Starting phenix.real_space_refine on Wed Jun 3 12:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzn_72367/06_2026/9xzn_72367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzn_72367/06_2026/9xzn_72367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xzn_72367/06_2026/9xzn_72367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzn_72367/06_2026/9xzn_72367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzn_72367/06_2026/9xzn_72367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzn_72367/06_2026/9xzn_72367.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 13 5.16 5 C 3109 2.51 5 N 727 2.21 5 O 819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4668 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4668 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 16, 'TRANS': 563} Time building chain proxies: 1.42, per 1000 atoms: 0.30 Number of scatterers: 4668 At special positions: 0 Unit cell: (74.63, 89.556, 106.238, 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 13 16.00 O 819 8.00 N 727 7.00 C 3109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 235.6 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid -96 through -82 removed outlier: 3.585A pdb=" N ASN B -85 " --> pdb=" O THR B -89 " (cutoff:3.500A) Processing helix chain 'B' and resid -81 through -78 removed outlier: 3.997A pdb=" N ALA B -78 " --> pdb=" O ILE B -81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid -81 through -78' Processing helix chain 'B' and resid -76 through -56 removed outlier: 3.961A pdb=" N LYS B -56 " --> pdb=" O LEU B -60 " (cutoff:3.500A) Processing helix chain 'B' and resid -43 through -18 removed outlier: 3.582A pdb=" N LEU B -20 " --> pdb=" O ASP B -24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B -18 " --> pdb=" O LEU B -22 " (cutoff:3.500A) Processing helix chain 'B' and resid -14 through 12 removed outlier: 4.098A pdb=" N GLN B -10 " --> pdb=" O VAL B -14 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B -9 " --> pdb=" O LYS B -13 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 removed outlier: 3.553A pdb=" N ASN B 18 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Proline residue: B 22 - end of helix removed outlier: 4.718A pdb=" N TYR B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.813A pdb=" N ALA B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 61 through 68 removed outlier: 4.432A pdb=" N ARG B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 4.763A pdb=" N ALA B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 131 through 139 removed outlier: 4.030A pdb=" N ASN B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 168 through 192 removed outlier: 3.840A pdb=" N TYR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 236 removed outlier: 3.730A pdb=" N LEU B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 4.249A pdb=" N VAL B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N MET B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 264 removed outlier: 4.084A pdb=" N VAL B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.562A pdb=" N TYR B 282 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 316 Proline residue: B 299 - end of helix Proline residue: B 309 - end of helix removed outlier: 3.591A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.562A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.852A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 378 removed outlier: 3.536A pdb=" N ILE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 406 removed outlier: 3.835A pdb=" N TYR B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.629A pdb=" N VAL B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 441 removed outlier: 4.056A pdb=" N ALA B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 471 Processing helix chain 'B' and resid 476 through 480 304 hydrogen bonds defined for protein. 