Starting phenix.real_space_refine on Wed Feb 14 19:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agf_11778/02_2024/7agf_11778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agf_11778/02_2024/7agf_11778.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/7agf_11778/02_2024/7agf_11778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agf_11778/02_2024/7agf_11778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agf_11778/02_2024/7agf_11778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7agf_11778/02_2024/7agf_11778.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= 0.000 sd= 0.001 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 36 5.16 5 C 6354 2.51 5 N 1641 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10071 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "D" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "E" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "F" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Time building chain proxies: 5.88, per 1000 atoms: 0.58 Number of scatterers: 10071 At special positions: 0 Unit cell: (126.75, 131.3, 98.8, 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 36 16.00 O 2040 8.00 N 1641 7.00 C 6354 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: 3.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 7.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU A 250 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.576A pdb=" N MET D 296 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.577A pdb=" N MET E 296 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 removed outlier: 3.578A pdb=" N MET F 296 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU B 250 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.852A pdb=" N GLU C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199 removed outlier: 5.609A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.316A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU D 128 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 173 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 242 through 245 removed outlier: 4.165A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.735A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.315A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU E 128 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 173 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 242 through 245 removed outlier: 4.164A pdb=" N THR E 242 " --> pdb=" O VAL E 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 259 through 265 removed outlier: 6.734A pdb=" N SER E 302 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 120 removed outlier: 6.315A pdb=" N PHE F 115 " --> pdb=" O GLN F 210 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG F 212 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY F 117 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU F 214 " --> pdb=" O GLY F 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 119 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR F 187 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU F 154 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR F 189 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 128 through 131 removed outlier: 6.698A pdb=" N LEU F 128 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR F 173 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 242 through 245 removed outlier: 4.165A pdb=" N THR F 242 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 265 removed outlier: 6.735A pdb=" N SER F 302 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.608A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AC4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AC5, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.608A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 219 through 220 258 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3318 1.34 - 1.46: 2243 1.46 - 1.58: 4648 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 10269 Sorted by residual: bond pdb=" CD ARG E 180 " pdb=" NE ARG E 180 " ideal model delta sigma weight residual 1.458 1.433 0.025 1.40e-02 5.10e+03 3.21e+00 bond pdb=" CD ARG D 180 " pdb=" NE ARG D 180 " ideal model delta sigma weight residual 1.458 1.433 0.025 1.40e-02 5.10e+03 3.19e+00 bond pdb=" CD ARG F 180 " pdb=" NE ARG F 180 " ideal model delta sigma weight residual 1.458 1.434 0.024 1.40e-02 5.10e+03 2.99e+00 bond pdb=" CZ ARG D 180 " pdb=" NH2 ARG D 180 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" CZ ARG E 180 " pdb=" NH2 ARG E 180 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.77e+00 ... (remaining 10264 not shown) Histogram of bond angle deviations from ideal: 99.90 - 107.18: 335 107.18 - 114.45: 6022 114.45 - 121.73: 5084 121.73 - 129.01: 2515 129.01 - 136.28: 54 Bond angle restraints: 14010 Sorted by residual: angle pdb=" C ARG D 316 " pdb=" N SER D 317 " pdb=" CA SER D 