Starting phenix.real_space_refine on Thu Oct 22 21:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7g_63682/10_2026/9m7g_63682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7g_63682/10_2026/9m7g_63682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m7g_63682/10_2026/9m7g_63682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7g_63682/10_2026/9m7g_63682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7g_63682/10_2026/9m7g_63682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7g_63682/10_2026/9m7g_63682.map" } resolution = 3.38 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= -0.001 sd= 0.093 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 20 5.16 5 C 3853 2.51 5 N 1009 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5972 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2247 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 5, 'TRANS': 276} Chain breaks: 2 Chain: "B" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 487 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "B" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1078 Unusual residues: {'CRO': 1} Classifications: {'peptide': 129, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 123, None: 1} Not linked: pdbres="CRO B 67 " pdbres="VAL B 69 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2160 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 8, 'TRANS': 278} Chain breaks: 1 Time building chain proxies: 1.49, per 1000 atoms: 0.25 Number of scatterers: 5972 At special positions: 0 Unit cell: (75.9, 102.3, 122.1, 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 20 16.00 O 1090 8.00 N 1009 7.00 C 3853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 257 " - pdb=" SG CYS C 186 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 210.1 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 52.8% alpha, 14.2% 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 136 through 163 Processing helix chain 'A' and resid 171 through 199 removed outlier: 3.820A pdb=" N ILE A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 252 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 275 through 287 Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.599A pdb=" N ILE A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 329 removed outlier: 3.504A pdb=" N PHE A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 369 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 377 through 390 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.577A pdb=" N SER A 409 " --> pdb=" O LYS A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 9 removed outlier: 4.106A pdb=" N GLU B 7 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 8 " --> pdb=" O GLY B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 76 through 83 removed outlier: 5.424A pdb=" N ARG B 81 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 17 through 25 removed outlier: 4.518A pdb=" N MET C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 removed outlier: 3.876A pdb=" N LEU C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 4.135A pdb=" N VAL C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 81 through 90 removed outlier: 4.104A pdb=" N GLU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.765A pdb=" N VAL C 117 " --> pdb=" O HIS C 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 175 through 181 Processing helix chain 'C' and resid 184 through 194 removed outlier: 3.893A pdb=" N ASP C 190 " --> pdb=" O CYS C 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 227 removed outlier: 3.624A pdb=" N VAL C 221 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.536A pdb=" N ILE C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 273 through 280 Processing helix chain 'C' and resid 286 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 1006 through 1015 removed outlier: 3.511A pdb=" N SER A1013 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A1028 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1015 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A1025 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 45 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A1029 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 43 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 33 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 34 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 186 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 162 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS B 167 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 150 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS A1006 " --> pdb=" O ILE B 153 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 921 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: 0.89 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1007 