Starting phenix.real_space_refine on Sat Jul 4 05:52:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2i_53531/07_2026/9r2i_53531_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2i_53531/07_2026/9r2i_53531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2i_53531/07_2026/9r2i_53531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2i_53531/07_2026/9r2i_53531.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2i_53531/07_2026/9r2i_53531_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2i_53531/07_2026/9r2i_53531_trim.cif" } resolution = 3.3 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= 1.000 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 5777 2.51 5 N 1556 2.21 5 O 1767 1.98 5 H 9103 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18248 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3826 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 4, 'TRANS': 233} Chain: "B" Number of atoms: 3768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3768 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "C" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5980 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain: "D" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4642 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 14, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.08, per 1000 atoms: 0.17 Number of scatterers: 18248 At special positions: 0 Unit cell: (85.0272, 99.1984, 133.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 38 16.00 P 6 15.00 Mg 1 11.99 O 1767 8.00 N 1556 7.00 C 5777 6.00 H 9103 1.00 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: 1.37 Conformation dependent library (CDL) restraints added in 466.6 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 65.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 19 through 33 Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.613A pdb=" N VAL A 53 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 107 removed outlier: 3.679A pdb=" N LYS A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 138 removed outlier: 3.862A pdb=" N VAL A 137 " --> pdb=" O TYR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 169 through 186 Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 19 through 33 removed outlier: 3.574A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 74 removed outlier: 3.643A pdb=" N ARG B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 107 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 140 through 165 Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 189 through 207 removed outlier: 3.846A pdb=" N GLU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 235 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 259 through 280 removed outlier: 3.696A pdb=" N GLN C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 291 Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 341 through 358 removed outlier: 3.667A pdb=" N MET C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 379 removed outlier: 3.679A pdb=" N ILE C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 407 through 412 removed outlier: 4.034A pdb=" N HIS C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 442 through 447 removed outlier: 5.924A pdb=" N PHE C 445 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.635A pdb=" N HIS C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.672A pdb=" N PHE D 57 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 115 through 133 Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.644A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 204 Processing helix chain 'D' and resid 212 through 229 Processing helix chain 'D' and resid 245 through 261 Processing helix chain 'D' and resid 267 through 284 Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 313 through 319 removed outlier: 3.765A pdb=" N ARG D 317 " --> pdb=" O TYR D 313 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 165 through 172 removed outlier: 3.571A pdb=" N ILE C 166 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS C 181 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS C 170 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL C 179 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY C 172 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA C 177 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 228 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU C 241 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU C 226 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA3, first strand: chain 'C' and resid 282 through 283 541 hydrogen bonds defined for protein. 