Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:10:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlr_27512/11_2022/8dlr_27512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlr_27512/11_2022/8dlr_27512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlr_27512/11_2022/8dlr_27512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlr_27512/11_2022/8dlr_27512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlr_27512/11_2022/8dlr_27512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlr_27512/11_2022/8dlr_27512.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 122": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4027 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2218 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 14, 'TRANS': 259} Chain breaks: 2 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.68, per 1000 atoms: 0.67 Number of scatterers: 4027 At special positions: 0 Unit cell: (92, 64, 108, 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 16 16.00 O 788 8.00 N 656 7.00 C 2567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 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 A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 694.7 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 7.9% alpha, 56.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.696A pdb=" N SER H 49 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.966A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 129 removed outlier: 4.142A pdb=" N LYS H 127 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.143A pdb=" N GLU L 102 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.012A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.663A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.835A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.318A pdb=" N GLU H 29 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE H 53 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.318A pdb=" N GLU H 29 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL H 133 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.403A pdb=" N TRP L 54 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 29 through 32 165 hydrogen bonds defined for protein. 405 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: 1.08 Time building geometry restraints manager: 1.51 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: 1253 1.34 - 1.47: 1107 1.47 - 1.59: 1744 1.59 - 1.71: 0 1.71 - 1.84: 21 Bond restraints: 4125 Sorted by residual: bond pdb=" CB ASN A 280 " pdb=" CG ASN A 280 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CA ASN A 280 " pdb=" CB ASN A 280 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.42e+00 bond pdb=" CB THR A 286 " pdb=" CG2 THR A 286 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CB VAL A 130 " pdb=" CG2 VAL A 130 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CG LEU A 117 " pdb=" CD1 LEU A 117 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 ... (remaining 4120 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 113 106.57 - 113.42: 2227 113.42 - 120.28: 1443 120.28 - 127.13: 1780 127.13 - 133.99: 46 Bond angle restraints: 5609 Sorted by residual: angle pdb=" C GLN L 69 " pdb=" N ASP L 70 " pdb=" CA ASP L 70 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C2 NAG A1306 " pdb=" N2 NAG A1306 " pdb=" C7 NAG A1306 " ideal model delta sigma weight residual 123.12 127.28 -4.16 1.28e+00 6.08e-01 1.05e+01 angle pdb=" CA ASN A 280 " pdb=" CB ASN A 280 " pdb=" CG ASN A 280 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.00e+00 1.00e+00 8.16e+00 angle pdb=" N GLY H 75 " pdb=" CA GLY H 75 " pdb=" C GLY H 75 " ideal model delta sigma weight residual 113.18 119.45 -6.27 2.37e+00 1.78e-01 7.00e+00 angle pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" C ASP A 287 " ideal model delta sigma weight residual 108.79 104.81 3.98 1.53e+00 4.27e-01 6.76e+00 ... (remaining 5604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2216 16.63 - 33.26: 160 33.26 - 49.90: 25 49.90 - 66.53: 3 66.53 - 83.16: 8 Dihedral angle restraints: 2412 sinusoidal: 948 harmonic: 1464 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -41.28 -44.72 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU H 74 " pdb=" C LEU H 74 " pdb=" N GLY H 75 " pdb=" CA GLY H 75 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 473 0.054 - 0.109: 128 0.109 - 0.163: 34 0.163 - 0.217: 3 0.217 - 0.271: 3 Chirality restraints: 641 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR A 63 " pdb=" CA THR A 63 " pdb=" OG1 THR A 63 " pdb=" CG2 THR A 63 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 227 " pdb=" CA VAL A 227 " pdb=" CG1 VAL A 227 " pdb=" CG2 VAL A 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 638 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 295 