Starting phenix.real_space_refine on Fri Aug 22 19:42:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy8_36723/08_2025/8jy8_36723.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy8_36723/08_2025/8jy8_36723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jy8_36723/08_2025/8jy8_36723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy8_36723/08_2025/8jy8_36723.map" model { file = "/net/cci-nas-00/data/ceres_data/8jy8_36723/08_2025/8jy8_36723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy8_36723/08_2025/8jy8_36723.cif" } resolution = 2.45 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= 0.260 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4988 2.51 5 N 1132 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7392 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1823 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PNT': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 1.25, per 1000 atoms: 0.17 Number of scatterers: 7392 At special positions: 0 Unit cell: (92.568, 92.568, 63.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1240 8.00 N 1132 7.00 C 4988 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: 0.64 Conformation dependent library (CDL) restraints added in 358.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 71 through 98 Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.678A pdb=" N VAL A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.508A pdb=" N THR A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 170 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.104A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 226 removed outlier: 3.659A pdb=" N ILE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 261 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.610A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 310 removed outlier: 3.523A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Proline residue: A 295 - end of helix Processing helix chain 'B' and resid 72 through 98 Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.678A pdb=" N VAL B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.508A pdb=" N THR B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 170 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.104A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 226 removed outlier: 3.659A pdb=" N ILE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 261 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.610A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 removed outlier: 3.523A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Proline residue: B 295 - end of helix Processing helix chain 'C' and resid 72 through 98 Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.678A pdb=" N VAL C 120 " --> pdb=" O MET C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 removed outlier: 3.509A pdb=" N THR C 134 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 170 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.104A pdb=" N PHE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 226 removed outlier: 3.659A pdb=" N ILE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 253 Processing helix chain 'C' and resid 261 through 276 Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.610A pdb=" N TYR C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 310 removed outlier: 3.522A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Proline residue: C 295 - end of helix Processing helix chain 'D' and resid 72 through 98 Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.678A pdb=" N VAL D 120 " --> pdb=" O MET D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 140 removed outlier: 3.508A pdb=" N THR D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 139 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 170 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.104A pdb=" N PHE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 226 removed outlier: 3.659A pdb=" N ILE D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 253 Processing helix chain 'D' and resid 261 through 276 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.610A pdb=" N TYR D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 removed outlier: 3.522A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Proline residue: D 295 - end of helix 481 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2196 1.34 - 1.46: 1735 1.46 - 1.57: 3641 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 7624 Sorted by residual: bond pdb=" C9 PNT A 401 " pdb=" N1 PNT A 401 " ideal model delta sigma weight residual 1.279 1.389 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C9 PNT B 401 " pdb=" N1 PNT B 401 " ideal model delta sigma weight residual 1.279 1.389 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C9 PNT C 401 " pdb=" N1 PNT C 401 " ideal model delta sigma weight residual 1.279 1.389 