Starting phenix.real_space_refine on Fri Dec 27 06:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qwl_14188/12_2024/7qwl_14188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qwl_14188/12_2024/7qwl_14188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qwl_14188/12_2024/7qwl_14188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qwl_14188/12_2024/7qwl_14188.map" model { file = "/net/cci-nas-00/data/ceres_data/7qwl_14188/12_2024/7qwl_14188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qwl_14188/12_2024/7qwl_14188.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.94, per 1000 atoms: 0.90 Number of scatterers: 3258 At special positions: 0 Unit cell: (105.8, 98.9, 31.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.69 Conformation dependent library (CDL) restraints added in 395.5 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.961A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA7, first strand: chain 'A' and resid 165 through 170 removed outlier: 6.459A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 165 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLN C 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 167 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLN C 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.412A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.464A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AB2, first strand: chain 'A' and resid 194 through 198 removed outlier: 8.237A pdb=" N ILE A 195 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N TYR A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.382A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AB5, first strand: chain 'A' and resid 214 through 218 Processing sheet with id=AB6, first strand: chain 'A' and resid 221 through 236 removed outlier: 8.501A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLN C 229 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N MET B 228 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR C 231 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 230 " --> pdb=" O THR C 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 221 through 236 removed outlier: 8.501A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 240 through 252 removed outlier: 6.851A pdb=" N VAL A 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP B 252 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 251 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP C 252 " --> pdb=" O VAL B 251 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 0.77 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 938 1.33 - 1.45: 521 1.45 - 1.57: 1817 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CB THR C 215 " pdb=" OG1 THR C 215 " ideal model delta sigma weight residual 1.433 1.387 0.046 1.60e-02 3.91e+03 8.14e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.62e+00 bond pdb=" CZ ARG C 247 " pdb=" NH2 ARG C 247 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.10e+00 bond pdb=" CZ ARG C 180 " pdb=" NH2 ARG C 180 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.55e+00 bond pdb=" CZ ARG A 247 " pdb=" NH2 ARG A 247 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 3544 2.61 - 5.23: 798 5.23 - 7.84: 147 7.84 - 10.45: 11 10.45 - 13.07: 3 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 109.07 122.14 -13.07 1.52e+00 4.33e-01 7.39e+01 angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" CB GLU C 246 " ideal model delta sigma weight residual 111.66 98.72 12.94 1.67e+00 3.59e-01 6.01e+01 angle pdb=" OD1 ASN A 164 " pdb=" CG ASN A 164 " pdb=" ND2 ASN A 164 " ideal model delta sigma weight residual 122.60 115.11 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" OD1 ASN C 164 " pdb=" CG ASN C 164 " pdb=" ND2 ASN C 164 " ideal model delta sigma weight residual 122.60 116.24 6.36 1.00e+00 1.00e+00 4.04e+01 angle pdb=" C ILE A 219 " pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 111.06 116.62 -5.56 8.80e-01 1.29e+00 3.99e+01 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.07: 1830 16.07 - 32.13: 122 32.13 - 48.19: 25 48.19 - 64.26: 9 64.26 - 80.32: 9 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" C ASN B 183 " pdb=" N ASN B 183 " pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " ideal model delta harmonic sigma weight