Starting phenix.real_space_refine on Tue Aug 4 16:39:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w02_65489/08_2026/9w02_65489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w02_65489/08_2026/9w02_65489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w02_65489/08_2026/9w02_65489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w02_65489/08_2026/9w02_65489.map" model { file = "/net/cci-nas-00/data/ceres_data/9w02_65489/08_2026/9w02_65489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w02_65489/08_2026/9w02_65489_neut.cif" } resolution = 2.72 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= 0.000 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 24 5.16 5 C 2888 2.51 5 N 909 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4900 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1898 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1961 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "C" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 774 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 14, 'rna3p': 22} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 0.98, per 1000 atoms: 0.20 Number of scatterers: 4900 At special positions: 0 Unit cell: (63.8, 65.975, 105.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 49 15.00 O 1030 8.00 N 909 7.00 C 2888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 85.7 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 71.6% alpha, 3.3% beta 6 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 65 through 97 removed outlier: 3.659A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 4.296A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.708A pdb=" N VAL A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.912A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.510A pdb=" N ARG A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.528A pdb=" N TYR A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'B' and resid 66 through 98 removed outlier: 3.500A pdb=" N GLN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 133 removed outlier: 3.570A pdb=" N LYS B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.598A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.818A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 4.187A pdb=" N TYR B 186 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.609A pdb=" N LYS B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 288 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 238 253 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 926 1.32 - 1.45: 1475 1.45 - 1.57: 2561 1.57 - 1.70: 97 1.70 - 1.82: 44 Bond restraints: 5103 Sorted by residual: bond pdb=" C SER A 237 " pdb=" N ARG A 238 " ideal model delta sigma weight residual 1.330 1.236 0.094 1.39e-02 5.18e+03 4.53e+01 bond pdb=" C ARG A 238 " pdb=" N ASN A 239 " ideal model delta sigma weight residual 1.330 1.247 0.083 1.38e-02 5.25e+03 3.60e+01 bond pdb=" C SER A 105 " pdb=" N THR A 106 " ideal model delta sigma weight residual 1.335 1.267 0.068 1.31e-02 5.83e+03 2.70e+01 bond pdb=" C ALA A 206 " pdb=" N ASN A 207 " ideal model delta sigma weight residual 1.335 1.265 0.070 1.38e-02 5.25e+03 2.57e+01 bond pdb=" CA ASN B 195 " pdb=" C ASN B 195 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.32e-02 5.74e+03 9.34e+00 ... (remaining 5098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5880 2.00 - 4.00: 1098 4.00 - 6.01: 130 6.01 - 8.01: 10 8.01 - 10.01: 1 Bond angle restraints: 7119 Sorted by residual: angle pdb=" N THR B 197 " pdb=" CA THR B 197 " pdb=" C THR B 197 " ideal model delta sigma weight residual 110.97 105.60 5.37 1.09e+00 8.42e-01 2.43e+01 angle pdb=" N ASN A 195 " pdb=" CA ASN A 195 " pdb=" C ASN A 195 " ideal model delta sigma weight residual 111.33 105.45 5.88 1.21e+00 6.83e-01 2.36e+01 angle pdb=" CB HIS B 296 " pdb=" CG HIS B 296 " pdb=" CD2 HIS B 296 " ideal model delta sigma weight residual 131.20 124.90 6.30 1.30e+00 5.92e-01 2.35e+01 angle pdb=" N VAL B 161 " pdb=" CA VAL B 161 " pdb=" C VAL B 161 " ideal model delta sigma weight residual 109.63 116.51 -6.88 1.44e+00 4.82e-01 2.28e+01 angle pdb=" CB HIS B 258 " pdb=" CG HIS B 258 " pdb=" CD2 HIS B 258 " ideal model delta sigma weight residual 131.20 125.21 5.99 1.30e+00 5.92e-01 2.12e+01 ... (remaining 7114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 2895 34.36 - 68.71: 162 68.71 - 103.07: 16 103.07 - 137.42: 0 137.42 - 171.78: 3 Dihedral angle restraints: 3076 sinusoidal: 1679 harmonic: 1397 Sorted by residual: dihedral pdb=" O4' C C 24 " pdb=" C1' C C 24 " pdb=" N1 C C 24 " pdb=" C2 C C 24 " ideal model delta sinusoidal sigma weight residual 200.00 36.54 163.46 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" C5' A C 29 " pdb=" C4' A C 29 " pdb=" C3' A C 29 " pdb=" O3' A C 29 " ideal model delta sinusoidal sigma weight residual 82.00 