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C9 PNT D 401 " pdb=" N1 PNT D 401 " ideal model delta sigma weight residual 1.279 1.389 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C9 PNT A 401 " pdb=" N2 PNT A 401 " ideal model delta sigma weight residual 1.368 1.311 0.057 2.00e-02 2.50e+03 8.23e+00 ... (remaining 7619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10272 2.36 - 4.73: 100 4.73 - 7.09: 16 7.09 - 9.46: 0 9.46 - 11.82: 8 Bond angle restraints: 10396 Sorted by residual: angle pdb=" C4 PNT C 401 " pdb=" C9 PNT C 401 " pdb=" N2 PNT C 401 " ideal model delta sigma weight residual 115.38 127.20 -11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4 PNT B 401 " pdb=" C9 PNT B 401 " pdb=" N2 PNT B 401 " ideal model delta sigma weight residual 115.38 127.20 -11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4 PNT A 401 " pdb=" C9 PNT A 401 " pdb=" N2 PNT A 401 " ideal model delta sigma weight residual 115.38 127.20 -11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4 PNT D 401 " pdb=" C9 PNT D 401 " pdb=" N2 PNT D 401 " ideal model delta sigma weight residual 115.38 127.17 -11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N1 PNT D 401 " pdb=" C9 PNT D 401 " pdb=" N2 PNT D 401 " ideal model delta sigma weight residual 125.71 114.42 11.29 3.00e+00 1.11e-01 1.42e+01 ... (remaining 10391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 4048 32.36 - 64.73: 152 64.73 - 97.09: 12 97.09 - 129.45: 0 129.45 - 161.81: 4 Dihedral angle restraints: 4216 sinusoidal: 1520 harmonic: 2696 Sorted by residual: dihedral pdb=" C10 PNT D 401 " pdb=" C7 PNT D 401 " pdb=" C8 PNT D 401 " pdb=" O1 PNT D 401 " ideal model delta sinusoidal sigma weight residual 180.84 19.03 161.81 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C10 PNT B 401 " pdb=" C7 PNT B 401 " pdb=" C8 PNT B 401 " pdb=" O1 PNT B 401 " ideal model delta sinusoidal sigma weight residual 180.84 19.04 161.80 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C10 PNT C 401 " pdb=" C7 PNT C 401 " pdb=" C8 PNT C 401 " pdb=" O1 PNT C 401 " ideal model delta sinusoidal sigma weight residual 180.84 19.06 161.78 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 4213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 719 0.032 - 0.065: 329 0.065 - 0.097: 74 0.097 - 0.129: 22 0.129 - 0.162: 4 Chirality restraints: 1148 Sorted by residual: chirality pdb=" CA ASN C 137 " pdb=" N ASN C 137 " pdb=" C ASN C 137 " pdb=" CB ASN C 137 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ASN D 137 " pdb=" N ASN D 137 " pdb=" C ASN D 137 " pdb=" CB ASN D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ASN B 137 " pdb=" N ASN B 137 " pdb=" C ASN B 137 " pdb=" CB ASN B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1145 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 137 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ASN D 137 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN D 137 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA D 138 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 137 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ASN C 137 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN C 137 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 138 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ASN A 137 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 138 " -0.015 2.00e-02 2.50e+03 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2717 2.85 - 3.37: 7150 3.37 - 3.88: 13091 3.88 - 4.39: 14895 4.39 - 4.90: 25485 Nonbonded interactions: 63338 Sorted by model distance: nonbonded pdb=" O MET B 156 " pdb=" OG1 THR B 159 " model vdw 2.343 3.040 nonbonded pdb=" O MET C 156 " pdb=" OG1 THR C 159 " model vdw 2.344 3.040 nonbonded pdb=" O MET D 156 " pdb=" OG1 THR D 159 " model vdw 2.344 3.040 nonbonded pdb=" O MET A 156 " pdb=" OG1 THR A 159 " model vdw 2.344 3.040 nonbonded pdb=" N ASP A 73 " pdb=" OD1 ASP A 73 " model vdw 2.367 3.120 ... (remaining 63333 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.260 Find NCS groups from input model: 0.060 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.005 0.110 7624 Z= 0.240 Angle : 0.690 11.821 10396 Z= 0.340 Chirality : 0.038 0.162 1148 Planarity : 0.006 0.030 1308 Dihedral : 17.048 161.815 2536 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 21.43 % Favored : 76.92 % 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 aren not related in a simple way. whole: 0.01 (0.27), residues: 960 helix: 0.82 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 146 TYR 0.007 0.001 TYR D 206 PHE 0.010 0.001 PHE A 246 TRP 0.005 0.001 TRP C 289 HIS 0.001 0.000 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 7624) covalent geometry : angle 0.68996 (10396) hydrogen bonds : bond 0.14668 ( 481) hydrogen bonds : angle 7.42200 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.163 Fit side-chains REVERT: A 172 ASP