1581 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: 3.34 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 9086 1.06 - 1.28: 1584 1.28 - 1.50: 3824 1.50 - 1.73: 3861 1.73 - 1.95: 58 Bond restraints: 18413 Sorted by residual: bond pdb=" O3B AGS C 502 " pdb=" PB AGS C 502 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3A AGS C 502 " pdb=" PA AGS C 502 " ideal model delta sigma weight residual 1.664 1.585 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3B AGS C 502 " pdb=" PG AGS C 502 " ideal model delta sigma weight residual 1.614 1.557 0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" O5' AGS C 502 " pdb=" PA AGS C 502 " ideal model delta sigma weight residual 1.634 1.578 0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" N GLY D 38 " pdb=" CA GLY D 38 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 ... (remaining 18408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 33298 4.21 - 8.42: 16 8.42 - 12.62: 3 12.62 - 16.83: 0 16.83 - 21.04: 1 Bond angle restraints: 33318 Sorted by residual: angle pdb=" C ALA D 65 " pdb=" N SEP D 66 " pdb=" H SEP D 66 " ideal model delta sigma weight residual 124.30 103.26 21.04 3.00e+00 1.11e-01 4.92e+01 angle pdb=" O3A AGS C 502 " pdb=" PB AGS C 502 " pdb=" O3B AGS C 502 " ideal model delta sigma weight residual 100.38 110.69 -10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" PB AGS C 502 " pdb=" O3B AGS C 502 " pdb=" PG AGS C 502 " ideal model delta sigma weight residual 129.21 119.36 9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N PRO C 139 " pdb=" CA PRO C 139 " pdb=" C PRO C 139 " ideal model delta sigma weight residual 112.47 118.75 -6.28 2.06e+00 2.36e-01 9.29e+00 angle pdb=" O1B AGS C 502 " pdb=" PB AGS C 502 " pdb=" O2B AGS C 502 " ideal model delta sigma weight residual 121.53 112.53 9.00 3.00e+00 1.11e-01 9.01e+00 ... (remaining 33313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.75: 8507 31.75 - 63.51: 119 63.51 - 95.26: 2 95.26 - 127.02: 2 127.02 - 158.77: 2 Dihedral angle restraints: 8632 sinusoidal: 4764 harmonic: 3868 Sorted by residual: dihedral pdb=" CA PRO C 139 " pdb=" C PRO C 139 " pdb=" N ILE C 140 " pdb=" CA ILE C 140 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" O2A AGS C 502 " pdb=" O3A AGS C 502 " pdb=" PA AGS C 502 " pdb=" PB AGS C 502 " ideal model delta sinusoidal sigma weight residual -52.28 106.49 -158.77 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" O2B AGS C 502 " pdb=" O3B AGS C 502 " pdb=" PB AGS C 502 " pdb=" PG AGS C 502 " ideal model delta sinusoidal sigma weight residual 7.37 140.45 -133.08 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 8629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1241 0.052 - 0.104: 137 0.104 - 0.156: 23 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" C3' AGS C 502 " pdb=" C2' AGS C 502 " pdb=" C4' AGS C 502 " pdb=" O3' AGS C 502 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA PRO C 139 " pdb=" N PRO C 139 " pdb=" C PRO C 139 " pdb=" CB PRO C 139 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE C 109 " pdb=" N ILE C 109 " pdb=" C ILE C 109 " pdb=" CB ILE C 109 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1400 not shown) Planarity restraints: 2695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 65 " 0.080 2.00e-02 2.50e+03 1.56e-01 2.44e+02 pdb=" N SEP D 66 " -0.269 2.00e-02 2.50e+03 pdb=" CA SEP D 66 " 0.074 2.00e-02 2.50e+03 pdb=" H SEP D 66 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 138 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 139 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 126 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO C 127 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 127 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 127 " 0.018 5.00e-02 4.00e+02 ... (remaining 2692 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 832 2.19 - 2.79: 37986 2.79 - 3.40: 50632 3.40 - 4.00: 63965 4.00 - 4.60: 102006 Nonbonded interactions: 255421 Sorted by model distance: nonbonded pdb=" OE1 GLU A 141 " pdb=" H GLU A 141 " model vdw 1.589 2.450 nonbonded pdb=" O VAL B 47 " pdb="HD21 ASN B 51 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU C 132 " pdb=" H GLU C 132 " model vdw 1.632 2.450 nonbonded pdb="HH21 ARG C 210 " pdb=" O VAL D 226 " model vdw 1.633 2.450 nonbonded pdb=" OE1 GLU B 213 " pdb=" H GLU B 213 " model vdw 1.640 2.450 ... (remaining 255416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 236) selection = chain 'B' } 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: 2.360 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: 0.080 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.004 0.090 9310 Z= 0.180 Angle : 0.525 10.308 12586 Z= 0.257 Chirality : 0.035 0.260 1403 Planarity : 0.003 0.042 1614 Dihedral : 10.178 158.772 3580 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 0.80 % Allowed : 3.71 % Favored : 95.49 % 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 are not related in a simple way. whole: 2.68 (0.27), residues: 1106 helix: 2.88 (0.20), residues: 696 sheet: -0.28 (0.97), residues: 32 loop : -0.20 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.017 0.001 TYR A 130 PHE 0.010 0.001 PHE A 158 TRP 0.007 0.001 TRP D 335 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 9310) covalent geometry : angle 0.52509 / 0.26 (12586) hydrogen bonds : bond 0.13186 / 8.91 ( 541) hydrogen bonds : angle 5.44414 / 4.00 ( 1581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8256 (m-40) cc_final: 0.8021 (m-40) REVERT: A 159 GLU cc_start: 0.7458 (tt0) cc_final: 0.7231 (mt-10) REVERT: A 213 GLU cc_start: 0.7461 (tp30) cc_final: 0.7190 (tp30) REVERT: B 10 ARG cc_start: 0.7030 (ttm110) cc_final: 0.6548 (ttt-90) REVERT: C 436 SER cc_start: 0.6922 (t) cc_final: 0.6470 (p) REVERT: D 140 MET cc_start: 0.5091 (mpp) cc_final: 0.4534 (ppp) REVERT: D 211 ASN cc_start: 0.8460 (p0) cc_final: 0.8156 (p0) REVERT: D 307 ARG cc_start: 0.6746 (mtp-110) cc_final: 0.6130 (ttp-110) REVERT: D 318 ARG cc_start: 0.3398 (OUTLIER) cc_final: 0.2522 (tpt170) REVERT: D 334 ARG cc_start: 0.4457 (OUTLIER) cc_final: 0.2133 (ttt90) outliers start: 8 outliers final: 2 residues processed: 123 average time/residue: 0.2523 time to fit residues: 40.8438 Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.242672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.187363 restraints weight = 25359.537| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.41 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9310 Z= 0.210 Angle : 0.541 6.605 12586 Z= 0.289 Chirality : 0.037 0.203 1403 Planarity : 0.004 0.052 1614 Dihedral : 9.626 157.270 1294 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.75 % Rotamer: Outliers : 0.70 % Allowed : 6.01 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.26), residues: 1106 helix: 2.63 (0.19), residues: 686 sheet: -0.58 (0.97), residues: 32 loop : -0.49 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.022 0.002 TYR A 130 PHE 0.012 0.002 PHE D 69 TRP 0.014 0.002 TRP D 212 HIS 0.007 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 9310) covalent geometry : angle 0.54082 / 0.29 (12586) hydrogen bonds : bond 0.05075 / 3.45 ( 541) hydrogen bonds : angle 4.44080 / 3.26 ( 1581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.7603 (ttt) cc_final: 0.7372 (ttt) REVERT: C 436 SER cc_start: 0.7571 (t) cc_final: 0.7192 (p) REVERT: D 236 ASP cc_start: 0.7250 (t0) cc_final: 0.6433 (m-30) REVERT: D 307 ARG cc_start: 0.7080 (mtp-110) cc_final: 0.6743 (ttp-110) REVERT: D 318 ARG cc_start: 0.3413 (OUTLIER) cc_final: 0.2749 (tpt170) REVERT: D 334 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.2737 (ttt90) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 0.2659 time to fit residues: 33.9208 Evaluate side-chains 84 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.244981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.189965 restraints weight = 25436.240| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.41 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9310 Z= 0.121 Angle : 0.458 6.280 12586 Z= 0.242 Chirality : 0.034 0.185 1403 Planarity : 0.004 0.047 