Starting phenix.real_space_refine on Wed Feb 12 05:47:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy8_36723/02_2025/8jy8_36723.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy8_36723/02_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_36723/02_2025/8jy8_36723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy8_36723/02_2025/8jy8_36723.map" model { file = "/net/cci-nas-00/data/ceres_data/8jy8_36723/02_2025/8jy8_36723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy8_36723/02_2025/8jy8_36723.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, D Time building chain proxies: 3.46, per 1000 atoms: 0.47 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.62 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: 2.00 Time building geometry restraints manager: 2.20 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 18.590 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- 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= 0.322 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (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 TRP 0.005 0.001 TRP C 289 HIS 0.001 0.000 HIS C 283 PHE 0.010 0.001 PHE A 246 TYR 0.007 0.001 TYR D 206 ARG 0.002 0.001 ARG D 146 *********************** 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 : 0.763 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: 0.9170 time to fit residues: 139.7552 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 : 0.760 ------------------------------------------------------------------------------- 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 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.188357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.166260 restraints weight = 7081.382| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.16 r_work: 0.3682 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7624 Z= 0.219 Angle : 0.586 7.433 10396 Z= 0.302 Chirality : 0.038 0.127 1148 Planarity : 0.005 0.037 1308 Dihedral : 12.686 145.582 1080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.88 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 960 helix: 1.84 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.43 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.002 0.001 HIS D 128 PHE 0.017 0.002 PHE D 246 TYR 0.009 0.001 TYR C 71 ARG 0.001 0.000 ARG B 269 *********************** 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 149 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.797 Fit side-chains REVERT: A 145 TRP cc_start: 0.7853 (m100) cc_final: 0.7414 (m100) REVERT: A 237 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: A 258 LEU cc_start: 0.7626 (tp) cc_final: 0.7377 (tp) REVERT: A 309 PHE cc_start: 0.6309 (m-10) cc_final: 0.6080 (m-10) REVERT: B 145 TRP cc_start: 0.7851 (m100) cc_final: 0.7412 (m100) REVERT: B 237 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: B 258 LEU cc_start: 0.7643 (tp) cc_final: 0.7372 (tp) REVERT: C 145 TRP cc_start: 0.7835 (m100) cc_final: 0.7405 (m100) REVERT: C 237 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: C 258 LEU cc_start: 0.7713 (tp) cc_final: 0.7434 (tp) REVERT: D 145 TRP cc_start: 0.7868 (m100) cc_final: 0.7442 (m100) REVERT: D 237 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: D 258 LEU cc_start: 0.7637 (tp) cc_final: 0.7388 (tp) REVERT: D 309 PHE cc_start: 0.6296 (m-10) cc_final: 0.6063 (m-10) outliers start: 21 outliers final: 6 residues processed: 136 average time/residue: 0.8750 time to fit residues: 128.2500 Evaluate side-chains 123 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 GLU 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 20 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.182073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.159460 restraints weight = 7116.543| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.16 r_work: 0.3602 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7624 Z= 0.345 Angle : 0.689 8.909 10396 Z= 0.358 Chirality : 0.042 0.126 1148 Planarity : 0.006 0.036 1308 Dihedral : 13.342 158.479 1080 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.95 % Allowed : 14.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 960 helix: 1.23 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.59 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.004 0.002 HIS C 128 PHE 0.020 0.003 PHE D 246 TYR 0.008 0.002 TYR B 197 ARG 0.001 0.000 ARG B 146 *********************** 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 152 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.831 Fit side-chains REVERT: B 258 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7922 (mt) REVERT: C 258 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 279 GLU cc_start: 0.7776 (pt0) cc_final: 0.7570 (pm20) REVERT: D 188 LYS cc_start: 0.6996 (ptpp) cc_final: 0.6651 (ptpt) outliers start: 36 outliers final: 22 residues processed: 134 average time/residue: 1.1137 time to fit residues: 158.7247 Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU 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 A residue 237 GLU Chi-restraints excluded: chain B residue 103 LEU 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 237 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 103 LEU 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 237 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 103 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 Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.180387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.157303 restraints weight = 6818.132| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.12 r_work: 0.3579 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7624 Z= 0.232 Angle : 0.602 9.171 10396 Z= 0.306 Chirality : 0.038 0.116 1148 Planarity : 0.005 0.038 1308 Dihedral : 13.467 168.281 1080 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.08 % Allowed : 13.