317 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ARG F 316 " pdb=" N SER F 317 " pdb=" CA SER F 317 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ARG E 316 " pdb=" N SER E 317 " pdb=" CA SER E 317 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C ILE E 284 " pdb=" N VAL E 285 " pdb=" CA VAL E 285 " ideal model delta sigma weight residual 122.91 117.62 5.29 1.43e+00 4.89e-01 1.37e+01 angle pdb=" C ILE D 284 " pdb=" N VAL D 285 " pdb=" CA VAL D 285 " ideal model delta sigma weight residual 122.91 117.63 5.28 1.43e+00 4.89e-01 1.36e+01 ... (remaining 14005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 5603 15.86 - 31.72: 414 31.72 - 47.58: 87 47.58 - 63.44: 25 63.44 - 79.30: 15 Dihedral angle restraints: 6144 sinusoidal: 2352 harmonic: 3792 Sorted by residual: dihedral pdb=" CA SER E 153 " pdb=" C SER E 153 " pdb=" N LEU E 154 " pdb=" CA LEU E 154 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER F 153 " pdb=" C SER F 153 " pdb=" N LEU F 154 " pdb=" CA LEU F 154 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER D 153 " pdb=" C SER D 153 " pdb=" N LEU D 154 " pdb=" CA LEU D 154 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 922 0.040 - 0.081: 514 0.081 - 0.121: 163 0.121 - 0.161: 44 0.161 - 0.201: 10 Chirality restraints: 1653 Sorted by residual: chirality pdb=" CA GLU E 155 " pdb=" N GLU E 155 " pdb=" C GLU E 155 " pdb=" CB GLU E 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU F 155 " pdb=" N GLU F 155 " pdb=" C GLU F 155 " pdb=" CB GLU F 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU D 155 " pdb=" N GLU D 155 " pdb=" C GLU D 155 " pdb=" CB GLU D 155 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1650 not shown) Planarity restraints: 1815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " -0.043 2.00e-02 2.50e+03 4.82e-02 5.81e+01 pdb=" CG TRP A 135 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 135 " -0.043 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP C 135 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP C 135 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 135 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 135 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 135 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP C 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 135 " 0.042 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP B 135 " -0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP B 135 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 135 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 135 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 135 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 135 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP B 135 " 0.003 2.00e-02 2.50e+03 ... (remaining 1812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 295 2.69 - 3.24: 9486 3.24 - 3.79: 16487 3.79 - 4.35: 22330 4.35 - 4.90: 36442 Nonbonded interactions: 85040 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR C 319 " model vdw 2.136 2.440 nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 2.142 2.440 nonbonded pdb=" OH TYR B 319 " pdb=" OH TYR C 319 " model vdw 2.145 2.440 nonbonded pdb=" OE1 GLU D 170 " pdb=" OH TYR D 172 " model vdw 2.244 2.440 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.244 2.440 ... (remaining 85035 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 7.220 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.006 0.050 10269 Z= 0.417 Angle : 0.878 11.283 14010 Z= 0.489 Chirality : 0.054 0.201 1653 Planarity : 0.005 0.048 1815 Dihedral : 13.216 79.297 3684 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -1.03 (0.24), residues: 1275 helix: -3.96 (0.41), residues: 36 sheet: -0.79 (0.24), residues: 453 loop : -0.36 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.011 TRP A 135 HIS 0.004 0.001 HIS C 266 PHE 0.019 0.003 PHE D 301 TYR 0.023 0.002 TYR C 174 ARG 0.010 0.002 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 300 ASP cc_start: 0.6668 (t0) cc_final: 0.6404 (t0) REVERT: C 276 MET cc_start: 0.6375 (mtp) cc_final: 0.6085 (mtm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2583 time to fit residues: 86.7856 Evaluate side-chains 183 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN D 165 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN E 165 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN F 165 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10269 Z= 0.200 Angle : 0.587 8.728 14010 Z= 0.307 Chirality : 0.045 0.144 1653 Planarity : 0.003 0.030 1815 Dihedral : 5.426 21.643 1365 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.57 % Allowed : 6.81 % Favored : 91.62 % 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: -0.87 (0.24), residues: 1275 helix: -3.74 (0.51), residues: 36 sheet: -0.84 (0.23), residues: 468 loop : -0.12 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP C 135 HIS 