1.31 - 1.44: 1604 1.44 - 1.56: 3458 1.56 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6099 Sorted by residual: bond pdb=" C1 CRO B 67 " pdb=" N2 CRO B 67 " ideal model delta sigma weight residual 1.289 1.423 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C2 CRO B 67 " pdb=" N3 CRO B 67 " ideal model delta sigma weight residual 1.375 1.482 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" CB2 CRO B 67 " pdb=" CG2 CRO B 67 " ideal model delta sigma weight residual 1.446 1.536 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 CRO B 67 " pdb=" N3 CRO B 67 " ideal model delta sigma weight residual 1.377 1.456 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C2 CRO B 67 " pdb=" CA2 CRO B 67 " ideal model delta sigma weight residual 1.480 1.542 -0.062 2.00e-02 2.50e+03 9.73e+00 ... (remaining 6094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 8220 3.35 - 6.71: 46 6.71 - 10.06: 5 10.06 - 13.42: 0 13.42 - 16.77: 2 Bond angle restraints: 8273 Sorted by residual: angle pdb=" N SER A 167 " pdb=" CA SER A 167 " pdb=" C SER A 167 " ideal model delta sigma weight residual 108.86 95.14 13.72 1.41e+00 5.03e-01 9.47e+01 angle pdb=" N LEU A 166 " pdb=" CA LEU A 166 " pdb=" C LEU A 166 " ideal model delta sigma weight residual 110.80 127.57 -16.77 2.13e+00 2.20e-01 6.20e+01 angle pdb=" N SER A 167 " pdb=" CA SER A 167 " pdb=" CB SER A 167 " ideal model delta sigma weight residual 111.31 120.16 -8.85 1.67e+00 3.59e-01 2.81e+01 angle pdb=" C LEU A 166 " pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " ideal model delta sigma weight residual 110.42 100.45 9.97 1.99e+00 2.53e-01 2.51e+01 angle pdb=" N VAL C 127 " pdb=" CA VAL C 127 " pdb=" C VAL C 127 " ideal model delta sigma weight residual 113.42 108.16 5.26 1.17e+00 7.31e-01 2.02e+01 ... (remaining 8268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3128 17.89 - 35.78: 349 35.78 - 53.67: 72 53.67 - 71.56: 15 71.56 - 89.44: 1 Dihedral angle restraints: 3565 sinusoidal: 1388 harmonic: 2177 Sorted by residual: dihedral pdb=" CB CYS A 257 " pdb=" SG CYS A 257 " pdb=" SG CYS C 186 " pdb=" CB CYS C 186 " ideal model delta sinusoidal sigma weight residual -86.00 -133.30 47.30 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS A 224 " pdb=" SG CYS A 224 " pdb=" SG CYS A 294 " pdb=" CB CYS A 294 " ideal model delta sinusoidal sigma weight residual 93.00 57.67 35.33 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA CYS C 186 " pdb=" C CYS C 186 " pdb=" N LYS C 187 " pdb=" CA LYS C 187 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 887 0.079 - 0.158: 53 0.158 - 0.236: 1 0.236 - 0.315: 0 0.315 - 0.394: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA1 CRO B 67 " pdb=" CB1 CRO B 67 " pdb=" C1 CRO B 67 " pdb=" N1 CRO B 67 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB1 CRO B 67 " pdb=" CG1 CRO B 67 " pdb=" OG1 CRO B 67 " pdb=" CA1 CRO B 67 " both_signs ideal model delta sigma weight residual False -2.35 -2.50 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 939 not shown) Planarity restraints: 1057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 89 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.48e+00 pdb=" N PRO B 90 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 273 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 274 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 274 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 274 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 104 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.026 5.00e-02 4.00e+02 ... (remaining 1054 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1226 2.78 - 3.31: 5408 3.31 - 3.84: 9141 3.84 - 4.37: 10195 4.37 - 4.90: 18092 Nonbonded interactions: 44062 Sorted by model distance: nonbonded pdb=" OG1 THR C 103 " pdb=" ND1 HIS C 106 " model vdw 2.251 3.120 nonbonded pdb=" N SER A 167 " pdb=" O SER A 167 " model vdw 2.300 2.496 nonbonded pdb=" O THR B 63 " pdb=" NH1 ARG B 97 " model vdw 2.308 3.120 nonbonded pdb=" N ASP C 202 " pdb=" OD1 ASP C 202 " model vdw 2.371 3.120 nonbonded pdb=" OH TYR A 239 " pdb=" OE1 GLU A 362 " model vdw 2.392 3.040 ... (remaining 44057 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: 1.260 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: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 0.134 6103 Z= 0.195 Angle : 0.679 16.769 8277 Z= 0.372 Chirality : 0.040 0.394 942 Planarity : 0.004 0.064 1057 Dihedral : 15.189 89.444 2159 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 16.75 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.13 (0.31), residues: 748 helix: 0.96 (0.28), residues: 355 sheet: 1.93 (0.52), residues: 93 loop : -1.64 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.010 0.001 TYR A 145 PHE 0.022 0.001 PHE C 275 TRP 0.015 0.001 TRP A 295 