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 960 helix: 1.53 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.003 0.001 HIS A 177 PHE 0.018 0.002 PHE D 246 TYR 0.006 0.001 TYR C 206 ARG 0.001 0.000 ARG B 269 *********************** 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 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.780 Fit side-chains REVERT: D 188 LYS cc_start: 0.7006 (ptpp) cc_final: 0.6708 (ptpt) outliers start: 37 outliers final: 14 residues processed: 135 average time/residue: 1.0278 time to fit residues: 147.9576 Evaluate side-chains 121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 56 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.181304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158367 restraints weight = 6813.443| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.13 r_work: 0.3591 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2700 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= 0.212 Angle : 0.586 8.916 10396 Z= 0.295 Chirality : 0.038 0.116 1148 Planarity : 0.005 0.039 1308 Dihedral : 13.106 165.211 1076 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.85 % Allowed : 14.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 960 helix: 1.90 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 PHE 0.016 0.002 PHE A 246 TYR 0.005 0.001 TYR D 236 ARG 0.002 0.000 ARG C 72 *********************** 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 130 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.757 Fit side-chains REVERT: B 258 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7777 (mt) REVERT: C 258 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7751 (mt) REVERT: D 188 LYS cc_start: 0.6892 (ptpp) cc_final: 0.6627 (ptpt) outliers start: 28 outliers final: 12 residues processed: 120 average time/residue: 1.0658 time to fit residues: 136.3679 Evaluate side-chains 116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 219 LEU 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 258 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 82 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.182684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.159934 restraints weight = 6885.415| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.13 r_work: 0.3604 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2696 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= 0.192 Angle : 0.565 8.745 10396 Z= 0.283 Chirality : 0.037 0.113 1148 Planarity : 0.005 0.039 1308 Dihedral : 12.984 165.967 1076 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.40 % Allowed : 14.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 960 helix: 2.04 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 PHE 0.014 0.001 PHE D 246 TYR 0.006 0.001 TYR D 236 ARG 0.002 0.000 ARG B 72 *********************** 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 127 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.808 Fit side-chains REVERT: A 146 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (tmm160) REVERT: A 188 LYS cc_start: 0.6933 (ptpp) cc_final: 0.6694 (ptpt) REVERT: B 258 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7712 (mt) REVERT: C 258 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7635 (mt) REVERT: D 188 LYS cc_start: 0.6884 (ptpp) cc_final: 0.6549 (ptpt) outliers start: 32 outliers final: 18 residues processed: 112 average time/residue: 1.0433 time to fit residues: 124.7971 Evaluate side-chains 115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 82 optimal weight: 0.0060 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.182616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.159831 restraints weight = 6829.566| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.14 r_work: 0.3607 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2719 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= 0.192 Angle : 0.565 8.694 10396 Z= 0.283 Chirality : 0.037 0.114 1148 Planarity : 0.006 0.039 1308 Dihedral : 12.903 166.081 1076 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.98 % Allowed : 15.25 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 960 helix: 2.02 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.23 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 PHE 0.015 0.002 PHE D 246 TYR 0.006 0.001 TYR B 236 ARG 0.001 0.000 ARG B 72 *********************** 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 126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.734 Fit side-chains REVERT: A 146 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7794 (tmm160) REVERT: A 188 LYS cc_start: 0.6923 (ptpp) cc_final: 0.6717 (ptpt) REVERT: B 258 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7699 (mt) REVERT: C 258 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7617 (mt) REVERT: D 188 LYS cc_start: 0.6925 (ptpp) cc_final: 0.6606 (ptpt) outliers start: 29 outliers final: 20 residues processed: 113 average time/residue: 1.0380 time to fit residues: 125.1513 Evaluate side-chains 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LEU 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 96 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.183533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.161019 restraints weight = 6833.261| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.13 r_work: 0.3618 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2728 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= 0.183 Angle : 0.553 8.510 10396 Z= 0.277 Chirality : 0.037 0.113 1148 Planarity : 0.005 0.039 1308 Dihedral : 12.762 166.139 1076 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 15.