0.001 0.000 HIS A 266 PHE 0.017 0.002 PHE D 301 TYR 0.026 0.001 TYR D 319 ARG 0.004 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7370 (pt) cc_final: 0.7032 (tp) REVERT: F 143 LEU cc_start: 0.7344 (pt) cc_final: 0.6994 (tp) outliers start: 18 outliers final: 14 residues processed: 191 average time/residue: 0.2433 time to fit residues: 63.0651 Evaluate side-chains 185 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 284 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.0570 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN C 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10269 Z= 0.218 Angle : 0.547 8.076 14010 Z= 0.289 Chirality : 0.045 0.144 1653 Planarity : 0.003 0.027 1815 Dihedral : 5.035 17.249 1365 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.92 % Allowed : 8.38 % Favored : 89.70 % 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: -0.64 (0.25), residues: 1275 helix: -3.42 (0.58), residues: 36 sheet: -0.73 (0.23), residues: 468 loop : 0.07 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 135 HIS 0.001 0.000 HIS A 266 PHE 0.019 0.002 PHE F 301 TYR 0.013 0.001 TYR D 186 ARG 0.003 0.001 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7341 (pt) cc_final: 0.7059 (tp) outliers start: 22 outliers final: 16 residues processed: 192 average time/residue: 0.2597 time to fit residues: 67.2306 Evaluate side-chains 186 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 284 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN D 165 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10269 Z= 0.163 Angle : 0.516 8.104 14010 Z= 0.273 Chirality : 0.045 0.142 1653 Planarity : 0.002 0.024 1815 Dihedral : 4.769 18.020 1365 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.18 % Allowed : 9.77 % Favored : 88.05 % 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: -0.49 (0.25), residues: 1275 helix: -3.17 (0.62), residues: 36 sheet: -0.59 (0.24), residues: 468 loop : 0.13 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 135 HIS 0.001 0.000 HIS C 266 PHE 0.014 0.001 PHE E 301 TYR 0.010 0.001 TYR D 319 ARG 0.004 0.001 ARG E 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7373 (pt) cc_final: 0.7082 (tp) REVERT: D 188 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8102 (mp) REVERT: F 143 LEU cc_start: 0.7333 (pt) cc_final: 0.6887 (tp) outliers start: 25 outliers final: 12 residues processed: 187 average time/residue: 0.2631 time to fit residues: 66.4196 Evaluate side-chains 177 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 284 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10269 Z= 0.352 Angle : 0.589 8.364 14010 Z= 0.311 Chirality : 0.046 0.145 1653 Planarity : 0.003 0.035 1815 Dihedral : 5.145 19.320 1365 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.79 % Allowed : 9.25 % Favored : 87.96 % 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: -0.51 (0.25), residues: 1275 helix: -2.57 (0.77), residues: 36 sheet: -0.61 (0.24), residues: 468 loop : 0.09 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 296 HIS 0.002 0.001 HIS B 266 PHE 0.019 0.002 PHE D 301 TYR 0.017 0.002 TYR B 256 ARG 0.007 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8426 (mp) outliers start: 32 outliers final: 24 residues processed: 194 average time/residue: 0.2343 time to fit residues: 62.4438 Evaluate side-chains 191 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 284 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10269 Z= 0.240 Angle : 0.550 8.334 14010 Z= 0.290 Chirality : 0.045 0.146 1653 Planarity : 0.003 0.026 1815 Dihedral : 4.945 18.107 1365 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.62 % Allowed : 10.56 % Favored : 86.82 % 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: -0.55 (0.25), residues: 1275 helix: -2.47 (0.78), residues: 36 sheet: -0.62 (0.24), residues: 468 loop : 0.05 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 296 HIS 0.002 0.000 HIS C 266 PHE 0.013 0.002 PHE F 272 TYR 0.011 0.001 TYR E 149 ARG 0.004 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7416 (pt) cc_final: 0.7057 (tp) REVERT: D 188 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8438 (mp) outliers start: 30 outliers final: 26 residues processed: 191 average time/residue: 0.2619 time to fit residues: 67.4702 Evaluate side-chains 197 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 324 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 0.0020 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10269 Z= 0.137 Angle : 0.508 7.947 14010 Z= 0.267 Chirality : 0.044 0.143 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.541 19.700 1365 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.66 % Allowed : 11.87 % Favored : 86.47 % 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: -0.49 (0.25), residues: 1275 helix: -2.35 (0.79), residues: 36 sheet: -0.50 (0.24), residues: 465 loop : 0.02 (0.25), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 