1614 Dihedral : 9.557 157.704 1294 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 0.90 % Allowed : 6.41 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.26), residues: 1106 helix: 2.74 (0.19), residues: 694 sheet: -0.74 (0.98), residues: 32 loop : -0.40 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.017 0.001 TYR A 130 PHE 0.008 0.001 PHE C 240 TRP 0.008 0.001 TRP D 212 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9310) covalent geometry : angle 0.45836 / 0.24 (12586) hydrogen bonds : bond 0.04266 / 2.88 ( 541) hydrogen bonds : angle 4.09253 / 3.00 ( 1581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7591 (t) cc_final: 0.7210 (p) REVERT: D 236 ASP cc_start: 0.7215 (t0) cc_final: 0.6398 (m-30) REVERT: D 307 ARG cc_start: 0.7154 (mtp-110) cc_final: 0.6749 (ttp-110) REVERT: D 318 ARG cc_start: 0.3330 (OUTLIER) cc_final: 0.2714 (tpt170) REVERT: D 334 ARG cc_start: 0.5119 (OUTLIER) cc_final: 0.2663 (ttt90) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.2465 time to fit residues: 29.3027 Evaluate side-chains 83 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.212660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160527 restraints weight = 25144.171| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.42 r_work: 0.3602 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9310 Z= 0.195 Angle : 0.513 5.878 12586 Z= 0.274 Chirality : 0.036 0.177 1403 Planarity : 0.004 0.048 1614 Dihedral : 9.653 162.123 1294 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.03 % Rotamer: Outliers : 1.20 % Allowed : 6.81 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.26), residues: 1106 helix: 2.48 (0.19), residues: 690 sheet: -0.77 (1.00), residues: 32 loop : -0.70 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 198 TYR 0.022 0.002 TYR A 130 PHE 0.013 0.001 PHE D 69 TRP 0.011 0.002 TRP C 346 HIS 0.006 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.19 ( 9310) covalent geometry : angle 0.51317 / 0.27 (12586) hydrogen bonds : bond 0.04788 / 3.27 ( 541) hydrogen bonds : angle 4.15895 / 3.04 ( 1581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7183 (t) cc_final: 0.6647 (p) REVERT: D 236 ASP cc_start: 0.6970 (t0) cc_final: 0.5917 (m-30) REVERT: D 307 ARG cc_start: 0.7247 (mtp-110) cc_final: 0.6171 (ttp-110) REVERT: D 318 ARG cc_start: 0.3298 (OUTLIER) cc_final: 0.2452 (tpt170) REVERT: D 334 ARG cc_start: 0.4729 (OUTLIER) cc_final: 0.2078 (ttt90) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.2272 time to fit residues: 27.4875 Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.216079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163162 restraints weight = 24908.258| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.50 r_work: 0.3686 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9310 Z= 0.111 Angle : 0.448 5.649 12586 Z= 0.235 Chirality : 0.034 0.168 1403 Planarity : 0.004 0.049 1614 Dihedral : 9.545 165.203 1294 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.20 % Rotamer: Outliers : 0.90 % Allowed : 7.72 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.26), residues: 1106 helix: 2.70 (0.19), residues: 692 sheet: -0.74 (1.00), residues: 32 loop : -0.56 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.015 0.001 TYR A 130 PHE 0.008 0.001 PHE C 240 TRP 0.008 0.001 TRP D 212 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 9310) covalent geometry : angle 0.44758 / 0.24 (12586) hydrogen bonds : bond 0.04030 / 2.73 ( 541) hydrogen bonds : angle 3.92199 / 2.87 ( 1581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7138 (t) cc_final: 0.6637 (p) REVERT: D 236 ASP cc_start: 0.7008 (t0) cc_final: 0.5986 (m-30) REVERT: D 307 ARG cc_start: 0.7208 (mtp-110) cc_final: 0.6079 (ttp-110) REVERT: D 318 ARG cc_start: 0.3260 (OUTLIER) cc_final: 0.2439 (tpt170) REVERT: D 334 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.2016 (ttt90) outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.2328 time to fit residues: 27.0849 Evaluate side-chains 82 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.213156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.161311 restraints weight = 24965.788| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.38 r_work: 0.3662 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9310 