Starting phenix.real_space_refine on Thu Dec 7 22:42:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/12_2023/7qb9_13882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/12_2023/7qb9_13882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/12_2023/7qb9_13882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/12_2023/7qb9_13882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/12_2023/7qb9_13882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qb9_13882/12_2023/7qb9_13882.pdb" } resolution = 3.1 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= 0.003 sd= 0.119 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 21 5.16 5 C 3732 2.51 5 N 732 2.21 5 O 934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5419 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2295 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2298 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Unusual residues: {'NAG': 2, 'Y01': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Unusual residues: {'NAG': 2, 'Y01': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.64, per 1000 atoms: 0.67 Number of scatterers: 5419 At special positions: 0 Unit cell: (81.2736, 83.8134, 100.745, 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 21 16.00 O 934 8.00 N 732 7.00 C 3732 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 25 " " NAG B 502 " - " ASN B 32 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 853.5 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 75.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.506A pdb=" N PHE A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 73 removed outlier: 3.638A pdb=" N SER A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.856A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.600A pdb=" N ILE A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.806A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 195 removed outlier: 4.070A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 3.705A pdb=" N PHE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.745A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.653A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 Proline residue: A 290 - end of helix removed outlier: 3.714A pdb=" N MET A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.505A pdb=" N PHE B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 73 removed outlier: 3.637A pdb=" N SER B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.857A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.601A pdb=" N ILE B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.806A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 195 removed outlier: 4.069A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 removed outlier: 3.668A pdb=" N PHE B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.746A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 Proline residue: B 290 - end of helix removed outlier: 3.714A pdb=" N MET B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 6.507A pdb=" N SER A 28 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28 removed outlier: 6.507A pdb=" N SER B 28 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 852 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: 1.29 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 749 1.31 - 1.44: 1357 1.44 - 1.56: 3413 1.56 - 1.68: 22 1.68 - 1.81: 38 Bond restraints: 5579 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 5574 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.15: 156 105.15 - 112.44: 3106 112.44 - 119.72: 2066 119.72 - 127.00: 2357 127.00 - 134.28: 32 Bond angle restraints: 7717 Sorted by residual: angle pdb=" N PHE B 204 " pdb=" CA PHE B 204 " pdb=" C PHE B 204 " ideal model delta sigma weight residual 111.54 106.03 5.51 1.36e+00 5.41e-01 1.64e+01 angle pdb=" N PHE A 204 " pdb=" CA PHE A 204 " pdb=" C PHE A 204 " ideal model delta sigma weight residual 111.54 106.24 5.30 1.36e+00 5.41e-01 1.52e+01 angle pdb=" N PHE B 235 " pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 111.28 107.10 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N TYR B 106 " pdb=" CA TYR B 106 " pdb=" C TYR B 106 " ideal model delta sigma weight residual 113.23 108.60 4.63 1.24e+00 6.50e-01 1.39e+01 angle pdb=" N PHE A 235 " pdb=" CA PHE A 235 " pdb=" C PHE A 235 " ideal model delta sigma weight residual 111.28 107.23 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 7712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 3918 15.26 - 30.52: 345 30.52 - 45.78: 83 45.78 - 61.03: 51 61.03 - 76.29: 4 Dihedral angle restraints: 4401 sinusoidal: 2643 harmonic: 1758 Sorted by residual: dihedral pdb=" CA ILE A 263 " pdb=" C ILE A 263 " pdb=" N LEU A 264 " pdb=" CA LEU A 264 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ILE B 263 " pdb=" C ILE B 263 " pdb=" N LEU B 264 " pdb=" CA LEU B 264 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" N ASN A 25 " pdb=" C ASN A 25 " pdb=" CA ASN A 25 " pdb=" CB ASN A 25 " ideal model delta harmonic sigma weight residual 122.80 114.48 8.32 