Starting phenix.real_space_refine on Fri Sep 11 01:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0b_65500/09_2026/9w0b_65500.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0b_65500/09_2026/9w0b_65500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w0b_65500/09_2026/9w0b_65500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0b_65500/09_2026/9w0b_65500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w0b_65500/09_2026/9w0b_65500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0b_65500/09_2026/9w0b_65500.map" } resolution = 2.52 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= 0.095 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 4069 2.51 5 N 1087 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6402 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2300 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1880 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1904 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.36, per 1000 atoms: 0.21 Number of scatterers: 6402 At special positions: 0 Unit cell: (98.115, 100.225, 84.4, 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 1205 8.00 N 1087 7.00 C 4069 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: 0.45 Conformation dependent library (CDL) restraints added in 272.4 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 15.5% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 removed outlier: 3.518A pdb=" N THR A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.815A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.833A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.632A pdb=" N ALA B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.828A pdb=" N ARG B 151 " --> pdb=" O LYS B 148 " (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 42 through 47 removed outlier: 4.118A pdb=" N MET C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 49 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.610A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 22 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.851A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.977A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.936A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.936A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.623A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.762A pdb=" N LEU C 80 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET C 196 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 82 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.246A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 513 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: 0.86 Time building geometry restraints manager: 0.56 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: 1178 1.33 - 1.45: 1697 1.45 - 1.57: 3621 1.57 - 1.69: 1 1.69 - 1.81: 68 Bond restraints: 6565 Sorted by residual: bond pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 1.462 1.384 0.077 1.15e-02 7.56e+03 4.51e+01 bond pdb=" CA MET A 241 " pdb=" C MET A 241 " ideal model delta sigma weight residual 1.523 1.450 0.074 1.18e-02 7.18e+03 3.89e+01 bond pdb=" C GLY C 63 " pdb=" N MET C 64 " ideal model delta sigma weight residual 1.332 1.261 0.070 1.52e-02 4.33e+03 2.14e+01 bond pdb=" N MET A 241 " pdb=" CA MET A 241 " ideal model delta sigma weight residual 1.454 1.403 0.051 1.19e-02 7.06e+03 1.87e+01 bond pdb=" C ALA A 214 " pdb=" N ASP A 215 " ideal model delta sigma weight residual 1.331 1.284 0.048 1.14e-02 7.69e+03 1.75e+01 ... (remaining 6560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 8891 3.22 - 6.44: 39 6.44 - 9.65: 8 9.65 - 12.87: 2 12.87 - 16.09: 3 Bond angle restraints: 8943 Sorted by residual: angle pdb=" N ASP A 215 " pdb=" CA ASP A 215 " pdb=" C ASP A 215 " ideal model delta sigma weight residual 112.25 100.00 12.25 1.36e+00 5.41e-01 8.11e+01 angle pdb=" C MET C 64 " pdb=" CA MET C 64 " pdb=" CB MET C 64 " ideal model delta sigma weight residual 110.11 126.20 -16.09 1.90e+00 2.77e-01 7.17e+01 angle pdb=" C GLY C 63 " pdb=" N MET C 64 " pdb=" CA MET C 64 " ideal model delta sigma weight residual 121.94 106.24 15.70 2.00e+00 2.50e-01 6.16e+01 angle pdb=" N ALA A 152 " pdb=" CA ALA A 152 " pdb=" C ALA A 152 " ideal model delta sigma weight residual 110.14 120.48 -10.34 1.55e+00 4.16e-01 4.45e+01 angle pdb=" C ALA A 152 " pdb=" N LEU A 153 " pdb=" CA LEU A 153 " ideal model delta sigma weight residual 121.50 130.83 -9.33 