cc_start: 0.6769 (t0) cc_final: 0.6429 (t0) REVERT: A 196 MET cc_start: 0.7386 (mmt) cc_final: 0.7173 (mmt) REVERT: A 308 TYR cc_start: 0.6031 (t80) cc_final: 0.5784 (t80) REVERT: B 172 ASP cc_start: 0.6718 (t0) cc_final: 0.6394 (t0) REVERT: B 196 MET cc_start: 0.7376 (mmt) cc_final: 0.7165 (mmt) REVERT: B 308 TYR cc_start: 0.6007 (t80) cc_final: 0.5779 (t80) REVERT: C 172 ASP cc_start: 0.6776 (t0) cc_final: 0.6437 (t0) REVERT: C 196 MET cc_start: 0.7430 (mmt) cc_final: 0.7203 (mmt) REVERT: C 308 TYR cc_start: 0.5999 (t80) cc_final: 0.5767 (t80) REVERT: D 172 ASP cc_start: 0.6768 (t0) cc_final: 0.6429 (t0) REVERT: D 196 MET cc_start: 0.7435 (mmt) cc_final: 0.7209 (mmt) REVERT: D 308 TYR cc_start: 0.6035 (t80) cc_final: 0.5781 (t80) outliers start: 12 outliers final: 4 residues processed: 142 average time/residue: 0.3831 time to fit residues: 58.2619 Evaluate side-chains 102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 250 ASN C 250 ASN D 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.188409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166313 restraints weight = 7199.204| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.16 r_work: 0.3682 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7624 Z= 0.152 Angle : 0.589 7.662 10396 Z= 0.303 Chirality : 0.039 0.122 1148 Planarity : 0.005 0.037 1308 Dihedral : 12.770 148.176 1080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.30 % Allowed : 17.58 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.27), residues: 960 helix: 1.87 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.010 0.001 TYR C 71 PHE 0.018 0.002 PHE D 246 TRP 0.003 0.001 TRP B 289 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7624) covalent geometry : angle 0.58852 (10396) hydrogen bonds : bond 0.05269 ( 481) hydrogen bonds : angle 4.57682 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.252 Fit side-chains REVERT: A 145 TRP cc_start: 0.7840 (m100) cc_final: 0.7381 (m100) REVERT: A 237 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 258 LEU cc_start: 0.7631 (tp) cc_final: 0.7381 (tp) REVERT: A 309 PHE cc_start: 0.6305 (m-10) cc_final: 0.6082 (m-10) REVERT: B 145 TRP cc_start: 0.7838 (m100) cc_final: 0.7376 (m100) REVERT: B 237 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: B 258 LEU cc_start: 0.7648 (tp) cc_final: 0.7374 (tp) REVERT: C 145 TRP cc_start: 0.7865 (m100) cc_final: 0.7420 (m100) REVERT: C 237 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: C 258 LEU cc_start: 0.7721 (tp) cc_final: 0.7443 (tp) REVERT: D 145 TRP cc_start: 0.7873 (m100) cc_final: 0.7432 (m100) REVERT: D 237 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: D 258 LEU cc_start: 0.7721 (tp) cc_final: 0.7465 (tp) REVERT: D 309 PHE cc_start: 0.6294 (m-10) cc_final: 0.6074 (m-10) outliers start: 24 outliers final: 9 residues processed: 141 average time/residue: 0.4086 time to fit residues: 61.9319 Evaluate side-chains 121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.188224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.166108 restraints weight = 7128.393| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.16 r_work: 0.3665 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7624 Z= 0.145 Angle : 0.570 8.397 10396 Z= 0.291 Chirality : 0.037 0.115 1148 Planarity : 0.005 0.037 1308 Dihedral : 13.950 178.433 1080 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.95 % Allowed : 13.87 % Favored : 81.18 % 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 aren not related in a simple way. whole: 1.31 (0.27), residues: 960 helix: 1.91 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 269 TYR 0.005 0.001 TYR A 197 PHE 0.015 0.002 PHE A 246 TRP 0.002 0.001 TRP A 289 HIS 0.003 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7624) covalent geometry : angle 0.56992 (10396) hydrogen bonds : bond 0.05188 ( 481) hydrogen bonds : angle 4.44386 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.185 Fit side-chains REVERT: D 211 GLU cc_start: 0.7615 (tp30) cc_final: 0.7394 (tp30) outliers start: 36 outliers final: 16 residues processed: 134 average time/residue: 0.3726 time to fit residues: 53.5530 Evaluate side-chains 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.184079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.161325 restraints weight = 6845.902| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.17 r_work: 0.3622 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7624 Z= 0.132 Angle : 0.554 8.466 10396 Z= 0.280 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.038 1308 Dihedral : 13.065 162.423 1076 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.40 % Allowed : 14.56 % Favored : 81.04 % 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 aren not related in a simple way. whole: 1.48 (0.27), residues: 960 helix: 2.15 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 269 TYR 0.006 0.001 TYR