903 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: 0.64 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1397 1.34 - 1.46: 764 1.46 - 1.57: 2592 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4777 Sorted by residual: bond pdb=" C TYR B 103 " pdb=" N PRO B 104 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.01e-01 bond pdb=" C VAL B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.76e-01 bond pdb=" CA TYR B 103 " pdb=" C TYR B 103 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.62e-01 bond pdb=" C ILE B 263 " pdb=" O ILE B 263 " ideal model delta sigma weight residual 1.245 1.236 0.010 1.41e-02 5.03e+03 4.62e-01 bond pdb=" CG1 ILE B 23 " pdb=" CD1 ILE B 23 " ideal model delta sigma weight residual 1.513 1.487 0.026 3.90e-02 6.57e+02 4.59e-01 ... (remaining 4772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 6303 1.20 - 2.40: 148 2.40 - 3.60: 26 3.60 - 4.80: 8 4.80 - 6.00: 8 Bond angle restraints: 6493 Sorted by residual: angle pdb=" N ILE B 263 " pdb=" CA ILE B 263 " pdb=" C ILE B 263 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" CA TYR B 103 " pdb=" CB TYR B 103 " pdb=" CG TYR B 103 " ideal model delta sigma weight residual 113.90 118.87 -4.97 1.80e+00 3.09e-01 7.63e+00 angle pdb=" CA TYR B 86 " pdb=" CB TYR B 86 " pdb=" CG TYR B 86 " ideal model delta sigma weight residual 113.90 118.72 -4.82 1.80e+00 3.09e-01 7.19e+00 angle pdb=" N GLY B 308 " pdb=" CA GLY B 308 " pdb=" C GLY B 308 " ideal model delta sigma weight residual 112.34 117.41 -5.07 2.04e+00 2.40e-01 6.17e+00 angle pdb=" C VAL B 446 " pdb=" N ILE B 447 " pdb=" CA ILE B 447 " ideal model delta sigma weight residual 121.97 126.19 -4.22 1.80e+00 3.09e-01 5.50e+00 ... (remaining 6488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2401 17.33 - 34.67: 286 34.67 - 52.00: 96 52.00 - 69.33: 16 69.33 - 86.66: 3 Dihedral angle restraints: 2802 sinusoidal: 1083 harmonic: 1719 Sorted by residual: dihedral pdb=" CA TYR B 86 " pdb=" C TYR B 86 " pdb=" N LEU B 87 " pdb=" CA LEU B 87 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CB GLU B 354 " pdb=" CG GLU B 354 " pdb=" CD GLU B 354 " pdb=" OE1 GLU B 354 " ideal model delta sinusoidal sigma weight residual 0.00 -86.66 86.66 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 2799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 474 0.027 - 0.055: 188 0.055 - 0.082: 80 0.082 - 0.110: 25 0.110 - 0.137: 6 Chirality restraints: 773 Sorted by residual: chirality pdb=" CA TYR B 86 " pdb=" N TYR B 86 " pdb=" C TYR B 86 " pdb=" CB TYR B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA PRO B 22 " pdb=" N PRO B 22 " pdb=" C PRO B 22 " pdb=" CB PRO B 22 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE B 195 " pdb=" N ILE B 195 " pdb=" C ILE B 195 " pdb=" CB ILE B 195 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 770 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 103 " -0.011 2.00e-02 2.50e+03 1.00e-02 2.02e+00 pdb=" CG TYR B 103 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 103 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 103 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 103 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 103 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 103 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 340 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" C ASP B 340 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP B 340 " -0.008 2.00e-02 2.50e+03 pdb=" N THR B 341 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 449 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO B 450 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 450 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 450 " -0.017 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2835 3.02 - 3.49: 5090 3.49 - 3.96: 7066 3.96 - 4.43: 8276 4.43 - 4.90: 12638 Nonbonded interactions: 35905 Sorted by model distance: nonbonded pdb=" O THR B -2 " pdb=" OD1 ASN B 1 " model vdw 2.553 3.040 nonbonded pdb=" C THR B -54 " pdb=" OG1 THR B -54 " model vdw 2.643 2.616 nonbonded pdb=" N LYS B 199 " pdb=" O LYS B 199 " model vdw 2.645 2.496 nonbonded pdb=" N ALA B -78 " pdb=" O ALA B -78 " model vdw 2.652 2.496 nonbonded pdb=" O ASN B 135 " pdb=" O GLU B 139 " model vdw 2.652 3.040 ... (remaining 35900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 4.760 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 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 : 0.002 0.031 4777 Z= 0.108 Angle : 0.503 5.996 6493 Z= 0.271 Chirality : 0.037 0.137 773 Planarity : 0.003 0.030 792 Dihedral : 16.715 86.664 1698 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.67 % Rotamer: Outliers : 1.17 % Allowed : 21.64 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.36), residues: 578 helix: 1.30 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -1.73 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 250 TYR 0.025 0.001 TYR B 103 PHE 0.010 0.001 PHE B 439 TRP 0.014 0.002 TRP B 190 HIS 0.002 0.001 HIS B -35 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 4777) covalent geometry : angle 0.50318 / 0.27 ( 6493) hydrogen bonds : bond 0.12192 / 8.50 ( 304) hydrogen bonds : angle 5.53324 / 4.01 ( 903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.157 Fit side-chains REVERT: B -31 ILE cc_start: 0.8087 (mt) cc_final: 0.7265 (tp) REVERT: B -27 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: B 200 ILE cc_start: 0.6564 (mt) cc_final: 0.6075 (tp) REVERT: B 389 THR cc_start: 0.5489 (p) cc_final: 0.5256 (p) outliers start: 6 outliers final: 5 residues processed: 119 average time/residue: 0.0705 time to fit residues: 10.7381 Evaluate side-chains 104 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.234868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.208133 restraints weight = 6835.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.211758 restraints weight = 4299.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.214169 restraints weight = 3091.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.215566 restraints weight = 2473.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.216690 restraints weight = 2146.007| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4777 Z= 0.133 Angle : 0.565 7.918 6493 Z= 0.293 Chirality : 0.039 0.151 773 Planarity : 0.004 0.034 792 Dihedral : 5.524 45.006 647 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.07 % Allowed : 21.44 % Favored : 73.49 % 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: 0.85 (0.36), residues: 578 helix: 1.44 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -1.80 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 250 TYR 0.032 0.001 TYR B 103 PHE 0.013 0.001 PHE B 129 TRP 0.006 0.001 TRP B 190 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 4777) covalent geometry : angle 0.56504 / 0.29 ( 6493) hydrogen bonds : bond 0.04186 / 2.92 ( 304) hydrogen bonds : angle 4.15499 / 3.10 ( 903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.190 Fit side-chains REVERT: B -82 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7685 (p) REVERT: B -31 ILE cc_start: 0.8154 (mt) cc_final: 0.7277 (tp) REVERT: B -27 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7025 (mp10) REVERT: B 40 TYR cc_start: 0.6974 (m-10) cc_final: 0.6771 (m-80) REVERT: B 114 LYS cc_start: 0.6918 (ttpp) cc_final: 0.5733 (tptp) REVERT: B 152 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: B 200 ILE cc_start: 0.6542 (mt) cc_final: 0.6056 (tp) REVERT: B 335 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7789 (mt) REVERT: B 465 SER cc_start: 0.7014 (OUTLIER) cc_final: 0.6500 (t) outliers start: 26 outliers final: 12 residues processed: 111 average time/residue: 0.0648 time to fit residues: 9.3676 Evaluate side-chains 113 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -82 VAL Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.230905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.203745 restraints weight = 6622.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.207388 restraints weight = 4170.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.209793 restraints weight = 2989.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.211344 restraints weight = 2383.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.212496 restraints weight = 2047.534| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4777 Z= 0.171 Angle : 0.609 7.708 6493 Z= 0.315 Chirality : 0.041 0.215 773 Planarity : 0.004 0.038 792 Dihedral : 5.519 47.462 645 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 7.41 % Allowed : 20.08 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.37), residues: 578 helix: 1.27 (0.26), residues: 423 sheet: None (None), residues: 0 loop : -1.82 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.038 0.002 TYR B 86 PHE 0.019 0.001 PHE B 330 TRP 0.005 0.001 TRP B -91 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 4777) covalent geometry : angle 0.60935 / 0.31 ( 6493) hydrogen bonds : bond 0.04396 / 3.02 ( 304) hydrogen bonds : angle 4.20780 / 3.15 ( 903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.155 Fit side-chains REVERT: B -82 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7642 (p) REVERT: B -31 ILE cc_start: 0.8238 (mt) cc_final: 0.7377 (tp) REVERT: B -27 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: B 118 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7569 (tt) REVERT: B 152 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7886 (mmm-85) REVERT: B 200 ILE cc_start: 0.6548 (mt) cc_final: 0.6086 (tp) REVERT: B 389 THR cc_start: 0.5694 (OUTLIER) cc_final: 0.5352 (p) REVERT: B 465 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6590 (t) outliers start: 38 outliers final: 21 residues processed: 117 average time/residue: 0.0613 time to fit residues: 9.4592 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -82 VAL Chi-restraints excluded: chain B residue -54 THR Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.232778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.207090 restraints weight = 6661.