1.43e+00 4.89e-01 4.26e+01 ... (remaining 8938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 3427 17.22 - 34.44: 339 34.44 - 51.66: 92 51.66 - 68.88: 38 68.88 - 86.10: 8 Dihedral angle restraints: 3904 sinusoidal: 1528 harmonic: 2376 Sorted by residual: dihedral pdb=" C MET C 64 " pdb=" N MET C 64 " pdb=" CA MET C 64 " pdb=" CB MET C 64 " ideal model delta harmonic sigma weight residual -122.60 -153.50 30.90 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" N MET C 64 " pdb=" C MET C 64 " pdb=" CA MET C 64 " pdb=" CB MET C 64 " ideal model delta harmonic sigma weight residual 122.80 149.35 -26.55 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" C MET A 241 " pdb=" N MET A 241 " pdb=" CA MET A 241 " pdb=" CB MET A 241 " ideal model delta harmonic sigma weight residual -122.60 -109.21 -13.39 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 3901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 1003 0.237 - 0.475: 1 0.475 - 0.712: 0 0.712 - 0.950: 0 0.950 - 1.187: 1 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CA MET C 64 " pdb=" N MET C 64 " pdb=" C MET C 64 " pdb=" CB MET C 64 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.52e+01 chirality pdb=" CA ALA A 152 " pdb=" N ALA A 152 " pdb=" C ALA A 152 " pdb=" CB ALA A 152 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.44 2.00e-01 2.50e+01 4.75e+00 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 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1002 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 63 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C GLY C 63 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY C 63 " 0.015 2.00e-02 2.50e+03 pdb=" N MET C 64 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 148 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C VAL A 148 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL A 148 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO A 149 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 240 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C TYR A 240 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR A 240 " -0.011 2.00e-02 2.50e+03 pdb=" N MET A 241 " -0.010 2.00e-02 2.50e+03 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1314 2.78 - 3.31: 5673 3.31 - 3.84: 10938 3.84 - 4.37: 13671 4.37 - 4.90: 22530 Nonbonded interactions: 54126 Sorted by model distance: nonbonded pdb=" O GLY C 63 " pdb=" CA MET C 64 " model vdw 2.256 2.776 nonbonded pdb=" O PRO A 213 " pdb=" OG1 THR A 216 " model vdw 2.299 3.040 nonbonded pdb=" N GLY A 151 " pdb=" N ALA A 152 " model vdw 2.486 2.560 nonbonded pdb=" N ASP A 215 " pdb=" N THR A 216 " model vdw 2.554 2.560 nonbonded pdb=" N ASP C 208 " pdb=" OD1 ASP C 208 " model vdw 2.563 3.120 ... (remaining 54121 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: 0.440 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.810 Find NCS groups from input model: 0.020 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:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.004 0.077 6565 Z= 0.244 Angle : 0.680 16.089 8943 Z= 0.387 Chirality : 0.058 1.187 1005 Planarity : 0.004 0.034 1157 Dihedral : 16.399 86.101 2370 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.69 % Allowed : 18.41 % Favored : 78.90 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 3.92 % 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: -0.55 (0.28), residues: 812 helix: -1.68 (0.63), residues: 60 sheet: 0.29 (0.37), residues: 197 loop : -0.44 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.010 0.001 TYR B 31 PHE 0.007 0.001 PHE C 178 TRP 0.008 0.001 TRP B 79 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.24 ( 6565) covalent geometry : angle 0.68006 / 0.39 ( 8943) hydrogen bonds : bond 0.18715 / 11.85 ( 172) hydrogen bonds : angle 8.33533 / 5.79 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8615 (ttpt) REVERT: A 19 GLU cc_start: 0.7981 (pm20) cc_final: 0.7416 (pp20) REVERT: A 102 GLN cc_start: 0.8614 (mm110) cc_final: 0.8354 (tp40) REVERT: A 136 MET cc_start: 0.5288 (ttt) cc_final: 0.2948 (mmm) REVERT: A 150 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7842 (p) REVERT: A 161 PHE cc_start: 0.8317 (m-80) cc_final: 0.7105 (p90) REVERT: C 74 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8363 (mm110) REVERT: C 78 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: C 114 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: C 205 