Z= 0.164 Angle : 0.480 5.369 12586 Z= 0.254 Chirality : 0.035 0.162 1403 Planarity : 0.004 0.047 1614 Dihedral : 9.484 170.677 1294 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.03 % Rotamer: Outliers : 1.00 % Allowed : 7.72 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.26), residues: 1106 helix: 2.56 (0.19), residues: 692 sheet: -0.92 (1.00), residues: 32 loop : -0.69 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 198 TYR 0.019 0.001 TYR A 130 PHE 0.011 0.001 PHE D 69 TRP 0.009 0.001 TRP C 346 HIS 0.005 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 9310) covalent geometry : angle 0.47997 / 0.25 (12586) hydrogen bonds : bond 0.04407 / 3.01 ( 541) hydrogen bonds : angle 3.98790 / 2.91 ( 1581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7268 (t) cc_final: 0.6716 (p) REVERT: D 236 ASP cc_start: 0.7026 (t0) cc_final: 0.5975 (m-30) REVERT: D 307 ARG cc_start: 0.7263 (mtp-110) cc_final: 0.6175 (ttp-110) REVERT: D 318 ARG cc_start: 0.3248 (OUTLIER) cc_final: 0.2445 (tpt170) REVERT: D 334 ARG cc_start: 0.4785 (OUTLIER) cc_final: 0.2084 (ttt90) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.2595 time to fit residues: 29.7161 Evaluate side-chains 83 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.215452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.164598 restraints weight = 24907.293| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.36 r_work: 0.3665 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9310 Z= 0.112 Angle : 0.441 5.170 12586 Z= 0.232 Chirality : 0.034 0.156 1403 Planarity : 0.004 0.051 1614 Dihedral : 9.455 176.164 1294 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.44 % Favored : 96.38 % Rotamer: Outliers : 1.00 % Allowed : 8.42 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.26), residues: 1106 helix: 2.71 (0.19), residues: 692 sheet: -0.88 (0.99), residues: 32 loop : -0.60 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.015 0.001 TYR D 118 PHE 0.008 0.001 PHE D 69 TRP 0.008 0.001 TRP D 212 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9310) covalent geometry : angle 0.44099 / 0.23 (12586) hydrogen bonds : bond 0.03926 / 2.67 ( 541) hydrogen bonds : angle 3.85959 / 2.81 ( 1581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7159 (t) cc_final: 0.6642 (p) REVERT: D 236 ASP cc_start: 0.6964 (t0) cc_final: 0.5912 (m-30) REVERT: D 307 ARG cc_start: 0.7247 (mtp-110) cc_final: 0.6135 (ttp-110) REVERT: D 318 ARG cc_start: 0.3202 (OUTLIER) cc_final: 0.2414 (tpt170) REVERT: D 334 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.2050 (ttt90) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.2539 time to fit residues: 29.4229 Evaluate side-chains 85 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.214267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.162508 restraints weight = 24979.053| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.57 r_work: 0.3652 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9310 Z= 0.129 Angle : 0.451 5.001 12586 Z= 0.238 Chirality : 0.034 0.152 1403 Planarity : 0.004 0.048 1614 Dihedral : 9.469 179.654 1294 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.84 % Rotamer: Outliers : 1.10 % Allowed : 8.52 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.26), residues: 1106 helix: 2.69 (0.19), residues: 692 sheet: -0.96 (1.00), residues: 32 loop : -0.64 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.017 0.001 TYR A 130 PHE 0.009 0.001 PHE D 69 TRP 0.007 0.001 TRP D 212 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9310) covalent geometry : angle 0.45060 / 0.24 (12586) hydrogen bonds : bond 0.04026 / 2.74 ( 541) hydrogen bonds : angle 3.85688 / 2.81 ( 1581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7176 (t) cc_final: 0.6668 (p) REVERT: D 236 ASP cc_start: 0.6971 (t0) cc_final: 0.5909 (m-30) REVERT: D 307 ARG cc_start: 0.7227 (mtp-110) cc_final: 0.6152 (ttp-110) REVERT: D 318 ARG cc_start: 0.3169 (OUTLIER) cc_final: 0.2380 (tpt170) REVERT: D 334 ARG cc_start: 0.4697 (OUTLIER) cc_final: 0.2053 (ttt90) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.2319 time to fit residues: 26.2302 Evaluate side-chains 84 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.214838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.165750 