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.210492 restraints weight = 4185.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.212894 restraints weight = 3015.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.214530 restraints weight = 2389.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.215249 restraints weight = 2040.039| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4777 Z= 0.129 Angle : 0.570 8.419 6493 Z= 0.295 Chirality : 0.039 0.161 773 Planarity : 0.003 0.035 792 Dihedral : 5.419 45.922 645 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.24 % Allowed : 20.86 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.36), residues: 578 helix: 1.37 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -1.73 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 250 TYR 0.027 0.001 TYR B 86 PHE 0.015 0.001 PHE B 330 TRP 0.004 0.001 TRP B 190 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 4777) covalent geometry : angle 0.56998 / 0.30 ( 6493) hydrogen bonds : bond 0.03954 / 2.71 ( 304) hydrogen bonds : angle 4.08146 / 3.06 ( 903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.138 Fit side-chains REVERT: B -82 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7526 (p) REVERT: B -31 ILE cc_start: 0.8257 (mt) cc_final: 0.7407 (tp) REVERT: B -27 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: B 79 ARG cc_start: 0.3586 (OUTLIER) cc_final: 0.3324 (ptm160) REVERT: B 114 LYS cc_start: 0.7092 (ttpp) cc_final: 0.5794 (tptp) REVERT: B 118 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7502 (tt) REVERT: B 200 ILE cc_start: 0.6517 (mt) cc_final: 0.6046 (tp) REVERT: B 389 THR cc_start: 0.5624 (OUTLIER) cc_final: 0.5320 (p) outliers start: 32 outliers final: 20 residues processed: 120 average time/residue: 0.0580 time to fit residues: 9.1540 Evaluate side-chains 120 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -82 VAL Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.0470 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.232626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.206887 restraints weight = 6683.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.210385 restraints weight = 4191.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.212673 restraints weight = 3013.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.213948 restraints weight = 2400.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.215117 restraints weight = 2087.501| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4777 Z= 0.132 Angle : 0.583 7.458 6493 Z= 0.301 Chirality : 0.039 0.173 773 Planarity : 0.003 0.035 792 Dihedral : 5.437 47.230 645 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 7.41 % Allowed : 19.49 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.36), residues: 578 helix: 1.36 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -1.77 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 250 TYR 0.028 0.001 TYR B 86 PHE 0.023 0.001 PHE B 129 TRP 0.007 0.001 TRP B 190 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4777) covalent geometry : angle 0.58315 / 0.30 ( 6493) hydrogen bonds : bond 0.03949 / 2.69 ( 304) hydrogen bonds : angle 4.08104 / 3.05 ( 903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: B -87 ASN cc_start: 0.7891 (m-40) cc_final: 0.7670 (m110) REVERT: B -82 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7421 (p) REVERT: B -31 ILE cc_start: 0.8312 (mt) cc_final: 0.7491 (tp) REVERT: B -27 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: B 1 ASN cc_start: 0.7487 (p0) cc_final: 0.7277 (m-40) REVERT: B 6 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7587 (tmtt) REVERT: B 79 ARG cc_start: 0.3703 (OUTLIER) cc_final: 0.3400 (ptm160) REVERT: B 114 LYS cc_start: 0.7131 (ttpp) cc_final: 0.5789 (tptp) REVERT: B 118 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 187 SER cc_start: 0.5981 (OUTLIER) cc_final: 0.5760 (p) REVERT: B 200 ILE cc_start: 0.6454 (mt) cc_final: 0.5973 (tp) REVERT: B 389 THR cc_start: 0.5669 (OUTLIER) cc_final: 0.5347 (p) REVERT: B 465 SER cc_start: 0.7002 (OUTLIER) cc_final: 0.6540 (t) outliers start: 38 outliers final: 23 residues processed: 119 average time/residue: 0.0665 time to fit residues: 10.3733 Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -82 VAL Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN B 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.233382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.207602 restraints weight = 6774.