C 206 PHE 0.014 0.002 PHE D 246 TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7624) covalent geometry : angle 0.55420 (10396) hydrogen bonds : bond 0.04777 ( 481) hydrogen bonds : angle 4.28408 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.248 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 131 average time/residue: 0.3364 time to fit residues: 47.3190 Evaluate side-chains 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.0030 chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 0.0170 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.186098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.163937 restraints weight = 6921.234| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.17 r_work: 0.3654 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7624 Z= 0.115 Angle : 0.533 7.888 10396 Z= 0.265 Chirality : 0.036 0.111 1148 Planarity : 0.005 0.037 1308 Dihedral : 12.953 163.996 1076 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.16 % Allowed : 16.35 % Favored : 80.49 % 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 aren not related in a simple way. whole: 1.70 (0.27), residues: 960 helix: 2.27 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.29 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 269 TYR 0.006 0.001 TYR B 236 PHE 0.013 0.001 PHE B 205 TRP 0.004 0.001 TRP A 289 HIS 0.001 0.000 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7624) covalent geometry : angle 0.53262 (10396) hydrogen bonds : bond 0.04188 ( 481) hydrogen bonds : angle 4.11854 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.176 Fit side-chains REVERT: C 279 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7368 (pm20) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.3585 time to fit residues: 47.6006 Evaluate side-chains 120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 165 CYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.182623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159512 restraints weight = 6857.639| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.18 r_work: 0.3603 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7624 Z= 0.147 Angle : 0.584 8.245 10396 Z= 0.294 Chirality : 0.038 0.117 1148 Planarity : 0.005 0.039 1308 Dihedral : 13.065 165.345 1076 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.95 % Allowed : 14.15 % Favored : 80.91 % 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 aren not related in a simple way. whole: 1.57 (0.27), residues: 960 helix: 2.22 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -1.37 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 269 TYR 0.007 0.001 TYR B 206 PHE 0.017 0.002 PHE A 246 TRP 0.002 0.001 TRP C 289 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7624) covalent geometry : angle 0.58358 (10396) hydrogen bonds : bond 0.05235 ( 481) hydrogen bonds : angle 4.32091 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.270 Fit side-chains REVERT: A 188 LYS cc_start: 0.6856 (ptpp) cc_final: 0.6618 (ptpt) REVERT: B 258 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7672 (mt) REVERT: C 258 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7667 (mt) outliers start: 36 outliers final: 20 residues processed: 126 average time/residue: 0.4118 time to fit residues: 55.5064 Evaluate side-chains 129 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.181228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.157935 restraints weight = 6884.975| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.15 r_work: 0.3583 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7624 Z= 0.157 Angle : 0.607 8.480 10396 Z= 0.305 Chirality : 0.038 0.116 1148 Planarity : 0.005 0.039 1308 Dihedral : 13.083 166.385 1076 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.08 % Allowed : 14.01 % Favored : 80.91 % 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 aren not related in a simple way. whole: 1.42 (0.26), residues: 960 helix: 2.07 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 269 TYR 0.007 0.001 TYR B 206 PHE 0.016 0.002 PHE D 246 TRP 0.002 0.001 TRP B 192 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7624) covalent geometry : angle 0.60697 (10396) hydrogen bonds : bond 0.05510 ( 481) hydrogen bonds : angle 4.40643 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.220 Fit side-chains REVERT: A 188 LYS cc_start: 0.6917 (ptpp) cc_final: 0.6701 (ptpt) REVERT: B 258 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7804 (mt) REVERT: C 258 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7782 (mt) outliers start: 37 outliers final: 18 residues processed: 125 average time/residue: 0.4185 time to fit residues: 55.9213 Evaluate side-chains 129 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.181824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.158690 restraints weight = 6920.419| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.15 