Starting phenix.real_space_refine on Tue Aug 4 17:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0d_65502/08_2026/9w0d_65502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0d_65502/08_2026/9w0d_65502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w0d_65502/08_2026/9w0d_65502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0d_65502/08_2026/9w0d_65502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w0d_65502/08_2026/9w0d_65502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0d_65502/08_2026/9w0d_65502.map" } resolution = 3.17 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 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= 0.004 sd= 0.062 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 41 5.16 5 C 3541 2.51 5 N 946 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5555 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1806 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1848 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 217} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Time building chain proxies: 1.20, per 1000 atoms: 0.22 Number of scatterers: 5555 At special positions: 0 Unit cell: (96.005, 98.115, 82.29, 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 41 16.00 O 1027 8.00 N 946 7.00 C 3541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.32 Conformation dependent library (CDL) restraints added in 141.2 milliseconds 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 13.7% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.954A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.722A pdb=" N TRP A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.799A pdb=" N THR A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.598A pdb=" N ASN B 87 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.571A pdb=" N ILE B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.520A pdb=" N ILE C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.552A pdb=" N GLU C 65 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.731A pdb=" N LEU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.767A pdb=" N ALA C 245 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.926A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 removed outlier: 5.189A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.101A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.625A pdb=" N LEU B 16 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 23 " --> pdb=" O LEU B 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.970A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.749A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.735A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 212 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 53 removed outlier: 4.663A pdb=" N GLY C 214 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 53 removed outlier: 4.663A pdb=" N GLY C 214 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.866A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 151 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.453A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 402 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: 1.16 Time building geometry restraints manager: 0.46 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: 1799 1.34 - 1.46: 1195 1.46 - 1.57: 2643 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 5705 Sorted by residual: bond pdb=" CA GLN C 235 " pdb=" C GLN C 235 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.23e-02 6.61e+03 7.53e+00 bond pdb=" N SER C 236 " pdb=" CA SER C 236 " ideal model delta sigma weight residual 1.459 1.432 0.027 1.20e-02 6.94e+03 5.01e+00 bond pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.26e-02 6.30e+03 2.84e+00 bond pdb=" CA HIS C 238 " pdb=" C HIS C 238 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.23e-02 6.61e+03 