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 230 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 48 " -0.014 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE H 48 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 48 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE H 48 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 48 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 48 " -0.001 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1131 2.81 - 3.33: 3161 3.33 - 3.86: 6983 3.86 - 4.38: 8076 4.38 - 4.90: 14213 Nonbonded interactions: 33564 Sorted by model distance: nonbonded pdb=" OH TYR A 144 " pdb=" OH TYR H 129 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR H 52 " pdb=" O THR H 120 " model vdw 2.320 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OG1 THR A 114 " model vdw 2.342 2.440 nonbonded pdb=" O ASP L 111 " pdb=" OG1 THR L 114 " model vdw 2.346 2.440 nonbonded pdb=" NE2 GLN A 14 " pdb=" O TYR A 160 " model vdw 2.347 2.520 ... (remaining 33559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2567 2.51 5 N 656 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 12.880 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 15.580 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 0.044 4125 Z= 0.389 Angle : 0.789 8.983 5609 Z= 0.439 Chirality : 0.056 0.271 641 Planarity : 0.007 0.070 705 Dihedral : 12.522 83.158 1461 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.36), residues: 495 helix: -0.46 (1.50), residues: 11 sheet: -0.36 (0.33), residues: 221 loop : -0.59 (0.37), residues: 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.1045 time to fit residues: 95.2114 Evaluate side-chains 70 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS L 85 ASN L 88 ASN L 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4125 Z= 0.283 Angle : 0.556 6.356 5609 Z= 0.297 Chirality : 0.046 0.236 641 Planarity : 0.005 0.050 705 Dihedral : 5.101 18.639 580 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.38 % 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: -0.64 (0.37), residues: 495 helix: -1.34 (1.26), residues: 17 sheet: -0.22 (0.33), residues: 216 loop : -0.43 (0.38), residues: 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.378 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 1.1041 time to fit residues: 88.1336 Evaluate side-chains 72 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 44 optimal weight: 0.0050 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 85 ASN L 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4125 Z= 0.232 Angle : 0.529 5.769 5609 Z= 0.281 Chirality : 0.044 0.216 641 Planarity : 0.004 0.044 705 Dihedral : 4.857 17.533 580 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.92 % 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: -0.46 (0.36), residues: 495 helix: -1.00 (1.33), residues: 17 sheet: -0.09 (0.34), residues: 210 loop : -0.33 (0.38), residues: 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.481 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 1.0693 time to fit residues: 83.2842 Evaluate side-chains 69 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0396 time to fit residues: 0.8702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 4125 Z= 0.260 Angle : 0.539 6.445 5609 Z= 0.285 Chirality : 0.044 0.212 641 Planarity : 0.004 0.042 705 Dihedral : 4.926 25.978 580 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 1.61 % 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: -0.32 (0.37), residues: 495 helix: -0.83 (1.35), residues: 17 sheet: -0.02 (0.34), residues: 210 loop : -0.21 (0.38), residues: 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.447 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 1.1221 time to fit residues: 84.9405 Evaluate side-chains 63 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.0470 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 4125 Z= 0.209 Angle : 0.522 7.519 5609 Z= 0.277 Chirality : 0.043 0.200 641 Planarity : 0.004 0.040 705 Dihedral : 4.793 26.915 580 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.38 % 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: -0.21 (0.37), residues: 495 helix: -0.75 (1.36), residues: 17 sheet: 0.03 (0.34), residues: 203 loop : -0.11 (0.38), residues: 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.501 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 1.1412 time to fit residues: 86.3332 Evaluate side-chains 70 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0988 time to fit residues: 0.