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: C 229 ASP cc_start: 0.8494 (m-30) cc_final: 0.7805 (m-30) outliers start: 19 outliers final: 9 residues processed: 128 average time/residue: 0.4868 time to fit residues: 65.6506 Evaluate side-chains 124 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 205 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 44 GLN A 219 ASN A 292 HIS B 45 HIS B 55 GLN B 206 GLN B 240 ASN C 235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.092618 restraints weight = 7630.227| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.90 r_work: 0.2937 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6565 Z= 0.141 Angle : 0.499 5.818 8943 Z= 0.258 Chirality : 0.043 0.148 1005 Planarity : 0.004 0.036 1157 Dihedral : 8.165 56.730 916 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.11 % Allowed : 16.57 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.41 (0.28), residues: 812 helix: -1.52 (0.64), residues: 60 sheet: 0.53 (0.36), residues: 207 loop : -0.42 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.014 0.001 TYR B 31 PHE 0.014 0.001 PHE C 215 TRP 0.005 0.001 TRP A 93 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6565) covalent geometry : angle 0.49934 / 0.26 ( 8943) hydrogen bonds : bond 0.04005 / 2.52 ( 172) hydrogen bonds : angle 5.97278 / 4.20 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8653 (ttpt) REVERT: A 19 GLU cc_start: 0.8049 (pm20) cc_final: 0.7426 (pp20) REVERT: A 98 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7739 (mttm) REVERT: A 102 GLN cc_start: 0.8608 (mm110) cc_final: 0.8294 (tp40) REVERT: A 136 MET cc_start: 0.5473 (ttt) cc_final: 0.2945 (mmm) REVERT: A 161 PHE cc_start: 0.8070 (m-80) cc_final: 0.6178 (p90) REVERT: A 164 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6662 (mp10) REVERT: B 74 ASN cc_start: 0.8607 (p0) cc_final: 0.8381 (p0) REVERT: C 41 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7999 (mtm180) REVERT: C 78 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: C 114 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7917 (pp20) REVERT: C 205 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 229 ASP cc_start: 0.8546 (m-30) cc_final: 0.7826 (m-30) outliers start: 29 outliers final: 12 residues processed: 132 average time/residue: 0.4879 time to fit residues: 67.8210 Evaluate side-chains 122 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 111 GLN B 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095427 restraints weight = 7549.853| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.89 r_work: 0.2972 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6565 Z= 0.085 Angle : 0.450 6.654 8943 Z= 0.233 Chirality : 0.042 0.147 1005 Planarity : 0.004 0.030 1157 Dihedral : 6.941 58.669 905 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.40 % Allowed : 17.56 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.35 (0.28), residues: 812 helix: -1.52 (0.63), residues: 61 sheet: 0.55 (0.36), residues: 213 loop : -0.37 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.012 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.005 0.001 TRP B 207 HIS 0.001 0.000 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 ( 6565) covalent geometry : angle 0.44997 / 0.23 ( 8943) hydrogen bonds : bond 0.03175 / 2.01 ( 172) hydrogen bonds : angle 5.55791 / 3.91 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8541 (ttpt) REVERT: A 102 GLN cc_start: 0.8588 (mm110) cc_final: 0.8278 (tp40) REVERT: A 136 MET cc_start: 0.5347 (ttt) cc_final: 0.2953 (mmm) REVERT: A 161 PHE cc_start: 0.8000 (m-80) cc_final: 0.6133 (p90) REVERT: A 164 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: B 74 ASN cc_start: 0.8631 (p0) cc_final: 0.8408 (p0) REVERT: C 74 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8319 (mm110) REVERT: C 114 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8026 (pp20) REVERT: C 145 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: C 205 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 229 ASP cc_start: 0.8422 (m-30) cc_final: 0.7753 (m-30) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.4769 time to fit residues: 67.9326 Evaluate side-chains 128 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.090212 restraints weight = 7822.842| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.86 r_work: 0.2906 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6565 Z= 0.185 Angle : 0.522 6.988 8943 Z= 