residual -122.60 -137.49 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA ASN B 183 " pdb=" C ASN B 183 " pdb=" N ILE B 184 " pdb=" CA ILE B 184 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N THR B 153 " pdb=" CA THR B 153 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 337 0.110 - 0.220: 156 0.220 - 0.329: 38 0.329 - 0.439: 10 0.439 - 0.549: 2 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN B 183 " pdb=" N ASN B 183 " pdb=" C ASN B 183 " pdb=" CB ASN B 183 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA GLN A 138 " pdb=" N GLN A 138 " pdb=" C GLN A 138 " pdb=" CB GLN A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " -0.134 2.00e-02 2.50e+03 8.25e-02 1.36e+02 pdb=" CG TYR B 135 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " 0.069 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 135 " -0.129 2.00e-02 2.50e+03 8.01e-02 1.28e+02 pdb=" CG TYR A 135 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 135 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 135 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 135 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 135 " 0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 135 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR A 135 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.153 2.00e-02 2.50e+03 7.96e-02 1.27e+02 pdb=" CG TYR C 143 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.107 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1602 2.98 - 3.46: 2809 3.46 - 3.94: 5234 3.94 - 4.42: 5555 4.42 - 4.90: 10249 Nonbonded interactions: 25449 Sorted by model distance: nonbonded pdb=" OE1 GLU A 161 " pdb=" OG SER B 120 " model vdw 2.501 3.040 nonbonded pdb=" OE1 GLU B 161 " pdb=" OG SER C 120 " model vdw 2.526 3.040 nonbonded pdb=" OD2 ASP C 212 " pdb=" OG1 THR C 215 " model vdw 2.550 3.040 nonbonded pdb=" OD2 ASP A 212 " pdb=" OG1 THR A 215 " model vdw 2.559 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" OG1 THR B 215 " model vdw 2.579 3.040 ... (remaining 25444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 12.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.012 0.046 3312 Z= 0.796 Angle : 2.274 13.066 4503 Z= 1.512 Chirality : 0.135 0.549 543 Planarity : 0.015 0.083 558 Dihedral : 13.778 80.320 1206 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.28 % Favored : 88.22 % Rotamer: Outliers : 1.06 % Allowed : 2.65 % Favored : 96.30 % Cbeta Deviations : 3.59 % 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: -3.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS A 239 PHE 0.047 0.013 PHE A 171 TYR 0.153 0.031 TYR C 143 ARG 0.002 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7814 (mttt) cc_final: 0.7568 (mtpt) REVERT: A 241 GLU cc_start: 0.7171 (tt0) cc_final: 0.6929 (tt0) REVERT: B 122 ASP cc_start: 0.7749 (t0) cc_final: 0.6593 (t0) REVERT: C 139 LYS cc_start: 0.8698 (mttt) cc_final: 0.8349 (mmmt) outliers start: 4 outliers final: 0 residues processed: 105 average time/residue: 0.1693 time to fit residues: 21.1630 Evaluate side-chains 69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN B 245 GLN C 155 ASN C 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.208 Angle : 0.746 6.759 4503 Z= 0.411 Chirality : 0.053 0.146 543 Planarity : 0.003 0.013 558 Dihedral : 8.049 23.491 447 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.48 % Rotamer: Outliers : 4.50 % Allowed : 10.05 % Favored : 85.45 % 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: -3.12 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.008 0.001 PHE C 237 TYR 0.026 0.002 TYR A 143 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.7249 (tt0) cc_final: 0.6980 (tt0) REVERT: B 150 LEU cc_start: 0.9038 (tp) cc_final: 0.8832 (tp) REVERT: B 178 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6576 (tptp) REVERT: B 207 MET cc_start: 0.7479 (ttt) cc_final: 0.7278 (ttm) REVERT: C 178 LYS cc_start: 0.7086 (mttp) cc_final: 0.6693 (tptt) REVERT: C 210 MET cc_start: 0.7614 (mtp) cc_final: 0.7254 (mtt) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.1847 time to fit residues: 19.5974 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3312 Z= 0.390 Angle : 0.743 5.332 4503 Z= 0.416 Chirality : 0.055 0.162 543 Planarity : 0.003 0.015 558 Dihedral : 8.076 23.809 447 