Starting phenix.real_space_refine on Fri Dec 27 17:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yqx_39509/12_2024/8yqx_39509.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yqx_39509/12_2024/8yqx_39509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yqx_39509/12_2024/8yqx_39509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yqx_39509/12_2024/8yqx_39509.map" model { file = "/net/cci-nas-00/data/ceres_data/8yqx_39509/12_2024/8yqx_39509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yqx_39509/12_2024/8yqx_39509.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.084 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 32 5.16 5 C 3952 2.51 5 N 1062 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6167 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2125 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 14, 'TRANS': 249} Chain breaks: 1 Chain: "F" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2698 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1344 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Time building chain proxies: 4.56, per 1000 atoms: 0.74 Number of scatterers: 6167 At special positions: 0 Unit cell: (84.84, 101.808, 96.96, 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 32 16.00 O 1121 8.00 N 1062 7.00 C 3952 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: 1.51 Conformation dependent library (CDL) restraints added in 903.9 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 38.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.668A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.793A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 171 through 194 removed outlier: 4.104A pdb=" N LYS F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 239 through 248 removed outlier: 3.568A pdb=" N LYS F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 314 Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.616A pdb=" N ILE F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.654A pdb=" N ARG F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 85 removed outlier: 3.865A pdb=" N ASP J 85 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.699A pdb=" N PHE J 142 " --> pdb=" O SER J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 163 Processing helix chain 'J' and resid 167 through 173 Processing helix chain 'J' and resid 193 through 211 removed outlier: 3.576A pdb=" N ILE J 197 " --> pdb=" O LYS J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 236 removed outlier: 3.506A pdb=" N ASN J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 4.823A pdb=" N GLN A 77 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.848A pdb=" N LEU A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.606A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 13 removed outlier: 6.305A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 2 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 86 through 87 removed outlier: 7.545A pdb=" N ILE F 154 " --> pdb=" O PRO F 115 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN F 95 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU F 101 " --> pdb=" O ILE F 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 237 through 238 removed outlier: 6.695A pdb=" N VAL F 163 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS F 287 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N HIS F 165 " --> pdb=" O CYS F 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 217 through 219 Processing sheet with id=AA9, first strand: chain 'J' and resid 115 through 119 removed outlier: 3.642A pdb=" N THR J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE J 91 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL J 92 " --> pdb=" O TYR J 128 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2009 1.34 - 1.46: 1353 1.46 - 1.58: 2883 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 6293 Sorted by residual: bond pdb=" CB ASN F 136 " pdb=" CG ASN F 136 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.69e+00 bond pdb=" CA GLY A 37 " pdb=" C GLY A 37 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.34e+00 bond pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.07e+00 bond pdb=" CB GLU F 282 " pdb=" CG GLU F 282 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB GLU A 113 " pdb=" CG GLU A 113 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.23e-01 ... (remaining 6288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 8366 1.67 - 3.33: 121 3.33 - 5.00: 16 5.00 - 6.66: 5 6.66 - 8.33: 2 Bond angle restraints: 8510 Sorted by residual: angle pdb=" N VAL F 123 " pdb=" CA VAL F 123 " pdb=" C VAL F 123 " ideal model delta sigma weight residual 112.96 107.95 5.01 1.00e+00 1.00e+00 2.51e+01 angle pdb=" CG ARG A 111 " pdb=" CD ARG A 111 " pdb=" NE ARG A 111 " ideal model delta sigma weight residual 112.00 118.92 -6.92 2.20e+00 2.07e-01 9.89e+00 angle pdb=" CB MET F 328 " pdb=" CG MET F 328 " pdb=" SD MET F 328 " ideal model delta sigma weight residual 112.70 121.03 -8.33 3.00e+00 1.11e-01 7.71e+00 angle pdb=" C ILE J 112 " pdb=" N ASN J 113 " pdb=" CA ASN J 113 " ideal model delta sigma weight residual 125.66 130.77 -5.11 1.85e+00 2.92e-01 7.64e+00 angle pdb=" CA LYS J 174 " pdb=" CB LYS J 174 " pdb=" CG LYS J 174 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.07e+00 ... (remaining 8505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3372 18.00 - 35.99: 342 35.99 - 53.98: 98 53.98 - 71.98: 19 71.98 - 89.97: 9 Dihedral angle restraints: 3840 sinusoidal: 1592 harmonic: 2248 Sorted by residual: dihedral pdb=" CA LYS J 174 " pdb=" C LYS J 174 " pdb=" N CYS J 175 " pdb=" CA CYS J 175 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CG ARG A 111 " pdb=" CD ARG A 111 " pdb=" NE ARG A 111 " pdb=" CZ ARG A 111 " ideal model delta sinusoidal sigma weight residual -90.00 -40.26 -49.74 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CA ASP J 235 " pdb=" CB ASP J 235 " pdb=" CG ASP J 235 " pdb=" OD1 ASP J 235 " ideal model delta sinusoidal sigma weight residual -30.00 -87.47 57.47 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 650 0.037 - 0.074: 221 0.074 - 0.112: 67 0.112 - 0.149: 24 0.149 - 0.186: 1 Chirality restraints: 963 Sorted by residual: chirality pdb=" CB VAL J 89 " pdb=" CA VAL J 89 " pdb=" CG1 VAL J 89 " pdb=" CG2 VAL J 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ASN F 122 " pdb=" N ASN F 122 " pdb=" C ASN F 122 " pdb=" CB ASN F 122 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE F 156 " pdb=" N ILE F 156 " pdb=" C ILE F 156 " pdb=" CB ILE F 156 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 960 not shown) Planarity restraints: 1086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 283 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO F 284 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 284 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 284 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 117 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 118 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 136 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ASN F 136 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN F 136 " 0.009 2.00e-02 2.50e+03 pdb=" N SER F 137 " 0.008 2.00e-02 2.50e+03 ... (remaining 1083 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 443 2.74 - 3.28: 5929 3.28 - 3.82: 10013 3.82 - 4.36: 12140 4.36 - 4.90: 20677 Nonbonded interactions: 49202 Sorted by model distance: nonbonded pdb=" OH TYR F 208 " pdb=" O ASN F 262 " model vdw 2.198 3.040 nonbonded pdb=" N GLU J 186 " pdb=" OE1 GLU J 186 " model vdw 2.223 3.120 nonbonded pdb=" NH2 ARG J 221 " pdb=" OE1 GLU J 224 " model vdw 2.274 3.120 nonbonded pdb=" N GLU F 282 " pdb=" OE1 GLU F 282 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU F 118 " pdb=" NE2 GLN F 120 " model vdw 2.324 3.120 ... (remaining 49197 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.330 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.003 0.033 6293 Z= 0.172 Angle : 0.523 8.330 8510 Z= 0.289 Chirality : 0.043 0.186 963 Planarity : 0.004 0.051 1086 Dihedral : 16.268 89.972 2382 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.72 % Allowed : 21.42 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.30), residues: 758 helix: 0.71 (0.30), residues: 279 sheet: -0.25 (0.52), residues: 89 loop : -0.65 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 327 HIS 0.002 0.001 HIS A 72 PHE 0.009 0.001 PHE F 7 TYR 0.011 0.001 TYR F 207 ARG 0.013 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 114 average time/residue: 1.1521 time to fit residues: 138.2001 Evaluate side-chains 111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain J residue 91 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 264 GLN F 22 ASN F 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6293 Z= 0.222 Angle : 0.506 7.058 8510 Z= 0.267 Chirality : 0.044 0.170 963 Planarity : 0.004 0.043 1086 Dihedral : 5.162 49.480 837 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.33 % Allowed : 18.81 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.29), residues: 758 helix: 0.83 (0.30), residues: 281 sheet: -0.63 (0.51), residues: 86 loop : -0.69 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 217 HIS 0.003 0.001 HIS J 215 PHE 0.011 0.001 PHE J 199 TYR 0.010 0.001 TYR A 112 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.725 Fit side-chains REVERT: A 111 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7732 (ttm-80) REVERT: A 123 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 172 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7983 (tp30) outliers start: 23 outliers final: 8 residues processed: 121 average time/residue: 1.0953 time to fit residues: 139.8255 Evaluate side-chains 114 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 171 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 245 GLN F 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6293 Z= 0.265 Angle : 0.525 6.907 8510 Z= 0.275 Chirality : 0.045 0.162 963 Planarity : 0.004 0.041 1086 Dihedral : 4.893 41.847 831 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.49 % Allowed : 18.09 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 758 helix: 0.90 (0.30), residues: 281 sheet: -0.75 (0.53), residues: 82 loop : -0.75 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 155 HIS 0.004 0.001 HIS J 215 PHE 0.014 0.001 PHE J 199 TYR 0.013 0.001 TYR J 207 