restraints weight = 24908.348| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.33 r_work: 0.3704 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9310 Z= 0.122 Angle : 0.450 6.590 12586 Z= 0.236 Chirality : 0.034 0.151 1403 Planarity : 0.004 0.048 1614 Dihedral : 9.457 179.439 1294 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 1.00 % Allowed : 8.92 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.26), residues: 1106 helix: 2.69 (0.19), residues: 692 sheet: -0.92 (0.99), residues: 32 loop : -0.65 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 172 TYR 0.015 0.001 TYR A 130 PHE 0.009 0.001 PHE D 69 TRP 0.008 0.001 TRP D 212 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 9310) covalent geometry : angle 0.45040 / 0.24 (12586) hydrogen bonds : bond 0.03951 / 2.69 ( 541) hydrogen bonds : angle 3.82055 / 2.78 ( 1581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: C 436 SER cc_start: 0.7209 (t) cc_final: 0.6709 (p) REVERT: D 236 ASP cc_start: 0.7004 (t0) cc_final: 0.5946 (m-30) REVERT: D 307 ARG cc_start: 0.7219 (mtp-110) cc_final: 0.6175 (ttp-110) REVERT: D 318 ARG cc_start: 0.3182 (OUTLIER) cc_final: 0.2438 (tpt170) REVERT: D 334 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.1981 (ttt90) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.2337 time to fit residues: 25.6227 Evaluate side-chains 81 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.214917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.163570 restraints weight = 24979.080| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.84 r_work: 0.3719 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9310 Z= 0.122 Angle : 0.449 5.663 12586 Z= 0.236 Chirality : 0.034 0.150 1403 Planarity : 0.004 0.048 1614 Dihedral : 9.427 179.196 1294 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.00 % Allowed : 8.82 % Favored : 90.18 % 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 are not related in a simple way. whole: 2.23 (0.26), residues: 1106 helix: 2.70 (0.19), residues: 692 sheet: -0.90 (1.00), residues: 32 loop : -0.67 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.015 0.001 TYR A 130 PHE 0.028 0.001 PHE C 362 TRP 0.008 0.001 TRP D 212 HIS 0.004 0.000 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 9310) covalent geometry : angle 0.44942 / 0.24 (12586) hydrogen bonds : bond 0.03935 / 2.67 ( 541) hydrogen bonds : angle 3.80781 / 2.77 ( 1581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 436 SER cc_start: 0.7126 (t) cc_final: 0.6623 (p) REVERT: D 236 ASP cc_start: 0.6966 (t0) cc_final: 0.5898 (m-30) REVERT: D 307 ARG cc_start: 0.7192 (mtp-110) cc_final: 0.6145 (ttp-110) REVERT: D 318 ARG cc_start: 0.3164 (OUTLIER) cc_final: 0.2421 (tpt170) REVERT: D 334 ARG cc_start: 0.4582 (OUTLIER) cc_final: 0.1916 (ttt90) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.2316 time to fit residues: 25.3578 Evaluate side-chains 82 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 176 TYR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 313 TYR Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 334 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.212950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.161972 restraints weight = 25024.739| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.47 r_work: 0.3648 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9310 Z= 0.163 Angle : 0.477 4.909 12586 Z= 0.252 Chirality : 0.035 0.149 1403 Planarity : 0.004 0.048 1614 Dihedral : 9.459 178.772 1294 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 1.00 % Allowed : 9.12 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.26), residues: 1106 helix: 2.62 (0.19), residues: 685 sheet: -0.98 (1.00), residues: 32 loop : -0.73 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 198 TYR 0.018 0.001 TYR A 130 PHE 0.022 0.001 PHE C 362 TRP 0.009 0.001 TRP C 346 HIS 0.005 0.001 HIS D 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.16 ( 9310) covalent geometry : angle 0.47735 / 0.25 (12586) hydrogen bonds : bond 0.04307 / 2.94 ( 541) hydrogen bonds : angle 3.90016 / 2.83 ( 1581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.24 seconds wall clock time: 58 minutes 46.23 seconds (3526.23 seconds total)