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 4398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 883 0.079 - 0.157: 98 0.157 - 0.236: 12 0.236 - 0.314: 5 0.314 - 0.393: 2 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CBC Y01 A 513 " pdb=" CAR Y01 A 513 " pdb=" CAV Y01 A 513 " pdb=" OAW Y01 A 513 " both_signs ideal model delta sigma weight residual False -2.54 -2.15 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CBC Y01 A 509 " pdb=" CAR Y01 A 509 " pdb=" CAV Y01 A 509 " pdb=" OAW Y01 A 509 " both_signs ideal model delta sigma weight residual False -2.54 -2.19 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA ASN A 25 " pdb=" N ASN A 25 " pdb=" C ASN A 25 " pdb=" CB ASN A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 997 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 269 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 270 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 269 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO B 270 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 247 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LEU B 247 " 0.068 2.00e-02 2.50e+03 pdb=" O LEU B 247 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU B 248 " -0.023 2.00e-02 2.50e+03 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1313 2.81 - 3.33: 4887 3.33 - 3.86: 7972 3.86 - 4.38: 9176 4.38 - 4.90: 16024 Nonbonded interactions: 39372 Sorted by model distance: nonbonded pdb=" O ILE B 175 " pdb=" OG1 THR B 179 " model vdw 2.291 2.440 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.291 2.440 nonbonded pdb=" O ALA B 61 " pdb=" OG1 THR B 65 " model vdw 2.317 2.440 nonbonded pdb=" O ALA A 61 " pdb=" OG1 THR A 65 " model vdw 2.317 2.440 nonbonded pdb=" O ASN A 46 " pdb=" OG1 THR A 50 " model vdw 2.340 2.440 ... (remaining 39367 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' and (resid 5 through 249 or (resid 250 and (name N or name CA or name \ C or name O or name CB )) or resid 251 through 303 or resid 501 through 513)) } 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: 0.820 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: 3.550 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 18.220 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.008 0.128 5579 Z= 0.473 Angle : 1.013 9.016 7717 Z= 0.545 Chirality : 0.056 0.393 1000 Planarity : 0.010 0.108 816 Dihedral : 12.615 76.292 3265 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -2.92 (0.29), residues: 594 helix: -1.69 (0.22), residues: 416 sheet: None (None), residues: 0 loop : -2.11 (0.37), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 70 HIS 0.004 0.002 HIS B 94 PHE 0.042 0.003 PHE A 262 TYR 0.025 0.002 TYR B 266 ARG 0.003 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.521 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1793 time to fit residues: 11.7668 Evaluate side-chains 42 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5579 Z= 0.185 Angle : 0.547 6.589 7717 Z= 0.271 Chirality : 0.039 0.232 1000 Planarity : 0.005 0.064 816 Dihedral : 9.599 59.070 2284 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.97 % Allowed : 6.60 % Favored : 92.43 % 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: -0.57 (0.32), residues: 594 helix: 0.29 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.023 0.002 PHE B 244 TYR 0.018 0.001 TYR B 266 ARG 0.003 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.468 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.1450 time to fit residues: 10.1705 Evaluate side-chains 42 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0502 time to fit residues: 0.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 0.0030 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5579 Z= 0.134 Angle : 0.469 5.599 7717 Z= 0.232 Chirality : 0.037 0.197 1000 Planarity : 0.004 0.051 816 Dihedral : 9.326 59.885 2284 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.55 % Allowed : 7.77 % Favored : 90.68 % 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: 0.72 (0.35), residues: 594 helix: 1.33 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -1.56 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.003 0.001 HIS B 94 PHE 0.014 0.001 PHE B 244 TYR 0.016 0.001 TYR A 266 ARG 0.001 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1470 time to fit residues: 10.6896 Evaluate side-chains 46 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0510 time to fit residues: 1.