Starting phenix.real_space_refine on Thu Jul 2 01:03:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w02_65489/07_2026/9w02_65489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w02_65489/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9w02_65489/07_2026/9w02_65489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w02_65489/07_2026/9w02_65489_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w02_65489/07_2026/9w02_65489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w02_65489/07_2026/9w02_65489.map" } 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-dev-6108/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: 0.85, per 1000 atoms: 0.17 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: 0.29 Conformation dependent library (CDL) restraints added in 108.1 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: 0.45 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: 0.64 Time building geometry restraints manager: 0.39 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: 5842 2.00 - 4.00: 1136 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: 640 0.104 - 0.207: 146 0.207 - 0.311: 11 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: 1.850 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- 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= 0.700 Angle : 1.525 10.010 7119 Z= 1.047 Chirality : 0.085 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 0.01078 / 0.70 ( 5103) covalent geometry : angle 1.52526 / 1.05 ( 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 : 0.129 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: 0.3795 time to fit residues: 27.8211 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 : 0.098 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 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: 7.9990 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 = 0.3619 r_free = 0.3619 target = 0.083861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068409 restraints weight = 13457.847| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.04 r_work: 0.3109 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5103 Z= 0.187 Angle : 0.667 9.532 7119 Z= 0.391 Chirality : 0.043 0.315 800 Planarity : 0.005 0.028 731 Dihedral : 22.596 175.969 1214 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.49 % Allowed : 10.67 % Favored : 87.84 % 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: 2.45 (0.36), residues: 476 helix: 2.15 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 0.63 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 238 TYR 0.027 0.002 TYR A 95 PHE 0.016 0.002 PHE A 269 TRP 0.007 0.001 TRP A 203 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 ( 5103) covalent geometry : angle 0.66744 / 0.39 ( 7119) hydrogen bonds : bond 0.07539 / 4.63 ( 268) hydrogen bonds : angle 4.12743 / 3.02 ( 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 : 0.158 Fit side-chains REVERT: A 82 MET cc_start: 0.9194 (tpp) cc_final: 0.8896 (tpp) REVERT: A 86 MET cc_start: 0.8634 (ttp) cc_final: 0.8190 (tmm) REVERT: A 105 SER cc_start: 0.9104 (m) cc_final: 0.8682 (t) REVERT: A 164 GLU cc_start: 0.8829 (tp30) cc_final: 0.8576 (tp30) REVERT: A 288 LEU cc_start: 0.8842 (mm) cc_final: 0.8560 (tp) REVERT: A 289 TYR cc_start: 0.8812 (m-80) cc_final: 0.8065 (m-10) REVERT: B 205 MET cc_start: 0.8379 (tpt) cc_final: 0.8118 (tpt) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.3864 time to fit residues: 21.1688 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 : 0.143 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.083318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068152 restraints weight = 13183.046| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.94 r_work: 0.3113 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5103 Z= 0.171 Angle : 0.593 9.079 7119 Z= 0.340 Chirality : 0.042 0.308 800 Planarity : 0.004 0.028 731 Dihedral : 22.551 176.242 1211 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.48 % Allowed : 13.90 % 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: 3.12 (0.37), residues: 476 helix: 2.67 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 0.88 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 213 TYR 0.026 0.002 TYR A 95 PHE 0.010 0.002 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 0.00333 / 0.17 ( 5103) covalent geometry : angle 0.59252 / 0.34 ( 7119) hydrogen bonds : bond 0.06303 / 3.85 ( 268) hydrogen bonds : angle 3.79533 / 2.82 ( 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 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.104 Fit side-chains REVERT: A 86 MET cc_start: 0.8609 (ttp) cc_final: 0.8045 (tmm) REVERT: A 105 SER cc_start: 0.9079 (m) cc_final: 0.8640 (t) REVERT: A 164 GLU cc_start: 0.8852 (tp30) cc_final: 0.8580 (tp30) REVERT: A 288 LEU cc_start: 0.8886 (mm) cc_final: 0.8603 (tp) REVERT: A 289 TYR cc_start: 0.8847 (m-80) cc_final: 0.8176 (m-10) REVERT: B 205 MET cc_start: 0.8485 (tpt) cc_final: 0.8265 (tpt) REVERT: B 274 TRP cc_start: 0.8579 (t60) cc_final: 0.8154 (t60) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.3476 time to fit residues: 18.5899 Evaluate side-chains 45 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 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 300 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.084448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069077 restraints weight = 13194.636| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.97 r_work: 0.3126 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5103 Z= 0.140 Angle : 0.559 7.639 7119 Z= 0.319 Chirality : 0.040 0.305 800 Planarity : 0.004 0.029 731 Dihedral : 22.385 174.735 1211 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.74 % Allowed : 14.64 % 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: 3.44 (0.37), residues: 476 helix: 2.90 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 1.02 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.023 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 