r_work: 0.3593 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7624 Z= 0.146 Angle : 0.595 8.412 10396 Z= 0.296 Chirality : 0.038 0.116 1148 Planarity : 0.005 0.040 1308 Dihedral : 12.969 165.757 1076 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.53 % Allowed : 14.42 % Favored : 81.04 % 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 aren not related in a simple way. whole: 1.55 (0.26), residues: 960 helix: 2.17 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 269 TYR 0.008 0.001 TYR B 206 PHE 0.016 0.002 PHE A 246 TRP 0.003 0.001 TRP A 289 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7624) covalent geometry : angle 0.59475 (10396) hydrogen bonds : bond 0.05200 ( 481) hydrogen bonds : angle 4.32532 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.257 Fit side-chains REVERT: A 188 LYS cc_start: 0.6938 (ptpp) cc_final: 0.6729 (ptpt) REVERT: B 258 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7722 (mt) REVERT: C 258 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7686 (mt) REVERT: D 188 LYS cc_start: 0.6822 (ptpp) cc_final: 0.6563 (ptpt) outliers start: 33 outliers final: 20 residues processed: 122 average time/residue: 0.4701 time to fit residues: 61.1610 Evaluate side-chains 129 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.181561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158454 restraints weight = 6813.684| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.14 r_work: 0.3590 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7624 Z= 0.149 Angle : 0.600 8.421 10396 Z= 0.300 Chirality : 0.038 0.116 1148 Planarity : 0.005 0.040 1308 Dihedral : 12.939 166.153 1076 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.98 % Allowed : 14.84 % Favored : 81.18 % 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 aren not related in a simple way. whole: 1.59 (0.26), residues: 960 helix: 2.20 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 269 TYR 0.009 0.001 TYR B 206 PHE 0.016 0.002 PHE A 246 TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7624) covalent geometry : angle 0.60026 (10396) hydrogen bonds : bond 0.05313 ( 481) hydrogen bonds : angle 4.35054 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.202 Fit side-chains REVERT: B 258 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7706 (mt) REVERT: B 307 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7241 (mttt) REVERT: C 258 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7697 (mt) outliers start: 29 outliers final: 20 residues processed: 126 average time/residue: 0.3991 time to fit residues: 53.9265 Evaluate side-chains 132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.177716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.153830 restraints weight = 6893.559| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.16 r_work: 0.3534 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7624 Z= 0.225 Angle : 0.704 8.375 10396 Z= 0.359 Chirality : 0.043 0.130 1148 Planarity : 0.006 0.040 1308 Dihedral : 13.166 167.517 1076 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.02 % Allowed : 15.80 % Favored : 81.18 % 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 aren not related in a simple way. whole: 1.18 (0.26), residues: 960 helix: 1.83 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 146 TYR 0.012 0.002 TYR D 119 PHE 0.019 0.003 PHE A 246 TRP 0.003 0.001 TRP A 192 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 7624) covalent geometry : angle 0.70366 (10396) hydrogen bonds : bond 0.06795 ( 481) hydrogen bonds : angle 4.75897 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.272 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 122 average time/residue: 0.5334 time to fit residues: 68.9180 Evaluate side-chains 125 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 14 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.182534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159863 restraints weight = 6902.344| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.14 r_work: 0.3607 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7624 Z= 0.131 Angle : 0.587 8.484 10396 Z= 0.289 Chirality : 0.037 0.114 1148 Planarity : 0.005 0.040 1308 Dihedral : 12.817 167.008 1076 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 16.35 % Favored : 81.32 % 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 aren not related in a simple way. whole: 1.67 (0.26), residues: 960 helix: 2.27 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 269 TYR 0.007 0.001 TYR D 236 PHE 0.012 0.001 PHE D 246 TRP 0.005 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7624) covalent geometry : angle 0.58675 (10396) hydrogen bonds : bond 0.04753 ( 481) hydrogen bonds : angle 4.27305 ( 1443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2451.84 seconds wall clock time: 42 minutes 26.88 seconds (2546.88 seconds total)