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.211116 restraints weight = 4205.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.213420 restraints weight = 2993.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.214976 restraints weight = 2379.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216053 restraints weight = 2038.734| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4777 Z= 0.124 Angle : 0.570 7.518 6493 Z= 0.295 Chirality : 0.039 0.179 773 Planarity : 0.003 0.034 792 Dihedral : 5.415 48.161 645 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 7.60 % Allowed : 20.27 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.36), residues: 578 helix: 1.44 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.81 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.027 0.001 TYR B 99 PHE 0.017 0.001 PHE B 150 TRP 0.008 0.001 TRP B 190 HIS 0.002 0.000 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 4777) covalent geometry : angle 0.57036 / 0.29 ( 6493) hydrogen bonds : bond 0.03758 / 2.56 ( 304) hydrogen bonds : angle 3.99295 / 2.99 ( 903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.184 Fit side-chains REVERT: B -87 ASN cc_start: 0.7947 (m-40) cc_final: 0.7700 (m110) REVERT: B -82 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7353 (p) REVERT: B -31 ILE cc_start: 0.8269 (mt) cc_final: 0.7433 (tp) REVERT: B -27 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: B 6 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7548 (tmtt) REVERT: B 40 TYR cc_start: 0.6713 (m-80) cc_final: 0.6386 (m-80) REVERT: B 79 ARG cc_start: 0.3690 (OUTLIER) cc_final: 0.3437 (ptm160) REVERT: B 114 LYS cc_start: 0.7149 (ttpp) cc_final: 0.5812 (tptp) REVERT: B 118 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7509 (tt) REVERT: B 200 ILE cc_start: 0.6467 (mt) cc_final: 0.5960 (tp) REVERT: B 389 THR cc_start: 0.5622 (OUTLIER) cc_final: 0.5357 (p) REVERT: B 465 SER cc_start: 0.6986 (OUTLIER) cc_final: 0.6512 (t) outliers start: 39 outliers final: 22 residues processed: 119 average time/residue: 0.0658 time to fit residues: 10.3103 Evaluate side-chains 123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -82 VAL Chi-restraints excluded: chain B residue -54 THR Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.233365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.207058 restraints weight = 6610.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210473 restraints weight = 4186.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.212334 restraints weight = 3020.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.214145 restraints weight = 2470.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.214804 restraints weight = 2123.074| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4777 Z= 0.137 Angle : 0.599 9.096 6493 Z= 0.304 Chirality : 0.040 0.187 773 Planarity : 0.003 0.035 792 Dihedral : 5.514 50.247 645 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 7.02 % Allowed : 21.44 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.36), residues: 578 helix: 1.36 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -1.81 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.029 0.001 TYR B 86 PHE 0.019 0.001 PHE B 439 TRP 0.020 0.002 TRP B 190 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 4777) covalent geometry : angle 0.59866 / 0.30 ( 6493) hydrogen bonds : bond 0.03844 / 2.62 ( 304) hydrogen bonds : angle 4.02029 / 3.03 ( 903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.212 Fit side-chains REVERT: B -87 ASN cc_start: 0.7985 (m-40) cc_final: 0.7761 (m110) REVERT: B -82 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7373 (p) REVERT: B -31 ILE cc_start: 0.8309 (mt) cc_final: 0.7483 (tp) REVERT: B -27 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: B 6 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7567 (tmtt) REVERT: B 40 TYR cc_start: 0.6647 (m-80) cc_final: 0.6365 (m-80) REVERT: B 79 ARG cc_start: 0.3737 (OUTLIER) cc_final: 0.3454 (ptm160) REVERT: B 118 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7558 (tt) REVERT: B 200 ILE cc_start: 0.6466 (mt) cc_final: 0.5982 (tp) REVERT: B 389 THR cc_start: 0.5723 (OUTLIER) cc_final: 0.5440 (p) REVERT: B 465 SER cc_start: 0.7005 (OUTLIER) cc_final: 0.6672 (t) outliers start: 36 outliers final: 24 residues processed: 115 average time/residue: 0.0654 time to fit residues: 9.8732 Evaluate side-chains 122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -82 VAL Chi-restraints excluded: chain B residue -54 THR Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.231933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.205200 restraints weight = 6690.