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 960 helix: 2.26 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 PHE 0.013 0.001 PHE A 246 TYR 0.007 0.001 TYR A 236 ARG 0.001 0.000 ARG B 72 *********************** 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 121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.865 Fit side-chains REVERT: A 146 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7781 (tmm160) REVERT: A 188 LYS cc_start: 0.6934 (ptpp) cc_final: 0.6732 (ptpt) REVERT: B 258 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7682 (mt) REVERT: C 258 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7594 (mt) REVERT: D 188 LYS cc_start: 0.6907 (ptpp) cc_final: 0.6595 (ptpt) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 1.0044 time to fit residues: 122.4654 Evaluate side-chains 118 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 96 LEU 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 96 LEU 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 258 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 0.0170 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.182070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158940 restraints weight = 6930.673| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.15 r_work: 0.3591 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2804 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= 0.207 Angle : 0.578 8.719 10396 Z= 0.291 Chirality : 0.038 0.116 1148 Planarity : 0.006 0.039 1308 Dihedral : 12.813 167.073 1076 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.57 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 960 helix: 2.20 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.34 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 289 HIS 0.002 0.001 HIS A 177 PHE 0.016 0.002 PHE D 246 TYR 0.006 0.001 TYR D 236 ARG 0.001 0.000 ARG D 72 *********************** 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 127 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.720 Fit side-chains REVERT: A 146 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7802 (tmm160) REVERT: A 188 LYS cc_start: 0.6984 (ptpp) cc_final: 0.6784 (ptpt) REVERT: B 258 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7725 (mt) REVERT: C 258 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7692 (mt) REVERT: D 188 LYS cc_start: 0.6914 (ptpp) cc_final: 0.6600 (ptpt) outliers start: 26 outliers final: 17 residues processed: 117 average time/residue: 1.0099 time to fit residues: 126.1676 Evaluate side-chains 121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 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 = 0.3953 r_free = 0.3953 target = 0.181573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.158204 restraints weight = 6958.435| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.17 r_work: 0.3585 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2854 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= 0.217 Angle : 0.602 8.866 10396 Z= 0.299 Chirality : 0.038 0.116 1148 Planarity : 0.006 0.039 1308 Dihedral : 12.792 167.198 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 : 2.61 % Allowed : 16.76 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 960 helix: 2.19 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 289 HIS 0.003 0.001 HIS A 177 PHE 0.017 0.002 PHE D 246 TYR 0.007 0.001 TYR B 206 ARG 0.001 0.000 ARG D 72 ********************** 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 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.902 Fit side-chains REVERT: A 146 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7803 (tmm160) REVERT: B 258 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7824 (mt) REVERT: C 258 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7793 (mt) REVERT: D 188 LYS cc_start: 0.6874 (ptpp) cc_final: 0.6558 (ptpt) outliers start: 19 outliers final: 15 residues processed: 107 average time/residue: 1.0940 time to fit residues: 124.9126 Evaluate side-chains 116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 B residue 258 LEU 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 14 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.182451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.159406 restraints weight = 6900.029| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.15 r_work: 0.3598 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2841 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= 0.199 Angle : 0.579 8.657 10396 Z= 0.288 Chirality : 0.037 0.115 1148 Planarity : 0.006 0.039 1308 Dihedral : 12.712 166.889 1076 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.02 % Allowed : 16.21 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 960 helix: 2.30 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS A 177 PHE 0.015 0.002 PHE D 246 TYR 0.007 0.001 TYR D 236 ARG 0.001 0.000 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.03 seconds wall clock time: 93 minutes 35.22 seconds (5615.22 seconds total)