296 HIS 0.001 0.000 HIS E 183 PHE 0.023 0.002 PHE D 301 TYR 0.011 0.001 TYR E 319 ARG 0.006 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7330 (pt) cc_final: 0.6992 (tp) REVERT: D 188 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8284 (mp) REVERT: F 143 LEU cc_start: 0.7292 (pt) cc_final: 0.6860 (tp) REVERT: C 236 MET cc_start: 0.8263 (mmp) cc_final: 0.8045 (mmt) outliers start: 19 outliers final: 12 residues processed: 189 average time/residue: 0.2887 time to fit residues: 72.9703 Evaluate side-chains 175 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 324 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 0.0270 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 10269 Z= 0.431 Angle : 0.637 10.953 14010 Z= 0.333 Chirality : 0.047 0.146 1653 Planarity : 0.003 0.028 1815 Dihedral : 5.162 20.627 1365 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.53 % Allowed : 11.61 % Favored : 85.86 % 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: -0.63 (0.25), residues: 1275 helix: -2.35 (0.81), residues: 36 sheet: -0.64 (0.24), residues: 468 loop : -0.04 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 296 HIS 0.003 0.001 HIS B 266 PHE 0.025 0.002 PHE D 301 TYR 0.024 0.002 TYR C 254 ARG 0.006 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7451 (pt) cc_final: 0.7077 (tp) REVERT: D 188 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8622 (mp) outliers start: 29 outliers final: 26 residues processed: 189 average time/residue: 0.2383 time to fit residues: 62.0957 Evaluate side-chains 193 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 324 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10269 Z= 0.199 Angle : 0.563 9.716 14010 Z= 0.294 Chirality : 0.046 0.319 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.821 18.667 1365 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.83 % Allowed : 12.48 % Favored : 85.69 % 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: -0.62 (0.25), residues: 1275 helix: -2.28 (0.81), residues: 36 sheet: -0.62 (0.24), residues: 468 loop : -0.05 (0.25), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 296 HIS 0.001 0.000 HIS B 266 PHE 0.016 0.002 PHE F 272 TYR 0.013 0.002 TYR E 158 ARG 0.006 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7375 (pt) cc_final: 0.7014 (tp) REVERT: D 188 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8471 (mp) outliers start: 21 outliers final: 18 residues processed: 182 average time/residue: 0.2456 time to fit residues: 60.8097 Evaluate side-chains 182 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 324 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 83 optimal weight: 0.0000 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 0.0060 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10269 Z= 0.162 Angle : 0.550 10.045 14010 Z= 0.286 Chirality : 0.045 0.209 1653 Planarity : 0.003 0.027 1815 Dihedral : 4.536 19.270 1365 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.66 % Allowed : 12.65 % Favored : 85.69 % 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 (0.25), residues: 1275 helix: -2.23 (0.80), residues: 36 sheet: -0.53 (0.24), residues: 465 loop : -0.06 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 296 HIS 0.001 0.000 HIS C 266 PHE 0.028 0.002 PHE D 301 TYR 0.015 0.001 TYR E 158 ARG 0.007 0.001 ARG C 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 LEU cc_start: 0.7356 (pt) cc_final: 0.6948 (tp) REVERT: D 188 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8365 (mp) REVERT: E 193 ARG cc_start: 0.7256 (tpp80) cc_final: 0.7014 (tpp80) REVERT: F 143 LEU cc_start: 0.7280 (pt) cc_final: 0.6857 (tp) outliers start: 19 outliers final: 17 residues processed: 179 average time/residue: 0.2520 time to fit residues: 61.1083 Evaluate side-chains 184 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 324 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** 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 = 0.3556 r_free = 0.3556 target = 0.102542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067716 restraints weight = 19971.159| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.46 r_work: 0.2791 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10269 Z= 0.228 Angle : 0.568 9.986 14010 Z= 0.294 Chirality : 0.045 0.208 1653 Planarity : 0.003 0.026 1815 Dihedral : 4.653 18.588 1365 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.83 % Allowed : 12.39 % Favored : 85.78 % 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: -0.53 (0.25), residues: 1275 helix: -2.23 (0.81), residues: 36 sheet: -0.51 (0.24), residues: 465 loop : -0.04 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 296 HIS 0.002 0.000 HIS B 266 PHE 0.026 0.002 PHE D 301 TYR 0.012 0.001 TYR E 319 ARG 0.008 0.001 ARG B 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.38 seconds wall clock time: 46 minutes 23.96 seconds (2783.96 seconds total)