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 ( 6099) covalent geometry : angle 0.67871 / 0.37 ( 8273) SS BOND : bond 0.00114 / 0.06 ( 2) SS BOND : angle 1.20686 / 0.56 ( 4) hydrogen bonds : bond 0.19471 / 13.03 ( 318) hydrogen bonds : angle 6.79437 / 5.23 ( 921) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.7273 (tp) cc_final: 0.6778 (tt) REVERT: A 245 GLU cc_start: 0.7531 (tp30) cc_final: 0.7182 (mt-10) REVERT: A 412 ARG cc_start: 0.6711 (ttm-80) cc_final: 0.6383 (tpp80) REVERT: B 6 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7449 (tm-30) REVERT: B 134 ASP cc_start: 0.6792 (p0) cc_final: 0.6475 (p0) REVERT: B 163 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7265 (mtmm) REVERT: C 4 LYS cc_start: 0.8005 (mppt) cc_final: 0.7719 (mtpt) REVERT: C 142 ILE cc_start: 0.8497 (tp) cc_final: 0.8185 (tp) REVERT: C 169 TYR cc_start: 0.8109 (p90) cc_final: 0.7631 (p90) REVERT: C 227 TYR cc_start: 0.7547 (m-80) cc_final: 0.7328 (m-10) REVERT: C 272 LYS cc_start: 0.7484 (mmmt) cc_final: 0.6956 (mtmt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0996 time to fit residues: 20.0761 Evaluate side-chains 94 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.0020 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 HIS C 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.193449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151044 restraints weight = 8021.871| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.99 r_work: 0.3530 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6103 Z= 0.132 Angle : 0.599 7.083 8277 Z= 0.310 Chirality : 0.040 0.153 942 Planarity : 0.005 0.060 1057 Dihedral : 4.442 24.492 808 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.03 % Allowed : 20.57 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 748 helix: 1.24 (0.28), residues: 354 sheet: 1.71 (0.48), residues: 92 loop : -1.67 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 81 TYR 0.012 0.001 TYR A 145 PHE 0.012 0.001 PHE A 141 TRP 0.012 0.002 TRP C 110 HIS 0.004 0.001 HIS A1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6099) covalent geometry : angle 0.59907 / 0.31 ( 8273) SS BOND : bond 0.00148 / 0.08 ( 2) SS BOND : angle 0.89116 / 0.41 ( 4) hydrogen bonds : bond 0.04808 / 3.34 ( 318) hydrogen bonds : angle 5.18529 / 4.00 ( 921) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: A 412 ARG cc_start: 0.7010 (ttm-80) cc_final: 0.6350 (tpm170) REVERT: B 27 LYS cc_start: 0.7602 (mttm) cc_final: 0.7362 (mttm) REVERT: B 163 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7674 (mtmm) REVERT: C 139 ASP cc_start: 0.7427 (m-30) cc_final: 0.7071 (m-30) REVERT: C 169 TYR cc_start: 0.8028 (p90) cc_final: 0.7571 (p90) REVERT: C 259 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7708 (tptt) REVERT: C 272 LYS cc_start: 0.7739 (mmmt) cc_final: 0.7259 (mtmt) outliers start: 19 outliers final: 8 residues processed: 102 average time/residue: 0.0916 time to fit residues: 11.8599 Evaluate side-chains 82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [3, 62, 17, 34, 26, 47, 1, 36, 55, 29, 0] chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141490 restraints weight = 7736.272| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.65 r_work: 0.3404 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6103 Z= 0.147 Angle : 0.602 8.346 8277 Z= 0.310 Chirality : 0.040 0.135 942 Planarity : 0.005 0.052 1057 Dihedral : 4.467 19.201 808 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.51 % Allowed : 20.41 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 748 helix: 1.46 (0.28), residues: 351 sheet: 1.17 (0.46), residues: 108 loop : -1.76 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 74 TYR 0.014 0.001 TYR A 239 PHE 0.016 0.001 PHE B 166 TRP 0.014 0.002 TRP C 110 HIS 0.006 0.001 HIS C 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6099) covalent geometry : angle 0.60138 / 0.31 ( 8273) SS BOND : bond 0.00156 / 0.08 ( 2) SS BOND : angle 0.94466 / 0.44 ( 4) hydrogen bonds : bond 0.05367 / 3.65 ( 318) hydrogen bonds : angle 4.91966 / 3.75 ( 921) Misc. bond : bond 0.00106 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 1025 MET cc_start: 0.8454 (ttp) cc_final: 0.8171 (ttm) REVERT: A 383 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.4913 (t80) REVERT: B 132 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7472 (mtpt) REVERT: B 163 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7510 (mtmm) REVERT: C 4 LYS cc_start: 0.8048 (mptt) cc_final: 0.7558 (mtpt) REVERT: C 139 ASP cc_start: 0.7654 (m-30) cc_final: 0.7414 (m-30) REVERT: C 186 CYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5037 (m) REVERT: C 259 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7771 (tptt) REVERT: C 272 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7298 (mtmt) outliers start: 22 outliers final: 10 residues