2.64e+00 bond pdb=" CA GLY C 241 " pdb=" C GLY C 241 " ideal model delta sigma weight residual 1.510 1.526 -0.016 1.46e-02 4.69e+03 1.15e+00 ... (remaining 5700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 7546 1.43 - 2.86: 178 2.86 - 4.29: 43 4.29 - 5.72: 6 5.72 - 7.15: 1 Bond angle restraints: 7774 Sorted by residual: angle pdb=" N SER C 236 " pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 111.14 105.87 5.27 1.08e+00 8.57e-01 2.38e+01 angle pdb=" C GLY C 234 " pdb=" N GLN C 235 " pdb=" CA GLN C 235 " ideal model delta sigma weight residual 122.77 119.04 3.73 1.33e+00 5.65e-01 7.89e+00 angle pdb=" N GLY A 218 " pdb=" CA GLY A 218 " pdb=" C GLY A 218 " ideal model delta sigma weight residual 110.20 113.72 -3.52 1.32e+00 5.74e-01 7.11e+00 angle pdb=" N GLN C 235 " pdb=" CA GLN C 235 " pdb=" C GLN C 235 " ideal model delta sigma weight residual 108.73 112.91 -4.18 1.63e+00 3.76e-01 6.56e+00 angle pdb=" C PRO B 56 " pdb=" N GLU B 57 " pdb=" CA GLU B 57 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.38e+00 ... (remaining 7769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.58: 2781 12.58 - 25.16: 345 25.16 - 37.74: 165 37.74 - 50.32: 59 50.32 - 62.90: 19 Dihedral angle restraints: 3369 sinusoidal: 1318 harmonic: 2051 Sorted by residual: dihedral pdb=" CA MET B 198 " pdb=" C MET B 198 " pdb=" N ASP B 199 " pdb=" CA ASP B 199 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN B 179 " pdb=" C ASN B 179 " pdb=" N LEU B 180 " pdb=" CA LEU B 180 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG B 181 " pdb=" CD ARG B 181 " pdb=" NE ARG B 181 " pdb=" CZ ARG B 181 " ideal model delta sinusoidal sigma weight residual 180.00 135.95 44.05 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 3366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 473 0.028 - 0.057: 256 0.057 - 0.085: 76 0.085 - 0.114: 44 0.114 - 0.142: 15 Chirality restraints: 864 Sorted by residual: chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE C 167 " pdb=" N ILE C 167 " pdb=" C ILE C 167 " pdb=" CB ILE C 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 861 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 88 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE C 88 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE C 88 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN C 89 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 230 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO C 231 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 231 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 231 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 26 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C GLN B 26 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 26 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU B 27 " 0.007 2.00e-02 2.50e+03 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 3364 3.05 - 3.51: 5303 3.51 - 3.97: 8577 3.97 - 4.44: 10481 4.44 - 4.90: 17033 Nonbonded interactions: 44758 Sorted by model distance: nonbonded pdb=" OG1 THR B 171 " pdb=" O GLU C 50 " model vdw 2.585 3.040 nonbonded pdb=" C SER B 185 " pdb=" OG SER B 185 " model vdw 2.601 2.616 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.604 3.120 nonbonded pdb=" N THR A 57 " pdb=" OG1 THR A 57 " model vdw 2.606 2.496 nonbonded pdb=" C SER A 70 " pdb=" OG SER A 70 " model vdw 2.611 2.616 ... (remaining 44753 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 ========== 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 6.890 Find NCS groups from input model: 0.050 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:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.005 0.043 5705 Z= 0.205 Angle : 0.583 7.151 7774 Z= 0.315 Chirality : 0.043 0.142 864 Planarity : 0.004 0.034 1003 Dihedral : 15.289 62.902 2047 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.94 % Allowed : 20.88 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.30), residues: 701 helix: -2.12 (0.60), residues: 63 sheet: 0.45 (0.38), residues: 180 loop : -0.53 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.015 0.001 TYR B 100 PHE 0.015 0.002 PHE A 161 TRP 0.010 0.001 TRP C 155 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 ( 5705) covalent geometry : angle 0.58322 / 0.31 ( 7774) hydrogen bonds : bond 0.19245 / 13.59 ( 146) hydrogen bonds : angle 9.21488 / 6.18 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8353 (t80) cc_final: 0.7800 (t80) REVERT: A 91 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7379 (p90) REVERT: A 118 GLU cc_start: 0.8793 (tt0) cc_final: 0.8513 (tt0) REVERT: A 174 LYS cc_start: 0.8826 (mttp) cc_final: 0.8581 (mtpp) REVERT: A 211 ILE cc_start: 0.8531 (tp) cc_final: 0.8177 (pt) REVERT: A 228 HIS cc_start: 0.6926 (p-80) cc_final: 0.6618 (p90) REVERT: A 244 LYS cc_start: 0.9099 (ptmt) cc_final: 0.8743 (ptpt) REVERT: B 72 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7778 (mt-10) REVERT: B 76 THR cc_start: 0.8776 (p) cc_final: 0.8557 (t) REVERT: B 113 ASN cc_start: 0.8083 (p0) cc_final: 0.7868 (m-40) REVERT: B 116 LYS cc_start: 0.8621 (mttp) cc_final: 0.8186 (ttmm) REVERT: B 119 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: B 136 ASP cc_start: 0.8611 (t0) cc_final: 0.8187 (t0) REVERT: B 184 ASN cc_start: 0.8710 (p0) cc_final: 0.8497 (p0) REVERT: B 193 MET cc_start: 0.8226 (tpp) cc_final: 0.7972 (tpp) REVERT: B 222 MET cc_start: 0.4164 (ptt) cc_final: 0.2537 (tpt) REVERT: C 54 GLU cc_start: 0.8223 (tt0) cc_final: 0.7910 (tt0) REVERT: C 148 MET cc_start: 0.5381 (ppp) cc_final: 0.5034 (ptt) REVERT: C 160 GLN cc_start: 0.7344 (pt0) cc_final: 0.7092 (pt0) outliers start: 18 outliers final: 12 residues processed: 120 average time/residue: 0.1010 time to fit residues: 15.4096 Evaluate side-chains 117 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.0270 chunk 27 optimal weight: 10.0000 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 206 GLN C 48 GLN C 74 GLN C 186 ASN C 235 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115351 restraints weight = 7361.637| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.77 r_work: 0.3207 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5705 Z= 0.106 Angle : 0.478 4.631 7774 Z= 0.244 Chirality : 0.041 0.143 864 Planarity : 0.004 0.032 1003 Dihedral : 6.908 60.561 783 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.77 % Allowed : 20.55 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.30), residues: 701 helix: -2.03 (0.60), residues: 63 sheet: 0.83 (0.37), residues: 180 loop : -0.47 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 203 TYR 0.013 0.001 TYR B 100 PHE 0.013 0.001 PHE B 117 TRP 0.006 0.001 TRP B 177 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 5705) covalent geometry : angle 0.47757 / 0.24 ( 7774) hydrogen bonds : bond 0.03171 / 2.14 ( 146) hydrogen bonds : angle 6.45560 / 4.18 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8650 (p) REVERT: A 76 TYR cc_start: 0.8411 (t80) cc_final: 0.7811 (t80) REVERT: A 91 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7154 (p90) REVERT: A 118 GLU cc_start: 0.8851 (tt0) cc_final: 0.8542 (tt0) REVERT: A 158 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7602 (tt0) REVERT: A 174 LYS cc_start: 0.8550 (mttp) cc_final: 0.8285 (mtpp) REVERT: A 211 ILE cc_start: 0.8545 (tp) cc_final: 0.8273 (pt) REVERT: A 228 HIS cc_start: 0.7013 (p-80) cc_final: 0.6676 (p90) REVERT: A 244 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8788 (ptmt) REVERT: A 247 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8343 (mtpt) REVERT: A 270 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6524 (mtm110) REVERT: B 72 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7811 (mt-10) REVERT: B 91 MET cc_start: 