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.866 Fit side-chains REVERT: A 123 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: F 1 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: F 187 MET cc_start: 0.7972 (ptt) cc_final: 0.7757 (ptp) REVERT: F 333 ARG cc_start: 0.6488 (mmm-85) cc_final: 0.5754 (mtt180) outliers start: 31 outliers final: 15 residues processed: 129 average time/residue: 1.0595 time to fit residues: 144.3843 Evaluate side-chains 117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 171 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6293 Z= 0.229 Angle : 0.517 7.735 8510 Z= 0.270 Chirality : 0.044 0.159 963 Planarity : 0.004 0.038 1086 Dihedral : 4.887 42.263 831 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.62 % Allowed : 20.26 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.29), residues: 758 helix: 0.94 (0.30), residues: 282 sheet: -0.78 (0.52), residues: 82 loop : -0.71 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 257 HIS 0.003 0.001 HIS J 215 PHE 0.012 0.001 PHE J 199 TYR 0.012 0.001 TYR J 207 ARG 0.006 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.722 Fit side-chains REVERT: A 123 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: A 172 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: F 1 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7448 (tpp) REVERT: F 187 MET cc_start: 0.7985 (ptt) cc_final: 0.7754 (ptp) REVERT: F 219 ASP cc_start: 0.7038 (t0) cc_final: 0.6563 (p0) REVERT: F 333 ARG cc_start: 0.6489 (mmm-85) cc_final: 0.5859 (mtt180) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 1.0091 time to fit residues: 130.4249 Evaluate side-chains 122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6293 Z= 0.206 Angle : 0.514 9.964 8510 Z= 0.266 Chirality : 0.044 0.164 963 Planarity : 0.004 0.036 1086 Dihedral : 4.839 42.080 831 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.34 % Allowed : 19.54 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 758 helix: 1.08 (0.30), residues: 281 sheet: -0.64 (0.52), residues: 84 loop : -0.69 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 257 HIS 0.002 0.001 HIS J 215 PHE 0.010 0.001 PHE J 199 TYR 0.012 0.001 TYR F 207 ARG 0.007 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.737 Fit side-chains REVERT: A 113 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: A 123 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 172 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: F 187 MET cc_start: 0.8012 (ptt) cc_final: 0.7764 (ptp) REVERT: F 333 ARG cc_start: 0.6458 (mmm-85) cc_final: 0.5873 (mtt180) REVERT: J 186 GLU cc_start: 0.6974 (pm20) cc_final: 0.6476 (tm-30) outliers start: 30 outliers final: 16 residues processed: 132 average time/residue: 1.0658 time to fit residues: 148.5367 Evaluate side-chains 123 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS F 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6293 Z= 0.202 Angle : 0.519 8.892 8510 Z= 0.269 Chirality : 0.044 0.190 963 Planarity : 0.004 0.036 1086 Dihedral : 4.880 44.812 831 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.34 % Allowed : 19.68 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 758 helix: 1.20 (0.30), residues: 281 sheet: -0.61 (0.52), residues: 86 loop : -0.67 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 257 HIS 0.002 0.001 HIS F 71 PHE 0.010 0.001 PHE J 199 TYR 0.012 0.001 TYR A 46 ARG 0.005 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.753 Fit side-chains REVERT: A 113 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: A 122 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 123 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 172 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: F 187 MET cc_start: 0.8038 (ptt) cc_final: 0.7763 (ptp) REVERT: F 219 ASP cc_start: 0.6968 (t0) cc_final: 0.6385 (p0) REVERT: F 333 ARG cc_start: 0.6419 (mmm-85) cc_final: 0.5844 (mtt180) REVERT: J 186 GLU cc_start: 0.7025 (pm20) cc_final: 0.6564 (tm-30) outliers start: 30 outliers final: 18 residues processed: 128 average time/residue: 1.0557 time to fit residues: 142.7908 Evaluate side-chains 125 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6293 Z= 0.257 Angle : 0.537 8.446 8510 Z= 0.276 Chirality : 0.045 0.156 963 Planarity : 0.004 0.035 1086 Dihedral : 5.016 47.496 831 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.34 % Allowed : 20.12 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 758 helix: 1.13 (0.30), residues: 280 sheet: -0.66 (0.53), residues: 86 loop : -0.73 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 181 HIS 0.003 0.001 HIS J 215 PHE 0.013 0.001 PHE J 199 TYR 0.013 0.001 TYR J 207 ARG 0.008 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.980 Fit side-chains REVERT: A 113 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: A 122 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 123 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: F 187 MET cc_start: 0.8055 (ptt) cc_final: 0.7770 (ptp) REVERT: F 333 ARG cc_start: 0.6433 (mmm-85) cc_final: 0.5859 (mtt180) REVERT: J 186 GLU cc_start: 0.7087 (pm20) cc_final: 0.6634 (tm-30) REVERT: J 226 MET cc_start: 0.6943 (mtp) cc_final: 0.6728 (mtp) outliers