processed: 94 average time/residue: 0.0870 time to fit residues: 10.5018 Evaluate side-chains 81 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [35, 51, 23, 39, 65, 38, 74, 7, 66, 19, 60] chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142345 restraints weight = 7795.883| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.75 r_work: 0.3420 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6103 Z= 0.123 Angle : 0.546 7.184 8277 Z= 0.283 Chirality : 0.039 0.131 942 Planarity : 0.004 0.053 1057 Dihedral : 4.296 19.068 808 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.47 % Allowed : 18.82 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.45 (0.31), residues: 748 helix: 1.63 (0.28), residues: 351 sheet: 1.18 (0.48), residues: 100 loop : -1.76 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 74 TYR 0.014 0.001 TYR A 145 PHE 0.015 0.001 PHE A 289 TRP 0.015 0.001 TRP C 110 HIS 0.004 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6099) covalent geometry : angle 0.54560 / 0.28 ( 8273) SS BOND : bond 0.00114 / 0.06 ( 2) SS BOND : angle 0.79612 / 0.36 ( 4) hydrogen bonds : bond 0.04545 / 3.08 ( 318) hydrogen bonds : angle 4.63116 / 3.53 ( 921) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 1025 MET cc_start: 0.8501 (ttp) cc_final: 0.8205 (ttm) REVERT: B 125 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: B 163 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7477 (mtmm) REVERT: C 60 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.5882 (t70) REVERT: C 139 ASP cc_start: 0.7583 (m-30) cc_final: 0.7291 (m-30) REVERT: C 272 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7204 (mtmt) outliers start: 28 outliers final: 10 residues processed: 100 average time/residue: 0.0823 time to fit residues: 10.7613 Evaluate side-chains 81 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [20, 68, 33, 61, 62, 41, 37, 55, 44, 16, 72] chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141791 restraints weight = 7994.609| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.89 r_work: 0.3381 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6103 Z= 0.120 Angle : 0.562 7.352 8277 Z= 0.288 Chirality : 0.038 0.130 942 Planarity : 0.004 0.053 1057 Dihedral : 4.211 18.415 808 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.35 % Allowed : 20.10 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.46 (0.31), residues: 748 helix: 1.60 (0.28), residues: 353 sheet: 1.08 (0.46), residues: 108 loop : -1.73 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 45 TYR 0.013 0.001 TYR A 145 PHE 0.012 0.001 PHE B 166 TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6099) covalent geometry : angle 0.55993 / 0.29 ( 8273) SS BOND : bond 0.00250 / 0.12 ( 2) SS BOND : angle 2.37036 / 1.16 ( 4) hydrogen bonds : bond 0.04474 / 3.03 ( 318) hydrogen bonds : angle 4.54007 / 3.46 ( 921) Misc. bond : bond 0.00039 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 1025 MET cc_start: 0.8436 (ttp) cc_final: 0.8219 (ttm) REVERT: A 383 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.4989 (t80) REVERT: B 125 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: B 163 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7507 (mtmm) REVERT: C 4 LYS cc_start: 0.7962 (mptt) cc_final: 0.7384 (mtpt) REVERT: C 60 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5752 (t70) REVERT: C 272 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7308 (mtmt) outliers start: 21 outliers final: 14 residues processed: 83 average time/residue: 0.0817 time to fit residues: 8.7921 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [33, 34, 74, 37, 24, 2, 19, 38, 14, 22, 64] chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.0060 chunk 74 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.185639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142394 restraints weight = 7866.848| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.69 r_work: 0.3424 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6103 Z= 0.112 Angle : 0.540 8.796 8277 Z= 0.275 Chirality : 0.037 0.129 942 Planarity : 0.004 0.053 1057 Dihedral : 4.129 17.456 808 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.35 % Allowed : 20.41 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 748 helix: 1.67 (0.28), residues: 352 sheet: 1.06 (0.47), residues: 108 loop : -1.73 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 74 TYR 0.011 0.001 TYR A 239 PHE 0.011 0.001 PHE B 166 TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6099) covalent geometry : angle 0.53868 / 0.28 ( 8273) SS BOND : bond 0.00332 / 0.16 ( 2) SS BOND : angle 1.48086 / 0.72 ( 4) hydrogen bonds : bond 0.04234 / 2.87 ( 318) hydrogen bonds : angle 4.42124 / 3.36 ( 921) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.272 Fit side-chains REVERT: A 253 