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 7.41 % Allowed : 10.58 % Favored : 82.01 % 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: -3.00 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 222 PHE 0.011 0.001 PHE B 171 TYR 0.023 0.003 TYR C 143 ARG 0.003 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.380 Fit side-chains REVERT: A 122 ASP cc_start: 0.8039 (t0) cc_final: 0.7514 (t0) REVERT: A 241 GLU cc_start: 0.7457 (tt0) cc_final: 0.7136 (tt0) REVERT: B 161 GLU cc_start: 0.8466 (tp30) cc_final: 0.8229 (tp30) REVERT: B 178 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6546 (tptp) REVERT: B 207 MET cc_start: 0.7534 (ttt) cc_final: 0.7333 (ttm) REVERT: B 212 ASP cc_start: 0.9074 (p0) cc_final: 0.8775 (p0) REVERT: C 178 LYS cc_start: 0.7240 (mttp) cc_final: 0.6666 (tptp) outliers start: 28 outliers final: 19 residues processed: 76 average time/residue: 0.1885 time to fit residues: 16.9138 Evaluate side-chains 77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3312 Z= 0.176 Angle : 0.610 5.778 4503 Z= 0.344 Chirality : 0.051 0.165 543 Planarity : 0.002 0.013 558 Dihedral : 7.183 20.729 447 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.03 % Allowed : 15.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.005 0.001 PHE A 213 TYR 0.017 0.002 TYR B 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.7385 (tt0) cc_final: 0.7129 (tt0) REVERT: B 178 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6490 (tptp) REVERT: B 241 GLU cc_start: 0.7277 (tt0) cc_final: 0.6970 (tt0) REVERT: C 147 THR cc_start: 0.7722 (m) cc_final: 0.7508 (m) REVERT: C 178 LYS cc_start: 0.7003 (mttp) cc_final: 0.6555 (tptt) outliers start: 19 outliers final: 9 residues processed: 77 average time/residue: 0.1813 time to fit residues: 16.5282 Evaluate side-chains 71 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3312 Z= 0.169 Angle : 0.594 5.861 4503 Z= 0.335 Chirality : 0.051 0.158 543 Planarity : 0.002 0.013 558 Dihedral : 6.786 19.670 447 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.76 % Allowed : 16.14 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.010 0.001 PHE C 237 TYR 0.020 0.002 TYR B 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 140 ARG cc_start: 0.6413 (ppt170) cc_final: 0.6016 (tmm160) REVERT: A 241 GLU cc_start: 0.7410 (tt0) cc_final: 0.7173 (tt0) REVERT: B 178 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6421 (tptp) REVERT: B 207 MET cc_start: 0.7840 (ttm) cc_final: 0.7570 (ttt) REVERT: B 241 GLU cc_start: 0.7279 (tt0) cc_final: 0.7065 (tt0) REVERT: C 147 THR cc_start: 0.7730 (m) cc_final: 0.7529 (m) REVERT: C 178 LYS cc_start: 0.6931 (mttp) cc_final: 0.6509 (tptt) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.2013 time to fit residues: 16.8949 Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.0040 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3312 Z= 0.304 Angle : 0.643 5.531 4503 Z= 0.365 Chirality : 0.052 0.154 543 Planarity : 0.002 0.013 558 Dihedral : 7.098 21.463 447 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 4.50 % Allowed : 16.67 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.019 0.002 PHE B 237 TYR 0.023 0.002 TYR B 143 ARG 0.002 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.381 Fit side-chains REVERT: A 241 GLU cc_start: 0.7470 (tt0) cc_final: 0.7186 (tt0) REVERT: B 178 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6415 (tptp) REVERT: B 212 ASP cc_start: 0.8836 (p0) cc_final: 0.8528 (p0) REVERT: C 178 LYS cc_start: 0.7067 (mttp) cc_final: 0.6500 (tptp) outliers start: 17 outliers final: 15 residues processed: 67 average time/residue: 0.1776 time to fit residues: 14.4013 Evaluate side-chains 69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN B 245 GLN C 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3312 Z= 0.359 Angle : 0.672 5.308 4503 Z= 0.379 Chirality : 0.054 0.197 543 Planarity : 0.002 0.013 558 Dihedral : 7.354 21.626 447 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.03 % Allowed : 16.40 % Favored : 78.57 % 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: -3.07 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.016 0.002 PHE B 237 TYR 0.024 0.002 TYR B 143 ARG 0.002 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.380 Fit side-chains REVERT: A 124 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7076 (mmmt) REVERT: A 140 ARG cc_start: 0.6844 (ppt170) cc_final: 0.6218 (ppt170) REVERT: A 241 GLU cc_start: 0.7456 (tt0) cc_final: 0.7139 (tt0) REVERT: B 178 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6447 (tptp) REVERT: B 212 ASP cc_start: 0.8960 (p0) cc_final: 0.8615 (p0) REVERT: C 178 LYS cc_start: 0.7134 (mttp) cc_final: 0.6351 (tptt) outliers start: 19 outliers final: 14 residues processed: 67 average time/residue: 0.1687 time to fit residues: 13.6549 Evaluate side-chains 71 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3312 Z= 0.360 Angle : 0.675 4.878 4503 Z= 0.379 Chirality : 0.053 0.160 543 Planarity : 0.002 0.013 558 Dihedral : 7.335 22.489 447 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.50 % Allowed : 17.20 % Favored : 78.31 % 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: -3.15 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.017 0.002 PHE C 237 TYR 0.022 0.002 TYR B 143 ARG 0.002 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.391 Fit side-chains REVERT: A 124 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.6925 (mmmt) REVERT: A 241 GLU cc_start: 0.7429 (tt0) cc_final: 0.7151 (tt0) REVERT: B 178 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6439 (tptp) REVERT: B 209 TYR cc_start: 0.8762 (m-80) cc_final: 0.8422 (m-80) REVERT: B 212 ASP cc_start: 0.8986 (p0) cc_final: 0.8627 (p0) REVERT: C 178 LYS cc_start: 0.7116 (mttp) cc_final: 0.6529 (tptt) outliers start: 17 outliers final: 13 residues processed: 66 average time/residue: 0.2104 time to fit residues: 16.5505 Evaluate side-chains 71 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3312 Z= 0.378 Angle : 0.701 5.266 4503 Z= 0.393 Chirality : 0.054 0.149 543 Planarity : 0.003 0.013 558 Dihedral : 7.379 22.041 447 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 17.20 % Favored : 78.04 % 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: -3.23 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.018 0.002 PHE C 237 TYR 0.022 0.003 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.386 Fit side-chains REVERT: A 124 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7189 (mmtt) REVERT: A 241 GLU cc_start: 0.7417 (tt0) cc_final: 0.7164 (tt0) REVERT: B 209 TYR cc_start: 0.8760 (m-80) cc_final: 0.8426 (m-80) REVERT: B 212 ASP cc_start: 0.8982 (p0) cc_final: 0.8648 (p0) REVERT: C 178 LYS cc_start: 0.7144 (mttp) cc_final: 0.6561 (tptt) outliers start: 18 outliers final: 15 residues processed: 68 average time/residue: 0.1790 time to fit residues: 14.5875 Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3312 Z= 0.161 Angle : 0.615 5.856 4503 Z= 0.341 Chirality : 0.051 0.139 543 Planarity : 0.002 0.014 558 Dihedral : 6.756 20.199 447 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.97 % Allowed : 17.72 % Favored : 78.31 % 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: -3.09 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.016 0.002 PHE B 237 TYR 0.018 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.383 Fit side-chains REVERT: A 140 ARG cc_start: 0.6625 (ppt170) cc_final: 0.6170 (tmm160) REVERT: A 163 GLU cc_start: 0.8084 (mp0) cc_final: 0.7698 (mp0) REVERT: A 241 GLU cc_start: 0.7377 (tt0) cc_final: 0.7134 (tt0) REVERT: A 247 ARG cc_start: 0.8408 (ptm160) cc_final: 0.8158 (ttt90) REVERT: B 178 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6421 (tptp) REVERT: C 178 LYS cc_start: 0.7081 (mttp) cc_final: 0.6524 (tptt) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.1976 time to fit residues: 18.2214 Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.130558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.114242 restraints weight = 4062.746| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.33 r_work: 0.3951 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3312 Z= 0.182 Angle : 0.618 5.245 4503 Z= 0.347 Chirality : 0.051 0.136 543 Planarity : 0.002 0.017 558 Dihedral : 6.648 20.939 447 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.17 % Allowed : 18.52 % Favored : 78.31 % 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: -3.11 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 239 PHE 0.016 0.001 PHE B 237 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.59 seconds wall clock time: 24 minutes 10.19 seconds (1450.19 seconds total)