128.05 -46.05 1 8.00e+00 1.56e-02 4.59e+01 dihedral pdb=" O4' A C 29 " pdb=" C4' A C 29 " pdb=" C3' A C 29 " pdb=" C2' A C 29 " ideal model delta sinusoidal sigma weight residual -35.00 10.27 -45.27 1 8.00e+00 1.56e-02 4.44e+01 ... (remaining 3073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 661 0.104 - 0.207: 126 0.207 - 0.311: 10 0.311 - 0.415: 1 0.415 - 0.518: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" P G C 36 " pdb=" OP1 G C 36 " pdb=" OP2 G C 36 " pdb=" O5' G C 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA TYR A 160 " pdb=" N TYR A 160 " pdb=" C TYR A 160 " pdb=" CB TYR A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 797 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 309 " 0.131 2.00e-02 2.50e+03 6.75e-02 1.14e+02 pdb=" CG TRP B 309 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 309 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 309 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 309 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP B 309 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP B 309 " -0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 309 " 0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 309 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP B 309 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 175 " 0.095 2.00e-02 2.50e+03 5.47e-02 5.99e+01 pdb=" CG TYR A 175 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 175 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 175 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 175 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR A 175 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 175 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 175 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 173 " -0.080 2.00e-02 2.50e+03 4.43e-02 4.91e+01 pdb=" CG TRP B 173 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 173 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 173 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP B 173 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP B 173 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 173 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 173 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 173 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 173 " -0.059 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1832 2.91 - 3.41: 5083 3.41 - 3.90: 9146 3.90 - 4.40: 10192 4.40 - 4.90: 15553 Nonbonded interactions: 41806 Sorted by model distance: nonbonded pdb=" OH TYR A 95 " pdb=" O ARG A 103 " model vdw 2.411 3.040 nonbonded pdb=" O4' C C 24 " pdb=" O2 C C 24 " model vdw 2.436 3.040 nonbonded pdb=" O2' C C 8 " pdb=" OP2 C C 9 " model vdw 2.458 3.040 nonbonded pdb=" O GLY A 194 " pdb=" C ASN A 195 " model vdw 2.461 3.270 nonbonded pdb=" N LYS B 133 " pdb=" O LYS B 133 " model vdw 2.474 2.496 ... (remaining 41801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 65 through 289 or resid 298 through 309)) } 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.011 0.094 5103 Z= 0.707 Angle : 1.508 10.010 7119 Z= 1.039 Chirality : 0.080 0.518 800 Planarity : 0.013 0.093 731 Dihedral : 19.612 171.778 2174 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.50 % Allowed : 5.21 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.34), residues: 476 helix: 0.06 (0.25), residues: 314 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 263 TYR 0.095 0.014 TYR A 175 PHE 0.035 0.009 PHE B 109 TRP 0.131 0.016 TRP B 309 HIS 0.011 0.003 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.01080 / 0.71 ( 5103) covalent geometry : angle 1.50814 / 1.04 ( 7119) hydrogen bonds : bond 0.18771 / 11.77 ( 268) hydrogen bonds : angle 6.77596 / 4.93 ( 773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9231 (tpp) cc_final: 0.9025 (tpp) REVERT: A 86 MET cc_start: 0.8592 (ttp) cc_final: 0.8243 (tmm) REVERT: A 90 ASN cc_start: 0.8283 (m-40) cc_final: 0.8022 (m110) REVERT: A 105 SER cc_start: 0.9221 (m) cc_final: 0.8932 (t) REVERT: A 164 GLU cc_start: 0.8777 (tp30) cc_final: 0.8554 (tp30) REVERT: A 288 LEU cc_start: 0.8799 (mm) cc_final: 0.8541 (tp) REVERT: A 289 TYR cc_start: 0.8699 (m-80) cc_final: 0.8191 (m-10) outliers start: 2 outliers final: 3 residues processed: 70 average time/residue: 0.3814 time to fit residues: 27.8895 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068478 restraints weight = 13456.310| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.03 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5103 Z= 0.188 Angle : 0.669 9.052 7119 Z= 0.387 Chirality : 0.043 0.336 800 Planarity : 0.005 0.028 731 Dihedral : 22.579 175.802 1214 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.49 % Allowed : 11.17 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.36), residues: 476 helix: 2.18 (0.27), residues: 319 sheet: None (None), residues: 0 loop : 0.59 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 238 TYR 0.027 0.002 TYR A 95 PHE 0.016 0.002 PHE A 269 TRP 0.008 0.002 TRP B 309 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 5103) covalent geometry : angle 0.66871 / 0.39 ( 7119) hydrogen bonds : bond 0.07606 / 4.60 ( 268) hydrogen bonds : angle 4.09824 / 3.01 ( 773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.091 Fit side-chains REVERT: A 82 MET cc_start: 0.9182 (tpp) cc_final: 0.8948 (tpp) REVERT: A 86 MET cc_start: 0.8645 (ttp) cc_final: 0.8215 (tmm) REVERT: A 105 SER cc_start: 0.9110 (m) cc_final: 0.8687 (t) REVERT: A 164 GLU cc_start: 0.8825 (tp30) cc_final: 0.8574 (tp30) REVERT: A 288 LEU cc_start: 0.8880 (mm) cc_final: 0.8595 (tp) REVERT: A 289 TYR cc_start: 0.8833 (m-80) cc_final: 0.8081 (m-10) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.3684 time to fit residues: 20.0619 Evaluate side-chains 42 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.083478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068263 restraints weight = 13136.356| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.94 r_work: 0.3103 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5103 Z= 0.158 Angle : 0.588 8.819 7119 Z= 0.335 Chirality : 0.041 0.331 800 Planarity : 0.004 0.028 731 Dihedral : 22.494 175.365 1211 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.23 % Allowed : 14.14 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.18 (0.37), residues: 476 helix: 2.69 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 0.95 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 238 TYR 0.029 0.002 TYR A 95 PHE 0.014 0.002 PHE A 269 TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 ( 5103) covalent geometry : angle 0.58834 / 0.33 ( 7119) hydrogen bonds : bond 0.06247 / 3.82 ( 268) hydrogen bonds : angle 3.77022 / 2.80 ( 773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.144 Fit side-chains REVERT: A 86 MET cc_start: 0.8618 (ttp) cc_final: 0.8048 (tmm) REVERT: A 105 SER cc_start: 0.9075 (m) cc_final: 0.8619 (t) REVERT: A 164 GLU cc_start: 0.8842 (tp30) cc_final: 0.8576 (tp30) REVERT: A 288 LEU cc_start: 0.8903 (mm) cc_final: 0.8608 (tp) REVERT: A 289 TYR cc_start: 0.8871 (m-80) cc_final: 0.8187 (m-10) REVERT: A 299 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 274 TRP cc_start: 0.8548 (t60) cc_final: 0.8126 (t60) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.3227 time to fit residues: 17.0421 Evaluate side-chains 46 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.084390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069314 restraints weight = 13117.477| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.92 r_work: 0.3142 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5103 Z= 0.136 Angle : 0.555 8.474 7119 Z= 0.316 Chirality : 0.040 0.325 800 Planarity : 0.004 0.029 731 Dihedral : 22.309 173.766 1211 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.99 % Allowed : 14.39 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.56 (0.37), residues: 476 helix: 2.96 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 1.14 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 218 TYR 0.023 0.001 TYR A 95 PHE 0.012 0.001 PHE A 269 TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 ( 5103) covalent geometry : angle 0.55499 / 0.32 ( 7119) hydrogen bonds : bond 0.05571 / 3.39 ( 268) hydrogen bonds : angle 3.59996 / 2.67 ( 773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.095 Fit side-chains REVERT: A 82 MET cc_start: 0.9057 (tpt) cc_final: 0.8809 (tpp) REVERT: A 86 MET cc_start: 0.8610 (ttp) cc_final: 0.8011 (tmm) REVERT: A 105 SER cc_start: 0.9052 (m) cc_final: 0.8569 (t) REVERT: A 164 GLU cc_start: 0.8829 (tp30) cc_final: 0.8566 (tp30) REVERT: A 288 LEU cc_start: 0.8929 (mm) cc_final: 0.8638 (tp) REVERT: A 289 TYR cc_start: 0.8891 (m-80) cc_final: 0.8310 (m-10) REVERT: B 205 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (tpt) REVERT: B 274 TRP cc_start: 0.8474 (t60) cc_final: 0.8098 (t60) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.3988 time to fit residues: 21.7533 Evaluate side-chains 46 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 205 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.084139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068796 restraints weight = 13471.226| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.00 r_work: 0.3136 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5103 Z= 0.139 Angle : 0.548 6.561 7119 Z= 0.311 Chirality : 0.040 0.323 800 Planarity : 0.004 0.029 731 Dihedral : 22.261 173.368 1211 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.99 % Allowed : 15.88 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.58 (0.37), residues: 476 helix: 2.97 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 