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 277 LEU cc_start: 0.6733 (tt) cc_final: 0.6481 (mt) REVERT: A 383 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5063 (t80) REVERT: B 125 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: B 163 LYS cc_start: 0.7804 (mmtp) cc_final: 0.7412 (mtmm) REVERT: B 186 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7555 (p0) REVERT: C 60 ASP cc_start: 0.6202 (OUTLIER) cc_final: 0.5843 (t70) REVERT: C 118 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: C 272 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7194 (mtmt) outliers start: 21 outliers final: 11 residues processed: 88 average time/residue: 0.0873 time to fit residues: 10.2107 Evaluate side-chains 86 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [21, 72, 5, 63, 15, 46, 10, 30, 16, 62, 53] chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 15 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 overall best weight: 0.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140009 restraints weight = 7977.803| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.19 r_work: 0.3424 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6103 Z= 0.112 Angle : 0.545 8.816 8277 Z= 0.277 Chirality : 0.038 0.129 942 Planarity : 0.004 0.053 1057 Dihedral : 4.076 17.413 808 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.83 % Allowed : 20.26 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.45 (0.31), residues: 748 helix: 1.60 (0.28), residues: 357 sheet: 1.34 (0.50), residues: 100 loop : -1.82 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.012 0.001 TYR A 239 PHE 0.011 0.001 PHE B 166 TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6099) covalent geometry : angle 0.54488 / 0.28 ( 8273) SS BOND : bond 0.00349 / 0.17 ( 2) SS BOND : angle 1.14427 / 0.55 ( 4) hydrogen bonds : bond 0.04180 / 2.81 ( 318) hydrogen bonds : angle 4.40180 / 3.35 ( 921) Misc. bond : bond 0.00037 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.231 Fit side-chains REVERT: A 253 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7810 (mp) REVERT: A 277 LEU cc_start: 0.6706 (tt) cc_final: 0.6497 (mt) REVERT: A 383 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.5089 (t80) REVERT: B 125 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: B 163 LYS cc_start: 0.7791 (mmtp) cc_final: 0.7401 (mtmm) REVERT: B 186 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7556 (p0) REVERT: C 60 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5846 (t70) REVERT: C 118 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: C 272 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6981 (mtmt) outliers start: 24 outliers final: 12 residues processed: 90 average time/residue: 0.0829 time to fit residues: 9.8198 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [25, 12, 49, 43, 18, 16, 45, 71, 39, 72, 70] chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138563 restraints weight = 7814.158| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.59 r_work: 0.3364 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6103 Z= 0.166 Angle : 0.615 8.833 8277 Z= 0.315 Chirality : 0.040 0.140 942 Planarity : 0.005 0.055 1057 Dihedral : 4.380 19.110 808 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.35 % Allowed : 20.73 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 748 helix: 1.48 (0.28), residues: 358 sheet: 0.92 (0.48), residues: 108 loop : -1.96 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.016 0.002 TYR A 239 PHE 0.016 0.001 PHE B 166 TRP 0.009 0.001 TRP C 110 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 6099) covalent geometry : angle 0.61490 / 0.32 ( 8273) SS BOND : bond 0.00573 / 0.27 ( 2) SS BOND : angle 1.16184 / 0.57 ( 4) hydrogen bonds : bond 0.05404 / 3.69 ( 318) hydrogen bonds : angle 4.64988 / 3.53 ( 921) Misc. bond : bond 0.00089 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.174 Fit side-chains REVERT: A 253 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 308 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7560 (mmp-170) REVERT: A 383 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.5294 (t80) REVERT: B 125 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: B 163 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7396 (mtmm) REVERT: B 186 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7701 (p0) REVERT: C 4 LYS cc_start: 0.7912 (mptt) cc_final: 0.7332 (mtpt) REVERT: C 60 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.6032 (t70) REVERT: C 272 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7103 (mtmt) outliers start: 21 outliers final: 12 residues processed: 87 average time/residue: 0.0826 time to fit residues: 9.4949 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [16, 24, 70, 59, 34, 36, 39, 18, 50, 54, 62] chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140466 