0.00261 / 0.14 ( 5103) covalent geometry : angle 0.55933 / 0.32 ( 7119) hydrogen bonds : bond 0.05694 / 3.47 ( 268) hydrogen bonds : angle 3.62946 / 2.70 ( 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 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.100 Fit side-chains REVERT: A 82 MET cc_start: 0.9071 (tpt) cc_final: 0.8851 (tpp) REVERT: A 86 MET cc_start: 0.8608 (ttp) cc_final: 0.8035 (tmm) REVERT: A 105 SER cc_start: 0.9058 (m) cc_final: 0.8577 (t) REVERT: A 164 GLU cc_start: 0.8832 (tp30) cc_final: 0.8569 (tp30) REVERT: A 288 LEU cc_start: 0.8911 (mm) cc_final: 0.8635 (tp) REVERT: A 289 TYR cc_start: 0.8875 (m-80) cc_final: 0.8273 (m-10) REVERT: B 205 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8274 (tpt) REVERT: B 274 TRP cc_start: 0.8492 (t60) cc_final: 0.8108 (t60) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.3848 time to fit residues: 19.8507 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 : 0.108 ------------------------------------------------------------------------------- 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 178 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: 0.8980 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.084504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069238 restraints weight = 13477.599| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.99 r_work: 0.3138 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5103 Z= 0.134 Angle : 0.551 7.283 7119 Z= 0.314 Chirality : 0.040 0.302 800 Planarity : 0.004 0.029 731 Dihedral : 22.322 174.172 1211 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.73 % Allowed : 14.89 % Favored : 82.38 % 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 (0.38), residues: 476 helix: 3.00 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 1.10 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.022 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 0.00248 / 0.13 ( 5103) covalent geometry : angle 0.55056 / 0.31 ( 7119) hydrogen bonds : bond 0.05403 / 3.29 ( 268) hydrogen bonds : angle 3.59804 / 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 56 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.128 Fit side-chains REVERT: A 82 MET cc_start: 0.9052 (tpt) cc_final: 0.8831 (tpp) REVERT: A 86 MET cc_start: 0.8597 (ttp) cc_final: 0.8030 (tmm) REVERT: A 105 SER cc_start: 0.9042 (m) cc_final: 0.8543 (t) REVERT: A 164 GLU cc_start: 0.8836 (tp30) cc_final: 0.8566 (tp30) REVERT: A 288 LEU cc_start: 0.8909 (mm) cc_final: 0.8618 (tp) REVERT: A 289 TYR cc_start: 0.8890 (m-80) cc_final: 0.8290 (m-10) REVERT: B 205 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8324 (tpt) REVERT: B 274 TRP cc_start: 0.8489 (t60) cc_final: 0.8127 (t60) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 0.3713 time to fit residues: 19.5548 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 209 MET 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: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.084273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068805 restraints weight = 13559.219| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.99 r_work: 0.3131 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5103 Z= 0.147 Angle : 0.553 8.490 7119 Z= 0.313 Chirality : 0.040 0.302 800 Planarity : 0.004 0.029 731 Dihedral : 22.247 174.076 1211 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.88 % 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: 3.65 (0.37), residues: 476 helix: 3.02 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 1.21 (0.50), 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 0.005 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 0.00291 / 0.15 ( 5103) covalent geometry : angle 0.55308 / 0.31 ( 7119) hydrogen bonds : bond 0.05308 / 3.26 ( 268) hydrogen bonds : angle 3.63140 / 2.70 ( 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 51 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.153 Fit side-chains REVERT: A 82 MET cc_start: 0.9044 (tpt) cc_final: 0.8816 (tpp) REVERT: A 105 SER cc_start: 0.9018 (m) cc_final: 0.8512 (t) REVERT: A 164 GLU cc_start: 0.8837 (tp30) cc_final: 0.8571 (tp30) REVERT: B 205 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8273 (tpp) REVERT: B 274 TRP cc_start: 0.8503 (t60) cc_final: 0.8151 (t60) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.3131 time to fit residues: 15.1943 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 : 0.196 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 209 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.084333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068982 restraints weight = 13423.280| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.98 r_work: 0.3129 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5103 Z= 0.143 Angle : 0.572 11.524 7119 Z= 0.311 Chirality : 0.040 0.306 800 Planarity : 0.004 0.029 731 Dihedral : 22.238 174.831 1211 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.48 % Allowed : 15.38 % 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: 3.86 (0.37), residues: 476 helix: 3.16 (0.27), residues: 319 sheet: None (None), residues: 0 loop : 1.37 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.020 0.001 TYR A 95 PHE 0.005 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 0.00281 / 0.14 ( 5103) covalent geometry : angle 0.57211 / 0.31 ( 7119) hydrogen bonds : bond 0.05080 / 3.09 ( 268) hydrogen bonds : angle 3.57092 / 2.66 ( 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 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.102 Fit side-chains REVERT: A 105 SER cc_start: 0.9008 (m) cc_final: 0.8619 (p) REVERT: A 164 GLU cc_start: 0.8836 (tp30) cc_final: 0.8580 (tp30) REVERT: A 288 LEU cc_start: 0.8932 (mm) cc_final: 0.8641 (tp) REVERT: A 289 TYR cc_start: 0.8920 (m-80) cc_final: 0.8251 (m-10) REVERT: B 205 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8344 (tpp) REVERT: B 274 TRP cc_start: 0.8494 (t60) cc_final: 0.8139 (t60) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 