0.270 Chirality : 0.044 0.175 1005 Planarity : 0.004 0.030 1157 Dihedral : 7.002 58.052 901 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.39 % Allowed : 17.00 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.34 (0.28), residues: 812 helix: -1.36 (0.65), residues: 60 sheet: 0.59 (0.36), residues: 207 loop : -0.39 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 65 TYR 0.016 0.001 TYR B 31 PHE 0.015 0.002 PHE C 117 TRP 0.008 0.001 TRP B 177 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 ( 6565) covalent geometry : angle 0.52239 / 0.27 ( 8943) hydrogen bonds : bond 0.03786 / 2.40 ( 172) hydrogen bonds : angle 5.58024 / 3.93 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8821 (ttpp) cc_final: 0.8575 (ttpt) REVERT: A 136 MET cc_start: 0.5585 (ttt) cc_final: 0.2929 (mmm) REVERT: A 161 PHE cc_start: 0.8045 (m-80) cc_final: 0.6157 (p90) REVERT: A 164 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: C 41 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8149 (mtm180) REVERT: C 114 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8012 (pp20) REVERT: C 145 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: C 205 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7401 (mt-10) REVERT: C 229 ASP cc_start: 0.8563 (m-30) cc_final: 0.7774 (m-30) outliers start: 31 outliers final: 13 residues processed: 127 average time/residue: 0.4806 time to fit residues: 64.2811 Evaluate side-chains 115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS B 111 GLN B 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.091849 restraints weight = 7707.297| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.90 r_work: 0.2920 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6565 Z= 0.134 Angle : 0.486 5.752 8943 Z= 0.252 Chirality : 0.043 0.148 1005 Planarity : 0.004 0.030 1157 Dihedral : 6.863 57.570 901 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.97 % Allowed : 17.00 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.32 (0.28), residues: 812 helix: -1.36 (0.64), residues: 60 sheet: 0.60 (0.36), residues: 207 loop : -0.37 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.014 0.001 TYR B 31 PHE 0.016 0.001 PHE C 123 TRP 0.005 0.001 TRP B 177 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6565) covalent geometry : angle 0.48598 / 0.25 ( 8943) hydrogen bonds : bond 0.03421 / 2.19 ( 172) hydrogen bonds : angle 5.44625 / 3.83 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8571 (ttpt) REVERT: A 102 GLN cc_start: 0.8604 (mm110) cc_final: 0.8310 (tp40) REVERT: A 136 MET cc_start: 0.5422 (ttt) cc_final: 0.2911 (mmm) REVERT: A 161 PHE cc_start: 0.8021 (m-80) cc_final: 0.6152 (p90) REVERT: A 164 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6672 (mp10) REVERT: C 41 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8148 (mtm180) REVERT: C 114 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7727 (pp20) REVERT: C 145 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: C 229 ASP cc_start: 0.8553 (m-30) cc_final: 0.7831 (m-30) outliers start: 28 outliers final: 15 residues processed: 123 average time/residue: 0.4757 time to fit residues: 61.6750 Evaluate side-chains 119 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN C 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087616 restraints weight = 7693.603| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.88 r_work: 0.2858 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 6565 Z= 0.336 Angle : 0.634 7.203 8943 Z= 0.330 Chirality : 0.049 0.206 1005 Planarity : 0.005 0.052 1157 Dihedral : 7.395 59.797 901 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.97 % Allowed : 16.29 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.53 (0.28), residues: 812 helix: -1.64 (0.59), residues: 66 sheet: 0.54 (0.38), residues: 189 loop : -0.49 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.019 0.002 TYR B 31 PHE 0.022 0.002 PHE C 117 TRP 0.011 0.002 TRP B 177 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.34 ( 6565) covalent geometry : angle 0.63430 / 0.33 ( 8943) hydrogen bonds : bond 0.04523 / 2.88 ( 172) hydrogen bonds : angle 5.76109 / 4.06 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8621 (ttpt) REVERT: A 19 GLU cc_start: 0.7972 (pm20) cc_final: 0.7204 (mm-30) REVERT: A 136 MET cc_start: 0.5460 (ttt) cc_final: 0.2806 (mmm) REVERT: A 161 PHE cc_start: 0.8156 (m-80) cc_final: 0.6226 (p90) REVERT: A 164 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: A 277 LEU cc_start: 0.8964 (tp) cc_final: 0.8745 (mt) REVERT: C 41 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8213 (mtm180) REVERT: C 114 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8062 (pp20) REVERT: C 145 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: C 229 ASP cc_start: 0.8621 (m-30) cc_final: 0.7815 (m-30) REVERT: D 42 LYS cc_start: 0.7682 (mttp) cc_final: 0.5493 (ttpt) outliers start: 28 outliers final: 14 residues processed: 122 average time/residue: 0.4999 time to fit residues: 64.1922 Evaluate side-chains 118 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092275 restraints weight = 7589.012| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.88 r_work: 0.2926 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6565 Z= 0.107 Angle : 0.479 7.282 8943 Z= 0.248 Chirality : 0.043 0.152 1005 Planarity : 0.004 0.032 1157 Dihedral : 6.825 55.394 901 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.54 % Allowed : 17.56 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.30 (0.28), residues: 812 helix: -1.23 (0.65), residues: 60 sheet: 0.50 (0.38), residues: 197 loop : -0.31 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.013 0.001 TYR B 31 PHE 0.012 0.001 PHE C 123 TRP 0.006 0.001 TRP B 79 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6565) covalent geometry : angle 0.47949 / 0.25 ( 8943) hydrogen bonds : bond 0.03214 / 2.07 ( 172) hydrogen bonds : angle 5.40785 / 3.80 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8817 (ttpp) cc_final: 0.8542 (ttpt) REVERT: A 102 GLN cc_start: 0.8592 (mm110) cc_final: 0.8315 (tp40) REVERT: A 136 MET cc_start: 0.5200 (ttt) cc_final: 0.2915 (mmm) REVERT: A 161 PHE cc_start: 0.8062 (m-80) cc_final: 0.6181 (p90) REVERT: A 164 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6565 (mp10) REVERT: C 41 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8165 (mtm180) REVERT: C 114 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: C 145 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: C 229 ASP cc_start: 0.8520 (m-30) cc_final: 0.7794 (m-30) outliers start: 25 outliers final: 16 residues processed: 124 average time/residue: 0.4970 time to fit residues: 65.0329 Evaluate side-chains 120 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN C 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.089339 restraints weight = 7579.644| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.87 r_work: 0.2879 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 6565 Z= 0.229 Angle : 0.565 8.000 8943 Z= 0.292 Chirality : 0.046 0.145 1005 Planarity : 0.004 0.036 1157 Dihedral : 7.116 57.967 901 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.68 % Allowed : 17.28 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.37 (0.28), residues: 812 helix: -1.30 (0.64), residues: 60 sheet: 0.48 (0.38), residues: 197 loop : -0.36 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 65 TYR 0.017 0.002 TYR B 31 PHE 0.022 0.002 PHE C 123 TRP 0.009 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 ( 6565) covalent geometry : angle 0.56451 / 0.29 ( 8943) hydrogen bonds : bond 0.03927 / 2.51 ( 172) hydrogen bonds : angle 5.54659 / 3.91 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8598 (ttpt) REVERT: A 98 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.7874 (mttm) REVERT: A 136 MET cc_start: 0.5221 (ttt) cc_final: 0.2726 (mmm) REVERT: A 161 PHE cc_start: 0.8108 (m-80) cc_final: 0.6165 (p90) REVERT: A 164 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: C 41 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8191 (mtm180) REVERT: C 114 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7973 (pp20) REVERT: C 145 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: C 229 ASP cc_start: 0.8569 (m-30) cc_final: 0.7767 (m-30) REVERT: D 42 LYS cc_start: 0.7661 (mttp) cc_final: 0.5477 (ttpt) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 0.4923 time to fit residues: 61.7118 Evaluate side-chains 117 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 overall best weight: 2.