0.6194 (ttm) cc_final: 0.5856 (ttt) REVERT: B 116 LYS cc_start: 0.8539 (mttp) cc_final: 0.8170 (ttmm) REVERT: B 136 ASP cc_start: 0.8601 (t0) cc_final: 0.8151 (t0) REVERT: B 193 MET cc_start: 0.8112 (tpp) cc_final: 0.7859 (tpp) REVERT: B 222 MET cc_start: 0.3806 (OUTLIER) cc_final: 0.2396 (ttp) REVERT: C 54 GLU cc_start: 0.8170 (tt0) cc_final: 0.7761 (tt0) REVERT: C 103 SER cc_start: 0.9056 (m) cc_final: 0.8763 (m) REVERT: C 148 MET cc_start: 0.5566 (ppp) cc_final: 0.5276 (ptp) REVERT: C 153 ILE cc_start: 0.8280 (tp) cc_final: 0.7978 (pt) REVERT: C 160 GLN cc_start: 0.7315 (pt0) cc_final: 0.6996 (pt0) outliers start: 17 outliers final: 8 residues processed: 122 average time/residue: 0.0895 time to fit residues: 13.9872 Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 238 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.0000 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115475 restraints weight = 7274.435| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.77 r_work: 0.3207 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5705 Z= 0.099 Angle : 0.460 7.479 7774 Z= 0.233 Chirality : 0.041 0.142 864 Planarity : 0.004 0.029 1003 Dihedral : 5.453 60.964 766 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.94 % Allowed : 20.55 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.31), residues: 701 helix: -1.95 (0.60), residues: 63 sheet: 0.78 (0.37), residues: 186 loop : -0.36 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 203 TYR 0.011 0.001 TYR B 100 PHE 0.013 0.001 PHE A 161 TRP 0.005 0.001 TRP A 249 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 5705) covalent geometry : angle 0.46005 / 0.23 ( 7774) hydrogen bonds : bond 0.03020 / 2.02 ( 146) hydrogen bonds : angle 5.95737 / 3.84 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8483 (t80) cc_final: 0.7845 (t80) REVERT: A 91 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7150 (p90) REVERT: A 118 GLU cc_start: 0.8807 (tt0) cc_final: 0.8554 (tt0) REVERT: A 158 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7598 (tt0) REVERT: A 174 LYS cc_start: 0.8507 (mttp) cc_final: 0.8241 (mtpp) REVERT: A 211 ILE cc_start: 0.8495 (tp) cc_final: 0.8235 (pt) REVERT: A 244 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8559 (ptpt) REVERT: B 72 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7847 (mt-10) REVERT: B 116 LYS cc_start: 0.8500 (mttp) cc_final: 0.8163 (ttmm) REVERT: B 136 ASP cc_start: 0.8583 (t0) cc_final: 0.8124 (t0) REVERT: B 193 MET cc_start: 0.8112 (tpp) cc_final: 0.7853 (tpp) REVERT: B 222 MET cc_start: 0.3825 (OUTLIER) cc_final: 0.2464 (tpp) REVERT: C 103 SER cc_start: 0.8970 (m) cc_final: 0.8694 (m) REVERT: C 148 MET cc_start: 0.5649 (ppp) cc_final: 0.5392 (ptp) REVERT: C 153 ILE cc_start: 0.8206 (tp) cc_final: 0.7913 (pt) REVERT: C 160 GLN cc_start: 0.7281 (pt0) cc_final: 0.6985 (pt0) REVERT: C 196 MET cc_start: 0.8217 (mtp) cc_final: 0.7924 (mtm) outliers start: 18 outliers final: 7 residues processed: 120 average time/residue: 0.0890 time to fit residues: 13.7680 Evaluate side-chains 116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 238 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108678 restraints weight = 7401.400| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.76 r_work: 0.3071 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 5705 Z= 0.315 Angle : 0.621 7.095 7774 Z= 0.318 Chirality : 0.045 0.153 864 Planarity : 0.005 0.034 1003 Dihedral : 6.210 62.886 765 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.24 % Allowed : 21.21 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.30), residues: 701 helix: -2.22 (0.59), residues: 55 sheet: 0.40 (0.36), residues: 188 loop : -0.36 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 104 TYR 0.016 0.002 TYR B 100 PHE 0.024 0.002 PHE A 91 TRP 0.008 0.001 TRP C 155 HIS 0.006 