1.19 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 218 TYR 0.021 0.001 TYR A 95 PHE 0.010 0.001 PHE A 269 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 5103) covalent geometry : angle 0.54770 / 0.31 ( 7119) hydrogen bonds : bond 0.05327 / 3.28 ( 268) hydrogen bonds : angle 3.61571 / 2.68 ( 773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.146 Fit side-chains REVERT: A 82 MET cc_start: 0.9048 (tpt) cc_final: 0.8826 (tpp) REVERT: A 86 MET cc_start: 0.8582 (ttp) cc_final: 0.7993 (tmm) REVERT: A 88 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8249 (ttp) REVERT: A 105 SER cc_start: 0.9023 (m) cc_final: 0.8525 (t) REVERT: A 164 GLU cc_start: 0.8846 (tp30) cc_final: 0.8581 (tp30) REVERT: A 288 LEU cc_start: 0.8917 (mm) cc_final: 0.8619 (tp) REVERT: A 289 TYR cc_start: 0.8896 (m-80) cc_final: 0.8298 (m-10) REVERT: B 274 TRP cc_start: 0.8492 (t60) cc_final: 0.8130 (t60) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.3226 time to fit residues: 16.3420 Evaluate side-chains 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.0000 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.085507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070229 restraints weight = 13519.725| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.01 r_work: 0.3166 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5103 Z= 0.127 Angle : 0.551 8.920 7119 Z= 0.305 Chirality : 0.039 0.323 800 Planarity : 0.004 0.028 731 Dihedral : 22.198 172.246 1211 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.99 % Allowed : 16.13 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.83 (0.38), residues: 476 helix: 3.13 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 1.38 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.019 0.001 TYR A 95 PHE 0.011 0.001 PHE A 269 TRP 0.010 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 ( 5103) covalent geometry : angle 0.55128 / 0.30 ( 7119) hydrogen bonds : bond 0.04981 / 3.05 ( 268) hydrogen bonds : angle 3.59806 / 2.67 ( 773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.157 Fit side-chains REVERT: A 82 MET cc_start: 0.9029 (tpt) cc_final: 0.8808 (tpp) REVERT: A 105 SER cc_start: 0.9002 (m) cc_final: 0.8606 (p) REVERT: A 164 GLU cc_start: 0.8832 (tp30) cc_final: 0.8568 (tp30) REVERT: A 288 LEU cc_start: 0.8935 (mm) cc_final: 0.8636 (tp) REVERT: A 289 TYR cc_start: 0.8862 (m-80) cc_final: 0.8285 (m-10) REVERT: B 205 MET cc_start: 0.8444 (tpt) cc_final: 0.8105 (tpp) REVERT: B 274 TRP cc_start: 0.8429 (t60) cc_final: 0.8101 (t60) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.3953 time to fit residues: 20.0377 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069431 restraints weight = 13434.541| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.01 r_work: 0.3130 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5103 Z= 0.139 Angle : 0.567 11.701 7119 Z= 0.305 Chirality : 0.039 0.325 800 Planarity : 0.004 0.029 731 Dihedral : 22.157 174.143 1211 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.23 % Allowed : 16.63 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.95 (0.38), residues: 476 helix: 3.21 (0.27), residues: 319 sheet: None (None), residues: 0 loop : 1.47 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.021 0.001 TYR A 95 PHE 0.010 0.001 PHE A 269 TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 5103) covalent geometry : angle 0.56713 / 0.31 ( 7119) hydrogen bonds : bond 0.04911 / 3.03 ( 268) hydrogen bonds : angle 3.52763 / 2.62 ( 773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 105 SER cc_start: 0.8990 (m) cc_final: 0.8610 (p) REVERT: A 164 GLU cc_start: 0.8846 (tp30) cc_final: 0.8583 (tp30) REVERT: B 205 MET cc_start: 0.8529 (tpt) cc_final: 0.8274 (tpp) REVERT: B 274 TRP cc_start: 0.8471 (t60) cc_final: 0.8147 (t60) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.3786 time to fit residues: 19.4958 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 226 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.085046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069645 restraints weight = 13320.167| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.99 r_work: 0.3138 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5103 Z= 0.138 Angle : 0.585 12.084 7119 Z= 0.311 Chirality : 0.039 0.330 800 Planarity : 0.004 0.029 731 Dihedral : 22.153 175.875 1211 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.99 % Allowed : 16.87 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.96 (0.38), residues: 476 helix: 3.23 (0.27), residues: 319 sheet: None (None), residues: 0 loop : 1.40 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.018 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 5103) covalent geometry : angle 0.58467 / 0.31 ( 7119) hydrogen bonds : bond 0.04872 / 2.99 ( 268) hydrogen bonds : angle 3.52051 / 2.62 ( 773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 105 SER cc_start: 0.8986 (m) cc_final: 0.8604 (p) REVERT: A 164 GLU cc_start: 0.8841 (tp30) cc_final: 0.8578 (tp30) REVERT: A 214 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8715 (mppt) REVERT: A 288 LEU cc_start: 0.8955 (mm) cc_final: 0.8642 (tp) REVERT: A 289 TYR cc_start: 0.8898 (m-80) cc_final: 0.8261 (m-10) REVERT: B 205 MET cc_start: 0.8527 (tpt) cc_final: 0.8295 (tpp) REVERT: B 274 TRP cc_start: 0.8454 (t60) cc_final: 0.8134 (t60) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.3655 time to fit residues: 19.6158 Evaluate side-chains 52 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 226 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.084423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069084 restraints weight = 13330.771| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.00 r_work: 0.3127 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5103 Z= 0.143 Angle : 0.614 13.196 7119 Z= 0.319 Chirality : 0.040 0.334 800 Planarity : 0.004 0.029 731 Dihedral : 22.190 176.872 1211 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.74 % Allowed : 17.37 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.93 (0.38), residues: 476 helix: 3.27 (0.27), residues: 318 sheet: None (None), residues: 0 loop : 1.28 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.018 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 5103) covalent geometry : angle 0.61374 / 0.32 ( 7119) hydrogen bonds : bond 0.04883 / 3.00 ( 268) hydrogen bonds : angle 3.58238 / 2.67 ( 773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 105 SER cc_start: 0.8994 (m) cc_final: 0.8628 (p) REVERT: A 164 GLU cc_start: 0.8831 (tp30) cc_final: 0.8582 (tp30) REVERT: A 214 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8765 (mppt) REVERT: B 205 MET cc_start: 0.8603 (tpt) cc_final: 0.8396 (tpp) REVERT: B 274 TRP cc_start: 0.8479 (t60) cc_final: 0.8189 (t60) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.4007 time to fit residues: 20.7109 Evaluate side-chains 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 226 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.084749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069294 restraints weight = 13401.635| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.01 r_work: 0.3149 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5103 Z= 0.136 Angle : 0.619 12.857 7119 Z= 0.318 Chirality : 0.039 0.338 800 Planarity : 0.004 0.029 731 Dihedral : 22.051 177.161 1211 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.99 % Allowed : 18.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.96 (0.38), residues: 476 helix: 3.29 (0.28), residues: 318 sheet: None (None), residues: 0 loop : 1.30 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.016 0.001 TYR A 95 PHE 0.006 0.001 PHE A 269 TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 5103) covalent geometry : angle 0.61943 / 0.32 ( 7119) hydrogen bonds : bond 0.04796 / 2.94 ( 268) hydrogen bonds : angle 3.58437 / 2.67 ( 773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 105 SER cc_start: 0.8968 (m) cc_final: 0.8600 (p) REVERT: A 164 GLU cc_start: 0.8826 (tp30) cc_final: 0.8582 (tp30) REVERT: A 214 LYS cc_start: 0.9083 (mmpt) cc_final: 0.8735 (mppt) REVERT: B 274 TRP cc_start: 0.8486 (t60) cc_final: 0.8220 (t60) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.3985 time to fit residues: 19.7445 Evaluate side-chains 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 226 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.1980 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 0.0050 chunk 17 optimal weight: 7.9990 chunk 45 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.3952 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.085910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070764 restraints weight = 13437.495| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.03 r_work: 0.3179 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5103 Z= 0.120 Angle : 0.603 12.637 7119 Z= 0.312 Chirality : 0.039 0.339 800 Planarity : 0.004 0.028 731 Dihedral : 22.023 177.778 1211 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.49 % Allowed : 17.62 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.99 (0.38), residues: 476 helix: 3.30 (0.28), residues: 317 sheet: None (None), residues: 0 loop : 1.34 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.017 0.001 TYR A 95 PHE 0.008 0.001 PHE B 269 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 ( 5103) covalent geometry : angle 0.60346 / 0.31 ( 7119) hydrogen bonds : bond 0.04591 / 2.80 ( 268) hydrogen bonds : angle 3.61129 / 2.69 ( 773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.66 seconds wall clock time: 25 minutes 28.60 seconds (1528.60 seconds total)