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.091325 restraints weight = 7773.760| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.90 r_work: 0.2910 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6565 Z= 0.137 Angle : 0.510 8.004 8943 Z= 0.263 Chirality : 0.043 0.150 1005 Planarity : 0.004 0.031 1157 Dihedral : 6.931 56.692 901 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.82 % Allowed : 17.28 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.31 (0.28), residues: 812 helix: -1.14 (0.65), residues: 60 sheet: 0.48 (0.38), residues: 197 loop : -0.32 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.015 0.001 TYR B 31 PHE 0.023 0.001 PHE C 123 TRP 0.006 0.001 TRP B 79 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6565) covalent geometry : angle 0.50994 / 0.26 ( 8943) hydrogen bonds : bond 0.03421 / 2.20 ( 172) hydrogen bonds : angle 5.41833 / 3.81 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8569 (ttpt) REVERT: A 98 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7883 (mttm) REVERT: A 102 GLN cc_start: 0.8606 (mm110) cc_final: 0.8321 (tp40) REVERT: A 136 MET cc_start: 0.5270 (ttt) cc_final: 0.2888 (mmm) REVERT: A 161 PHE cc_start: 0.8071 (m-80) cc_final: 0.6159 (p90) REVERT: A 164 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6564 (mp10) REVERT: A 227 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8029 (tt0) REVERT: C 41 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8170 (mtm180) REVERT: C 114 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7854 (pp20) REVERT: C 145 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: C 229 ASP cc_start: 0.8542 (m-30) cc_final: 0.7813 (m-30) REVERT: D 42 LYS cc_start: 0.7667 (mttp) cc_final: 0.5463 (ttpt) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.4901 time to fit residues: 63.5078 Evaluate side-chains 125 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.091598 restraints weight = 7604.231| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.87 r_work: 0.2917 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6565 Z= 0.133 Angle : 0.508 7.978 8943 Z= 0.262 Chirality : 0.043 0.149 1005 Planarity : 0.004 0.031 1157 Dihedral : 6.881 56.743 901 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.82 % Allowed : 17.42 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.28 (0.28), residues: 812 helix: -1.08 (0.66), residues: 60 sheet: 0.49 (0.38), residues: 197 loop : -0.30 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.015 0.001 TYR B 31 PHE 0.023 0.001 PHE C 123 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6565) covalent geometry : angle 0.50755 / 0.26 ( 8943) hydrogen bonds : bond 0.03390 / 2.17 ( 172) hydrogen bonds : angle 5.39569 / 3.80 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8564 (ttpt) REVERT: A 98 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7868 (mttm) REVERT: A 102 GLN cc_start: 0.8606 (mm110) cc_final: 0.8320 (tp40) REVERT: A 136 MET cc_start: 0.5229 (ttt) cc_final: 0.2864 (mmm) REVERT: A 161 PHE cc_start: 0.8060 (m-80) cc_final: 0.6150 (p90) REVERT: A 164 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6603 (mp10) REVERT: A 227 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8033 (tt0) REVERT: C 41 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8169 (mtm180) REVERT: C 114 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7743 (pp20) REVERT: C 145 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: C 229 ASP cc_start: 0.8539 (m-30) cc_final: 0.7808 (m-30) outliers start: 27 outliers final: 17 residues processed: 122 average time/residue: 0.4935 time to fit residues: 63.4355 Evaluate side-chains 123 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 HIS B 111 GLN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.090771 restraints weight = 7753.968| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.84 r_work: 0.2913 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 6565 Z= 0.250 Angle : 1.023 59.180 8943 Z= 0.613 Chirality : 0.045 0.178 1005 Planarity : 0.004 0.031 1157 Dihedral : 6.898 56.873 901 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.40 % Allowed : 17.42 % Favored : 79.18 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.92 % 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: -0.28 (0.28), residues: 812 helix: -1.10 (0.66), residues: 60 sheet: 0.50 (0.38), residues: 197 loop : -0.30 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.015 0.001 TYR B 31 PHE 0.025 0.002 PHE C 123 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.25 ( 6565) covalent geometry : angle 1.02310 / 0.61 ( 8943) hydrogen bonds : bond 0.03425 / 2.19 ( 172) hydrogen bonds : angle 5.39386 / 3.80 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2525.18 seconds wall clock time: 43 minutes 47.85 seconds (2627.85 seconds total)