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.31 ( 5705) covalent geometry : angle 0.62097 / 0.32 ( 7774) hydrogen bonds : bond 0.03721 / 2.53 ( 146) hydrogen bonds : angle 6.17668 / 3.98 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.226 Fit side-chains REVERT: A 76 TYR cc_start: 0.8650 (t80) cc_final: 0.8085 (t80) REVERT: A 91 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.6951 (p90) REVERT: A 118 GLU cc_start: 0.8853 (tt0) cc_final: 0.8540 (tt0) REVERT: A 158 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7546 (tt0) REVERT: A 211 ILE cc_start: 0.8571 (tp) cc_final: 0.8311 (pt) REVERT: A 244 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8637 (ptmt) REVERT: B 27 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.3072 (pm20) REVERT: B 72 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7907 (mt-10) REVERT: B 116 LYS cc_start: 0.8611 (mttp) cc_final: 0.8113 (ttmm) REVERT: B 136 ASP cc_start: 0.8574 (t0) cc_final: 0.8215 (t0) REVERT: B 222 MET cc_start: 0.4169 (OUTLIER) cc_final: 0.2840 (tpp) REVERT: C 43 MET cc_start: 0.9248 (mmm) cc_final: 0.8833 (mmm) REVERT: C 65 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7821 (mp0) REVERT: C 78 ASP cc_start: 0.7884 (m-30) cc_final: 0.7581 (m-30) REVERT: C 148 MET cc_start: 0.6318 (ppp) cc_final: 0.6056 (ptm) REVERT: C 153 ILE cc_start: 0.8037 (tp) cc_final: 0.7681 (pt) REVERT: C 160 GLN cc_start: 0.7365 (pt0) cc_final: 0.7057 (pt0) REVERT: C 196 MET cc_start: 0.8149 (mtp) cc_final: 0.7836 (mtm) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.0853 time to fit residues: 12.9143 Evaluate side-chains 119 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 238 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112827 restraints weight = 7448.429| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.77 r_work: 0.3108 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5705 Z= 0.099 Angle : 0.474 5.779 7774 Z= 0.242 Chirality : 0.041 0.140 864 Planarity : 0.004 0.029 1003 Dihedral : 5.764 61.871 765 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.10 % Allowed : 22.02 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.31), residues: 701 helix: -2.18 (0.56), residues: 63 sheet: 0.58 (0.36), residues: 186 loop : -0.30 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.014 0.001 TYR B 100 PHE 0.015 0.001 PHE A 161 TRP 0.006 0.001 TRP C 169 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 5705) covalent geometry : angle 0.47402 / 0.24 ( 7774) hydrogen bonds : bond 0.02845 / 1.91 ( 146) hydrogen bonds : angle 5.73032 / 3.68 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8606 (t80) cc_final: 0.8139 (t80) REVERT: A 91 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7318 (p90) REVERT: A 118 GLU cc_start: 0.8801 (tt0) cc_final: 0.8471 (tt0) REVERT: A 158 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7501 (tt0) REVERT: A 174 LYS cc_start: 0.8606 (mttp) cc_final: 0.8306 (mtpp) REVERT: A 211 ILE cc_start: 0.8460 (tp) cc_final: 0.8229 (pt) REVERT: A 244 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8643 (ptmt) REVERT: B 27 GLU cc_start: 0.3501 (OUTLIER) cc_final: 0.3261 (pm20) REVERT: B 72 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7888 (mt-10) REVERT: B 116 LYS cc_start: 0.8603 (mttp) cc_final: 0.8141 (ttmm) REVERT: B 136 ASP cc_start: 0.8582 (t0) cc_final: 0.8212 (t0) REVERT: B 222 MET cc_start: 0.4224 (OUTLIER) cc_final: 0.2961 (ttp) REVERT: C 103 SER cc_start: 0.8990 (m) cc_final: 0.8697 (m) REVERT: C 153 ILE cc_start: 0.8097 (tp) cc_final: 0.7737 (pt) REVERT: C 160 GLN cc_start: 0.7435 (pt0) cc_final: 0.7119 (pt0) REVERT: C 196 MET cc_start: 0.8058 (mtp) cc_final: 0.7685 (mtp) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.0636 time to fit residues: 9.6189 Evaluate side-chains 121 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 238 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 