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.208690 restraints weight = 4207.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.211059 restraints weight = 3023.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.212610 restraints weight = 2410.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.213404 restraints weight = 2075.698| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4777 Z= 0.144 Angle : 0.614 8.581 6493 Z= 0.315 Chirality : 0.040 0.182 773 Planarity : 0.003 0.035 792 Dihedral : 5.669 53.888 645 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.82 % Allowed : 21.64 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.36), residues: 578 helix: 1.32 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -1.87 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.031 0.002 TYR B 86 PHE 0.019 0.001 PHE B 150 TRP 0.015 0.002 TRP B 190 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4777) covalent geometry : angle 0.61401 / 0.31 ( 6493) hydrogen bonds : bond 0.03953 / 2.71 ( 304) hydrogen bonds : angle 4.03970 / 3.05 ( 903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.179 Fit side-chains REVERT: B -87 ASN cc_start: 0.8092 (m-40) cc_final: 0.7875 (m110) REVERT: B -31 ILE cc_start: 0.8250 (mt) cc_final: 0.7431 (tp) REVERT: B -27 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: B 6 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7600 (tmtt) REVERT: B 40 TYR cc_start: 0.6677 (m-80) cc_final: 0.6342 (m-80) REVERT: B 79 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.3461 (ptm160) REVERT: B 99 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.7139 (t80) REVERT: B 118 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7546 (tt) REVERT: B 200 ILE cc_start: 0.6550 (mt) cc_final: 0.6037 (tp) REVERT: B 389 THR cc_start: 0.5731 (OUTLIER) cc_final: 0.5441 (p) REVERT: B 465 SER cc_start: 0.7114 (OUTLIER) cc_final: 0.6619 (t) outliers start: 35 outliers final: 23 residues processed: 113 average time/residue: 0.0655 time to fit residues: 9.6153 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -54 THR Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.233544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.207845 restraints weight = 6582.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.211140 restraints weight = 4132.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.212927 restraints weight = 2989.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.214754 restraints weight = 2446.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.215529 restraints weight = 2090.405| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4777 Z= 0.126 Angle : 0.604 8.572 6493 Z= 0.309 Chirality : 0.041 0.185 773 Planarity : 0.003 0.034 792 Dihedral : 5.577 53.083 645 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.43 % Allowed : 21.64 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.36), residues: 578 helix: 1.44 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -1.85 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.028 0.001 TYR B 99 PHE 0.020 0.001 PHE B 439 TRP 0.006 0.001 TRP B 190 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 4777) covalent geometry : angle 0.60381 / 0.31 ( 6493) hydrogen bonds : bond 0.03784 / 2.59 ( 304) hydrogen bonds : angle 3.98292 / 2.99 ( 903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.218 Fit side-chains REVERT: B -87 ASN cc_start: 0.8028 (m-40) cc_final: 0.7800 (m110) REVERT: B -31 ILE cc_start: 0.8242 (mt) cc_final: 0.7436 (tp) REVERT: B -27 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: B 6 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7544 (tmtt) REVERT: B 40 TYR cc_start: 0.6582 (m-80) cc_final: 0.6283 (m-80) REVERT: B 79 ARG cc_start: 0.3655 (OUTLIER) cc_final: 0.3363 (ptm160) REVERT: B 101 LEU cc_start: 0.8142 (mm) cc_final: 0.7798 (mt) REVERT: B 114 LYS cc_start: 0.7172 (ttpp) cc_final: 0.5764 (tptp) REVERT: B 118 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (tt) REVERT: B 187 SER cc_start: 0.6148 (OUTLIER) cc_final: 0.5883 (p) REVERT: B 200 ILE cc_start: 0.6514 (mt) cc_final: 0.5984 (tp) REVERT: B 389 THR cc_start: 0.5671 (OUTLIER) cc_final: 0.5374 (p) REVERT: B 465 SER cc_start: 0.7075 (OUTLIER) cc_final: 0.6668 (t) REVERT: B 466 TYR cc_start: 0.7060 (t80) cc_final: 0.6825 (t80) outliers start: 33 outliers final: 24 residues processed: 118 average time/residue: 0.0732 time to fit residues: 11.1859 Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -54 THR Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.231053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.204427 restraints weight = 6760.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.207834 restraints weight = 4258.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.210173 restraints weight = 3081.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.211730 restraints weight = 2459.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.212696 restraints weight = 2109.136| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4777 Z= 0.153 Angle : 0.642 8.331 6493 Z= 0.329 Chirality : 0.042 0.199 773 Planarity : 0.004 0.035 792 Dihedral : 5.753 56.537 645 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 6.04 % Allowed : 22.61 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.36), residues: 578 helix: 1.26 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -1.94 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.032 0.002 TYR B 99 PHE 0.011 0.001 PHE B 330 TRP 0.006 0.001 TRP B 190 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 4777) covalent geometry : angle 0.64193 / 0.33 ( 6493) hydrogen bonds : bond 0.04020 / 2.76 ( 304) hydrogen bonds : angle 4.06991 / 3.07 ( 903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.179 Fit side-chains REVERT: B -87 ASN cc_start: 0.8085 (m-40) cc_final: 0.7862 (m110) REVERT: B -31 ILE cc_start: 0.8283 (mt) cc_final: 0.7459 (tp) REVERT: B -27 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: B 6 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7618 (tmtt) REVERT: B 40 TYR cc_start: 0.6674 (m-80) cc_final: 0.6421 (m-80) REVERT: B 79 ARG cc_start: 0.3831 (OUTLIER) cc_final: 0.3488 (ptm160) REVERT: B 99 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.7083 (t80) REVERT: B 101 LEU cc_start: 0.8144 (mm) cc_final: 0.7755 (mt) REVERT: B 200 ILE cc_start: 0.6523 (mt) cc_final: 0.6103 (tp) REVERT: B 389 THR cc_start: 0.5681 (OUTLIER) cc_final: 0.5428 (p) REVERT: B 465 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6802 (t) outliers start: 31 outliers final: 24 residues processed: 103 average time/residue: 0.0673 time to fit residues: 9.0604 Evaluate side-chains 116 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -95 LEU Chi-restraints excluded: chain B residue -54 THR Chi-restraints excluded: chain B residue -27 GLN Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 0.0030 chunk 31 optimal weight: 0.0040 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.234926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.208960 restraints weight = 6608.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.212470 restraints weight = 4090.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.214844 restraints weight = 2922.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.216398 restraints weight = 2320.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.217194 restraints weight = 1983.483| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4777 Z= 0.123 Angle : 0.608 8.895 6493 Z= 0.310 Chirality : 0.040 0.195 773 Planarity : 0.003 0.033 792 Dihedral : 5.581 54.662 645 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.26 % Allowed : 23.39 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.36), residues: 578 helix: 1.46 (0.26), residues: 418 sheet: None (None), residues: 0 loop : -1.88 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.028 0.001 TYR B 99 PHE 0.021 0.001 PHE B 150 TRP 0.003 0.001 TRP B 190 HIS 0.001 0.000 HIS B -35 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4777) covalent geometry : angle 0.60809 / 0.31 ( 6493) hydrogen bonds : bond 0.03647 / 2.50 ( 304) hydrogen bonds : angle 3.93220 / 2.96 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1082.51 seconds wall clock time: 19 minutes 23.04 seconds (1163.04 seconds total)