 minutes 21.28 seconds (1881.28 seconds total)