0.0870 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 23 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110099 restraints weight = 7435.706| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.73 r_work: 0.3132 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5705 Z= 0.235 Angle : 0.549 5.363 7774 Z= 0.278 Chirality : 0.043 0.146 864 Planarity : 0.004 0.031 1003 Dihedral : 5.944 61.227 765 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.08 % Allowed : 21.04 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.31), residues: 701 helix: -2.26 (0.57), residues: 56 sheet: 0.44 (0.36), residues: 186 loop : -0.34 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 270 TYR 0.012 0.001 TYR B 100 PHE 0.020 0.002 PHE A 91 TRP 0.006 0.001 TRP C 155 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 ( 5705) covalent geometry : angle 0.54854 / 0.28 ( 7774) hydrogen bonds : bond 0.03272 / 2.17 ( 146) hydrogen bonds : angle 5.81446 / 3.74 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.191 Fit side-chains REVERT: A 76 TYR cc_start: 0.8626 (t80) cc_final: 0.8169 (t80) REVERT: A 118 GLU cc_start: 0.8875 (tt0) cc_final: 0.8548 (tt0) REVERT: A 158 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7508 (tt0) REVERT: A 211 ILE cc_start: 0.8409 (tp) cc_final: 0.8179 (pt) REVERT: A 244 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8542 (ptmt) REVERT: B 27 GLU cc_start: 0.3570 (OUTLIER) cc_final: 0.3316 (pm20) REVERT: B 72 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7937 (mt-10) REVERT: B 116 LYS cc_start: 0.8647 (mttp) cc_final: 0.8139 (ttmm) REVERT: B 136 ASP cc_start: 0.8576 (t0) cc_final: 0.8214 (t0) REVERT: B 222 MET cc_start: 0.4234 (OUTLIER) cc_final: 0.3148 (ttm) REVERT: C 65 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7886 (mp0) REVERT: C 153 ILE cc_start: 0.8066 (tp) cc_final: 0.7712 (pt) REVERT: C 160 GLN cc_start: 0.7310 (pt0) cc_final: 0.6985 (pt0) REVERT: C 196 MET cc_start: 0.8012 (mtp) cc_final: 0.7662 (mtp) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 0.0624 time to fit residues: 9.5834 Evaluate side-chains 123 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110947 restraints weight = 7383.740| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.73 r_work: 0.3131 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5705 Z= 0.179 Angle : 0.524 8.388 7774 Z= 0.263 Chirality : 0.042 0.142 864 Planarity : 0.004 0.029 1003 Dihedral : 5.794 61.388 765 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.24 % Allowed : 20.88 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.31), residues: 701 helix: -2.15 (0.58), residues: 56 sheet: 0.63 (0.37), residues: 180 loop : -0.36 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.010 0.001 TYR B 100 PHE 0.017 0.001 PHE A 91 TRP 0.006 0.001 TRP A 249 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 5705) covalent geometry : angle 0.52414 / 0.26 ( 7774) hydrogen bonds : bond 0.03012 / 1.99 ( 146) hydrogen bonds : angle 5.70680 / 3.67 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8860 (tt0) cc_final: 0.8553 (tt0) REVERT: A 158 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7478 (tt0) REVERT: A 174 LYS cc_start: 0.8810 (mttp) cc_final: 0.8495 (mtpp) REVERT: A 211 ILE cc_start: 0.8386 (tp) cc_final: 0.8165 (pt) REVERT: A 244 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8561 (ptmt) REVERT: A 270 ARG cc_start: 0.7466 (ttm110) cc_final: 0.7105 (ttm-80) REVERT: B 27 GLU cc_start: 0.3568 (OUTLIER) cc_final: 0.3300 (pm20) REVERT: B 72 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7905 (mt-10) REVERT: B 116 LYS cc_start: 0.8628 (mttp) cc_final: 0.8144 (ttmm) REVERT: B 136 ASP cc_start: 0.8557 (t0) cc_final: 0.8218 (t0) REVERT: B 222 MET cc_start: 0.4310 (OUTLIER) cc_final: 0.3342 (ttm) REVERT: C 153 ILE cc_start: 0.8002 (tp) cc_final: 0.7681 (pt) REVERT: C 160 