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 4125 Z= 0.283 Angle : 0.559 7.616 5609 Z= 0.295 Chirality : 0.044 0.208 641 Planarity : 0.004 0.040 705 Dihedral : 4.928 28.071 580 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.61 % 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: -0.32 (0.37), residues: 495 helix: -0.71 (1.37), residues: 17 sheet: 0.02 (0.34), residues: 205 loop : -0.26 (0.38), residues: 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.479 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 1.1312 time to fit residues: 85.6762 Evaluate side-chains 65 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1771 time to fit residues: 0.8357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.0050 chunk 39 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 4125 Z= 0.239 Angle : 0.544 7.966 5609 Z= 0.287 Chirality : 0.044 0.199 641 Planarity : 0.004 0.040 705 Dihedral : 4.826 27.439 580 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.15 % 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: -0.12 (0.37), residues: 495 helix: -0.68 (1.37), residues: 17 sheet: 0.13 (0.34), residues: 202 loop : -0.09 (0.38), residues: 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.490 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 1.1280 time to fit residues: 80.8292 Evaluate side-chains 67 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1573 time to fit residues: 0.7866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 4125 Z= 0.280 Angle : 0.555 9.098 5609 Z= 0.294 Chirality : 0.044 0.202 641 Planarity : 0.004 0.040 705 Dihedral : 4.876 27.398 580 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.61 % 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: -0.25 (0.37), residues: 495 helix: -0.69 (1.38), residues: 17 sheet: 0.05 (0.34), residues: 205 loop : -0.19 (0.38), residues: 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.395 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 1.1446 time to fit residues: 79.5476 Evaluate side-chains 65 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1888 time to fit residues: 0.8904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 4125 Z= 0.238 Angle : 0.552 8.553 5609 Z= 0.293 Chirality : 0.044 0.198 641 Planarity : 0.004 0.040 705 Dihedral : 4.817 26.473 580 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.38 % 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: -0.16 (0.37), residues: 495 helix: -0.68 (1.37), residues: 17 sheet: 0.09 (0.33), residues: 213 loop : -0.11 (0.39), residues: 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.477 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 1.2265 time to fit residues: 83.9916 Evaluate side-chains 65 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.2634 time to fit residues: 1.1776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 4125 Z= 0.305 Angle : 0.582 9.724 5609 Z= 0.309 Chirality : 0.045 0.207 641 Planarity : 0.004 0.040 705 Dihedral : 4.920 26.637 580 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.92 % 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: -0.24 (0.37), residues: 495 helix: -0.68 (1.39), residues: 17 sheet: 0.03 (0.35), residues: 206 loop : -0.16 (0.38), residues: 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.490 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.1246 time to fit residues: 74.6643 Evaluate side-chains 63 residues out of total 436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN H 25 GLN L 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.073402 restraints weight = 6013.283| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.56 r_work: 0.2900 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.2875 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work: 0.2862 rms_B_bonded: 2.37 restraints_weight: 0.0625 r_work: 0.2849 rms_B_bonded: 2.44 restraints_weight: 0.0312 r_work: 0.2835 rms_B_bonded: 2.54 restraints_weight: 0.0156 r_work: 0.2821 rms_B_bonded: 2.66 restraints_weight: 0.0078 r_work: 0.2807 rms_B_bonded: 2.80 restraints_weight: 0.0039 r_work: 0.2791 rms_B_bonded: 2.97 restraints_weight: 0.0020 r_work: 0.2776 rms_B_bonded: 3.16 restraints_weight: 0.0010 r_work: 0.2759 rms_B_bonded: 3.39 restraints_weight: 0.0005 r_work: 0.2742 rms_B_bonded: 3.64 restraints_weight: 0.0002 r_work: 0.2723 rms_B_bonded: 3.93 restraints_weight: 0.0001 r_work: 0.2703 rms_B_bonded: 4.25 restraints_weight: 0.0001 r_work: 0.2683 rms_B_bonded: 4.62 restraints_weight: 0.0000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4125 Z= 0.207 Angle : 0.540 8.635 5609 Z= 0.288 Chirality : 0.044 0.190 641 Planarity : 0.004 0.039 705 Dihedral : 4.734 24.247 580 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.38 % 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: -0.08 (0.37), residues: 495 helix: -0.67 (1.36), residues: 17 sheet: 0.10 (0.33), residues: 214 loop : -0.01 (0.40), residues: 264 =============================================================================== Job complete usr+sys time: 2074.15 seconds wall clock time: 38 minutes 16.39 seconds (2296.39 seconds total)