start: 30 outliers final: 20 residues processed: 126 average time/residue: 1.0797 time to fit residues: 143.2343 Evaluate side-chains 126 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 0.0060 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS F 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6293 Z= 0.154 Angle : 0.503 8.132 8510 Z= 0.260 Chirality : 0.043 0.154 963 Planarity : 0.004 0.037 1086 Dihedral : 4.837 51.956 831 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.18 % Allowed : 21.71 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.30), residues: 758 helix: 1.39 (0.30), residues: 280 sheet: -0.54 (0.53), residues: 86 loop : -0.60 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 257 HIS 0.001 0.000 HIS F 165 PHE 0.008 0.001 PHE F 58 TYR 0.013 0.001 TYR A 46 ARG 0.009 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.674 Fit side-chains REVERT: A 122 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8046 (mp) REVERT: A 123 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: A 172 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: F 182 VAL cc_start: 0.8542 (t) cc_final: 0.8317 (p) REVERT: F 187 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7734 (ptp) REVERT: F 219 ASP cc_start: 0.6822 (t0) cc_final: 0.6249 (p0) REVERT: F 333 ARG cc_start: 0.6317 (mmm-85) cc_final: 0.5798 (mtt180) REVERT: J 186 GLU cc_start: 0.7173 (pm20) cc_final: 0.6708 (tm-30) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.9883 time to fit residues: 131.7889 Evaluate side-chains 117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS F 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6293 Z= 0.214 Angle : 0.529 7.870 8510 Z= 0.271 Chirality : 0.045 0.168 963 Planarity : 0.004 0.036 1086 Dihedral : 4.770 52.097 829 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.33 % Allowed : 22.00 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.30), residues: 758 helix: 1.24 (0.30), residues: 282 sheet: -0.57 (0.53), residues: 86 loop : -0.58 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 155 HIS 0.002 0.001 HIS F 71 PHE 0.010 0.001 PHE J 199 TYR 0.011 0.001 TYR J 207 ARG 0.002 0.000 ARG F 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.665 Fit side-chains REVERT: A 113 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: A 122 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 123 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 172 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: F 219 ASP cc_start: 0.6887 (t0) cc_final: 0.6254 (p0) REVERT: F 333 ARG cc_start: 0.6345 (mmm-85) cc_final: 0.5810 (mtt180) REVERT: J 186 GLU cc_start: 0.7178 (pm20) cc_final: 0.6754 (tm-30) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 1.0581 time to fit residues: 137.5393 Evaluate side-chains 122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 74 optimal weight: 0.0020 chunk 68 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS F 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6293 Z= 0.160 Angle : 0.521 9.039 8510 Z= 0.268 Chirality : 0.044 0.166 963 Planarity : 0.004 0.035 1086 Dihedral : 4.741 53.916 829 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.46 % Allowed : 23.30 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 758 helix: 1.29 (0.30), residues: 282 sheet: -0.51 (0.54), residues: 86 loop : -0.56 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 257 HIS 0.002 0.000 HIS F 71 PHE 0.008 0.001 PHE F 58 TYR 0.010 0.001 TYR F 207 ARG 0.009 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.730 Fit side-chains REVERT: A 113 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7028 (tp30) REVERT: A 122 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 123 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: A 172 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: F 219 ASP cc_start: 0.6838 (t0) cc_final: 0.6239 (p0) REVERT: F 333 ARG cc_start: 0.6289 (mmm-85) cc_final: 0.5807 (mtt180) REVERT: J 186 GLU cc_start: 0.7198 (pm20) cc_final: 0.6773 (tm-30) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 1.0118 time to fit residues: 127.3918 Evaluate side-chains 118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 237 CYS Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.0470 chunk 43 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS F 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.193786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155096 restraints weight = 6758.677| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.78 r_work: 0.3439 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6293 Z= 0.174 Angle : 0.519 8.692 8510 Z= 0.267 Chirality : 0.044 0.180 963 Planarity : 0.004 0.049 1086 Dihedral : 4.729 54.496 829 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.60 % Allowed : 23.30 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 758 helix: 1.30 (0.30), residues: 282 sheet: -0.46 (0.54), residues: 86 loop : -0.53 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 257 HIS 0.002 0.000 HIS F 71 PHE 0.008 0.001 PHE J 199 TYR 0.010 0.001 TYR F 207 ARG 0.011 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.38 seconds wall clock time: 50 minutes 31.49 seconds (3031.49 seconds total)