GLN cc_start: 0.7341 (pt0) cc_final: 0.7077 (pt0) REVERT: C 196 MET cc_start: 0.8022 (mtp) cc_final: 0.7723 (mtp) REVERT: C 205 GLU cc_start: 0.6916 (tt0) cc_final: 0.6689 (pt0) outliers start: 26 outliers final: 20 residues processed: 119 average time/residue: 0.0717 time to fit residues: 11.1077 Evaluate side-chains 126 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 238 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111685 restraints weight = 7277.219| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.71 r_work: 0.3080 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5705 Z= 0.146 Angle : 0.504 8.605 7774 Z= 0.253 Chirality : 0.041 0.141 864 Planarity : 0.004 0.030 1003 Dihedral : 5.657 60.350 765 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.08 % Allowed : 21.53 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.31), residues: 701 helix: -2.21 (0.54), residues: 63 sheet: 0.68 (0.37), residues: 180 loop : -0.31 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 203 TYR 0.009 0.001 TYR B 100 PHE 0.014 0.001 PHE A 91 TRP 0.005 0.001 TRP A 249 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5705) covalent geometry : angle 0.50421 / 0.25 ( 7774) hydrogen bonds : bond 0.02898 / 1.91 ( 146) hydrogen bonds : angle 5.60392 / 3.60 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8813 (tt0) cc_final: 0.8579 (tt0) REVERT: A 158 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7460 (tt0) REVERT: A 174 LYS cc_start: 0.8654 (mttp) cc_final: 0.8343 (mtpp) REVERT: A 211 ILE cc_start: 0.8343 (tp) cc_final: 0.8121 (pt) REVERT: A 244 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8606 (ptpt) REVERT: A 270 ARG cc_start: 0.7434 (ttm110) cc_final: 0.7049 (ttm-80) REVERT: B 27 GLU cc_start: 0.3544 (OUTLIER) cc_final: 0.3278 (pm20) REVERT: B 72 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7897 (mt-10) REVERT: B 116 LYS cc_start: 0.8604 (mttp) cc_final: 0.8115 (ttmm) REVERT: B 136 ASP cc_start: 0.8548 (t0) cc_final: 0.8199 (t0) REVERT: B 222 MET cc_start: 0.4056 (OUTLIER) cc_final: 0.3420 (ttm) REVERT: C 153 ILE cc_start: 0.7940 (tp) cc_final: 0.7595 (pt) REVERT: C 160 GLN cc_start: 0.7259 (pt0) cc_final: 0.6962 (pt0) REVERT: C 196 MET cc_start: 0.8026 (mtp) cc_final: 0.7708 (mtp) REVERT: C 205 GLU cc_start: 0.6990 (tt0) cc_final: 0.6747 (pt0) outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.0836 time to fit residues: 13.1313 Evaluate side-chains 129 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 238 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109914 restraints weight = 7309.393| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.71 r_work: 0.3102 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5705 Z= 0.216 Angle : 0.561 9.385 7774 Z= 0.280 Chirality : 0.043 0.145 864 Planarity : 0.004 0.029 1003 Dihedral : 5.813 60.500 765 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.75 % Allowed : 21.86 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.31), residues: 701 helix: -2.13 (0.58), residues: 56 sheet: 0.51 (0.37), residues: 180 loop : -0.38 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 203 TYR 0.012 0.001 TYR A 135 PHE 0.021 0.002 PHE A 91 TRP 0.007 0.001 TRP C 155 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 ( 5705) covalent geometry : angle 0.56061 / 0.28 ( 7774) hydrogen bonds : bond 0.03169 / 2.10 ( 146) hydrogen bonds : angle 5.75010 / 3.69 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8894 (tt0) cc_final: 0.8601 (tt0) REVERT: A 158 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7479 (tt0) REVERT: A 211 ILE cc_start: 0.8386 (tp) cc_final: 0.8164 (pt) REVERT: A 244 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8478 (ptmt) REVERT: A 270 ARG cc_start: 0.7414 (ttm110) cc_final: 0.7008 (ttm-80) REVERT: B 18 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6020 (mm) REVERT: B 72 