restraints weight = 7876.826| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.79 r_work: 0.3368 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6103 Z= 0.123 Angle : 0.581 9.019 8277 Z= 0.294 Chirality : 0.038 0.131 942 Planarity : 0.004 0.053 1057 Dihedral : 4.236 18.467 808 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.87 % Allowed : 20.89 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 748 helix: 1.54 (0.28), residues: 358 sheet: 1.25 (0.50), residues: 100 loop : -2.02 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.012 0.001 TYR A 145 PHE 0.012 0.001 PHE B 166 TRP 0.013 0.001 TRP C 110 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6099) covalent geometry : angle 0.58034 / 0.29 ( 8273) SS BOND : bond 0.00547 / 0.26 ( 2) SS BOND : angle 1.18479 / 0.58 ( 4) hydrogen bonds : bond 0.04565 / 3.10 ( 318) hydrogen bonds : angle 4.50077 / 3.42 ( 921) Misc. bond : bond 0.00046 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.213 Fit side-chains REVERT: A 253 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 383 PHE cc_start: 0.5996 (OUTLIER) cc_final: 0.5333 (t80) REVERT: B 125 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: B 163 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7455 (mtmm) REVERT: B 186 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7709 (p0) REVERT: C 4 LYS cc_start: 0.7959 (mptt) cc_final: 0.7413 (mmmt) REVERT: C 60 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6030 (t70) REVERT: C 272 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7128 (mtmt) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.0728 time to fit residues: 8.5774 Evaluate side-chains 83 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [15, 72, 53, 66, 67, 30, 12, 42, 27, 54, 50] chunk 15 optimal weight: 0.0060 chunk 72 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 67 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.183775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139289 restraints weight = 7814.682| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.91 r_work: 0.3386 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6103 Z= 0.120 Angle : 0.593 8.971 8277 Z= 0.297 Chirality : 0.038 0.153 942 Planarity : 0.004 0.053 1057 Dihedral : 4.165 19.707 808 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.23 % Allowed : 21.85 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 748 helix: 1.59 (0.28), residues: 358 sheet: 1.33 (0.50), residues: 100 loop : -2.00 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.013 0.001 TYR A 145 PHE 0.013 0.001 PHE A 289 TRP 0.012 0.001 TRP C 110 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6099) covalent geometry : angle 0.59112 / 0.30 ( 8273) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 2.34093 / 1.05 ( 4) hydrogen bonds : bond 0.04329 / 2.93 ( 318) hydrogen bonds : angle 4.44246 / 3.37 ( 921) Misc. bond : bond 0.00039 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.212 Fit side-chains REVERT: A 383 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5250 (t80) REVERT: B 163 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7394 (mtmm) REVERT: C 4 LYS cc_start: 0.7894 (mptt) cc_final: 0.7356 (mmmt) REVERT: C 60 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.6035 (t70) REVERT: C 272 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7084 (mtmt) outliers start: 14 outliers final: 10 residues processed: 80 average time/residue: 0.0740 time to fit residues: 7.9670 Evaluate side-chains 82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 253 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: [20, 45, 67, 6, 19, 10, 60, 1, 55, 21, 32] chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136169 restraints weight = 7843.320| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.90 r_work: 0.3305 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6103 Z= 0.161 Angle : 0.633 8.919 8277 Z= 0.321 Chirality : 0.040 0.148 942 Planarity : 0.005 0.054 1057 Dihedral : 4.434 19.599 808 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.55 % Allowed : 21.37 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.31), residues: 748 helix: 1.59 (0.28), residues: 351 sheet: 1.06 (0.47), residues: 114 loop : -2.07 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.014 0.002 TYR A 239 PHE 0.015 0.001 PHE B 166 TRP 0.010 0.001 TRP C 110 HIS 0.005 0.001 HIS C 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 6099) covalent geometry : angle 0.62967 / 0.32 ( 8273) SS BOND : bond 0.00148 / 0.07 ( 2) SS BOND : angle 2.80775 / 1.29 ( 4) hydrogen bonds : bond 0.05436 / 3.70 ( 318) hydrogen bonds : angle 4.68139 / 3.55 ( 921) Misc. bond : bond 0.00085 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.89 seconds wall clock time: 26 minutes 23.62 seconds (1583.62 seconds total)