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5579 Z= 0.184 Angle : 0.514 5.934 7717 Z= 0.249 Chirality : 0.038 0.202 1000 Planarity : 0.004 0.046 816 Dihedral : 9.190 59.813 2284 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.17 % Allowed : 10.29 % Favored : 88.54 % 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: 1.10 (0.35), residues: 594 helix: 1.61 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.004 0.001 HIS B 94 PHE 0.017 0.002 PHE B 55 TYR 0.014 0.001 TYR A 266 ARG 0.003 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 49 average time/residue: 0.1588 time to fit residues: 10.8621 Evaluate side-chains 41 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0533 time to fit residues: 0.8306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5579 Z= 0.377 Angle : 0.687 7.760 7717 Z= 0.320 Chirality : 0.045 0.174 1000 Planarity : 0.004 0.046 816 Dihedral : 10.110 59.039 2284 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.36 % Allowed : 10.87 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 594 helix: 1.30 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.60 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 295 HIS 0.006 0.002 HIS A 94 PHE 0.021 0.002 PHE B 55 TYR 0.018 0.002 TYR B 266 ARG 0.006 0.001 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 51 average time/residue: 0.1636 time to fit residues: 11.4031 Evaluate side-chains 51 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0515 time to fit residues: 1.3731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5579 Z= 0.168 Angle : 0.515 5.060 7717 Z= 0.246 Chirality : 0.039 0.203 1000 Planarity : 0.003 0.043 816 Dihedral : 9.494 58.487 2284 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 10.68 % Favored : 88.54 % 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: 1.26 (0.35), residues: 594 helix: 1.83 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.014 0.001 PHE B 244 TYR 0.014 0.001 TYR A 266 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.1657 time to fit residues: 11.9292 Evaluate side-chains 49 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0629 time to fit residues: 1.0974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5579 Z= 0.188 Angle : 0.524 5.085 7717 Z= 0.248 Chirality : 0.039 0.263 1000 Planarity : 0.003 0.043 816 Dihedral : 9.357 58.557 2284 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.55 % Allowed : 11.65 % Favored : 86.80 % 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: 1.46 (0.35), residues: 594 helix: 1.98 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.39 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.014 0.001 PHE A 55 TYR 0.014 0.001 TYR A 266 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.1494 time to fit residues: 11.1541 Evaluate side-chains 50 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0528 time to fit residues: 1.0770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 48 optimal weight: 0.0770 chunk 52 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5579 Z= 0.115 Angle : 0.456 4.912 7717 Z= 0.221 Chirality : 0.037 0.231 1000 Planarity : 0.003 0.043 816 Dihedral : 8.998 59.905 2284 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.36), residues: 594 helix: 2.44 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.21 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 70 HIS 0.003 0.001 HIS B 94 PHE 0.017 0.001 PHE A 171 TYR 0.013 0.001 TYR A 266 ARG 0.001 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1555 time to fit residues: 11.0969 Evaluate side-chains 48 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5579 Z= 0.187 Angle : 0.495 5.061 7717 Z= 0.236 Chirality : 0.039 0.216 1000 Planarity : 0.003 0.044 816 Dihedral : 9.064 59.314 2284 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.19 % Allowed : 14.37 % Favored : 85.44 % 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: 2.04 (0.36), residues: 594 helix: 2.44 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.015 0.001 PHE A 171 TYR 0.015 0.001 TYR B 266 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.1497 time to fit residues: 9.8844 Evaluate side-chains 47 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5579 Z= 0.157 Angle : 0.480 5.041 7717 Z= 0.229 Chirality : 0.038 0.200 1000 Planarity : 0.003 0.044 816 Dihedral : 8.956 59.459 2284 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.19 % Allowed : 14.56 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.36), residues: 594 helix: 2.47 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.14 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 PHE 0.016 0.001 PHE B 171 TYR 0.014 0.001 TYR B 266 ARG 0.002 0.000 ARG B 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.1517 time to fit residues: 10.6517 Evaluate side-chains 47 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.0050 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122945 restraints weight = 5582.300| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.32 r_work: 0.3258 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5579 Z= 0.117 Angle : 0.442 4.967 7717 Z= 0.213 Chirality : 0.036 0.184 1000 Planarity : 0.003 0.044 816 Dihedral : 8.696 59.451 2284 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.19 % Allowed : 15.15 % Favored : 84.66 % 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: 2.48 (0.36), residues: 594 helix: 2.69 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.02 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.003 0.001 HIS A 94 PHE 0.017 0.001 PHE A 171 TYR 0.014 0.001 TYR B 266 ARG 0.001 0.000 ARG A 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.55 seconds wall clock time: 23 minutes 8.02 seconds (1388.02 seconds total)