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7916 (mt-10) REVERT: B 76 THR cc_start: 0.8747 (p) cc_final: 0.8508 (t) REVERT: B 116 LYS cc_start: 0.8656 (mttp) cc_final: 0.8133 (ttmm) REVERT: B 136 ASP cc_start: 0.8570 (t0) cc_final: 0.8217 (t0) REVERT: B 222 MET cc_start: 0.4146 (OUTLIER) cc_final: 0.3546 (ttm) REVERT: C 65 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7833 (mp0) REVERT: C 153 ILE cc_start: 0.7983 (tp) cc_final: 0.7636 (pt) REVERT: C 160 GLN cc_start: 0.7214 (pt0) cc_final: 0.6901 (pt0) REVERT: C 196 MET cc_start: 0.8047 (mtp) cc_final: 0.7726 (mtp) REVERT: C 205 GLU cc_start: 0.7041 (tt0) cc_final: 0.6711 (mm-30) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.0816 time to fit residues: 12.3045 Evaluate side-chains 123 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111912 restraints weight = 7275.404| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.98 r_work: 0.3169 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5705 Z= 0.088 Angle : 0.484 9.617 7774 Z= 0.243 Chirality : 0.041 0.142 864 Planarity : 0.004 0.030 1003 Dihedral : 5.540 62.311 765 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.31 % Allowed : 24.47 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.31), residues: 701 helix: -2.09 (0.56), residues: 63 sheet: 0.76 (0.36), residues: 192 loop : -0.24 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.007 0.001 TYR B 100 PHE 0.007 0.001 PHE C 157 TRP 0.018 0.001 TRP B 207 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 5705) covalent geometry : angle 0.48446 / 0.24 ( 7774) hydrogen bonds : bond 0.02633 / 1.73 ( 146) hydrogen bonds : angle 5.39685 / 3.46 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8576 (p) REVERT: A 118 GLU cc_start: 0.8823 (tt0) cc_final: 0.8612 (tt0) REVERT: A 174 LYS cc_start: 0.8586 (mttp) cc_final: 0.8322 (mtpp) REVERT: A 211 ILE cc_start: 0.8403 (tp) cc_final: 0.8189 (pt) REVERT: A 244 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8646 (ptpt) REVERT: A 270 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7232 (ttm-80) REVERT: B 63 PHE cc_start: 0.8023 (m-10) cc_final: 0.7675 (m-10) REVERT: B 72 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7987 (mt-10) REVERT: B 116 LYS cc_start: 0.8579 (mttp) cc_final: 0.8162 (ttmm) REVERT: B 136 ASP cc_start: 0.8546 (t0) cc_final: 0.8177 (t0) REVERT: B 222 MET cc_start: 0.4080 (OUTLIER) cc_final: 0.3618 (ttp) REVERT: C 103 SER cc_start: 0.9016 (m) cc_final: 0.8760 (m) REVERT: C 153 ILE cc_start: 0.8102 (tp) cc_final: 0.7796 (pt) REVERT: C 160 GLN cc_start: 0.7238 (pt0) cc_final: 0.6981 (pt0) REVERT: C 205 GLU cc_start: 0.6907 (tt0) cc_final: 0.6561 (pt0) outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.0776 time to fit residues: 11.2882 Evaluate side-chains 115 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 0.0370 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110276 restraints weight = 7250.254| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.95 r_work: 0.3144 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5705 Z= 0.144 Angle : 0.493 9.404 7774 Z= 0.247 Chirality : 0.041 0.143 864 Planarity : 0.004 0.030 1003 Dihedral : 5.505 60.617 765 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.47 % Allowed : 24.31 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.31), residues: 701 helix: -2.05 (0.56), residues: 63 sheet: 0.81 (0.36), residues: 192 loop : -0.26 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.008 0.001 TYR B 159 PHE 0.011 0.001 PHE A 91 TRP 0.006 0.001 TRP A 249 HIS 0.005 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 5705) covalent geometry : angle 0.49333 / 0.25 ( 7774) hydrogen bonds : bond 0.02769 / 1.82 ( 146) hydrogen bonds : angle 5.40308 / 3.47 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.24 seconds wall clock time: 22 minutes 22.87 seconds (1342.87 seconds total)