0.3500 time to fit residues: 17.7039 Evaluate side-chains 48 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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 205 MET Chi-restraints excluded: chain B residue 209 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.085129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070395 restraints weight = 13439.163| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.98 r_work: 0.3143 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5103 Z= 0.130 Angle : 0.584 12.294 7119 Z= 0.313 Chirality : 0.039 0.306 800 Planarity : 0.003 0.028 731 Dihedral : 22.218 176.224 1211 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.74 % Allowed : 16.87 % Favored : 81.39 % 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: 3.23 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 1.34 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.019 0.001 TYR A 95 PHE 0.003 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 0.00248 / 0.13 ( 5103) covalent geometry : angle 0.58393 / 0.31 ( 7119) hydrogen bonds : bond 0.04878 / 2.96 ( 268) hydrogen bonds : angle 3.54806 / 2.65 ( 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 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.101 Fit side-chains REVERT: A 105 SER cc_start: 0.8991 (m) cc_final: 0.8601 (p) REVERT: A 164 GLU cc_start: 0.8833 (tp30) cc_final: 0.8575 (tp30) REVERT: A 214 LYS cc_start: 0.9063 (mmpt) cc_final: 0.8766 (mppt) REVERT: B 274 TRP cc_start: 0.8484 (t60) cc_final: 0.8193 (t60) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.3205 time to fit residues: 16.5993 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 : 0.119 ------------------------------------------------------------------------------- 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 209 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.084820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069320 restraints weight = 13421.811| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.04 r_work: 0.3123 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3495 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= 0.149 Angle : 0.624 13.243 7119 Z= 0.326 Chirality : 0.040 0.307 800 Planarity : 0.004 0.029 731 Dihedral : 22.226 177.827 1211 Min Nonbonded Distance : 2.471 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: 3.83 (0.38), residues: 476 helix: 3.22 (0.28), residues: 317 sheet: None (None), residues: 0 loop : 1.19 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 218 TYR 0.019 0.001 TYR A 95 PHE 0.005 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 0.00305 / 0.15 ( 5103) covalent geometry : angle 0.62403 / 0.33 ( 7119) hydrogen bonds : bond 0.04862 / 2.98 ( 268) hydrogen bonds : angle 3.59683 / 2.69 ( 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 49 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.119 Fit side-chains REVERT: A 105 SER cc_start: 0.9000 (m) cc_final: 0.8621 (p) REVERT: A 164 GLU cc_start: 0.8834 (tp30) cc_final: 0.8588 (tp30) REVERT: A 214 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8771 (mppt) REVERT: B 205 MET cc_start: 0.8445 (tpt) cc_final: 0.8058 (tpp) REVERT: B 274 TRP cc_start: 0.8488 (t60) cc_final: 0.8200 (t60) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.3571 time to fit residues: 17.2706 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 : 0.111 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.085250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070690 restraints weight = 13569.056| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.99 r_work: 0.3139 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5103 Z= 0.140 Angle : 0.626 13.463 7119 Z= 0.323 Chirality : 0.039 0.310 800 Planarity : 0.003 0.029 731 Dihedral : 22.171 179.231 1211 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 3.87 (0.38), residues: 476 helix: 3.25 (0.28), residues: 317 sheet: None (None), residues: 0 loop : 1.19 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.019 0.001 TYR A 95 PHE 0.004 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 0.00284 / 0.14 ( 5103) covalent geometry : angle 0.62563 / 0.32 ( 7119) hydrogen bonds : bond 0.04795 / 2.91 ( 268) hydrogen bonds : angle 3.59575 / 2.69 ( 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 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.104 Fit side-chains REVERT: A 105 SER cc_start: 0.8981 (m) cc_final: 0.8607 (p) REVERT: A 164 GLU cc_start: 0.8811 (tp30) cc_final: 0.8571 (tp30) REVERT: A 214 LYS cc_start: 0.9112 (mmpt) cc_final: 0.8775 (mppt) REVERT: B 205 MET cc_start: 0.8506 (tpt) cc_final: 0.8115 (tpp) REVERT: B 274 TRP cc_start: 0.8488 (t60) cc_final: 0.8224 (t60) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.3242 time to fit residues: 15.6956 Evaluate side-chains 44 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.0570 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.085304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069998 restraints weight = 13490.952| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.05 r_work: 0.3154 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3716 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= 0.127 Angle : 0.612 12.649 7119 Z= 0.317 Chirality : 0.040 0.314 800 Planarity : 0.004 0.032 731 Dihedral : 22.112 179.375 1211 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.99 % Allowed : 18.36 % Favored : 80.65 % 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: 3.84 (0.38), residues: 476 helix: 3.21 (0.28), residues: 317 sheet: None (None), residues: 0 loop : 1.24 (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 0.003 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 0.00253 / 0.13 ( 5103) covalent geometry : angle 0.61185 / 0.32 ( 7119) hydrogen bonds : bond 0.04621 / 2.79 ( 268) hydrogen bonds : angle 3.59218 / 2.68 ( 773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1261.45 seconds wall clock time: 22 minutes 18.17 seconds (1338.17 seconds total)