Starting phenix.real_space_refine on Thu Jul 2 20:40:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9of0_70416/07_2026/9of0_70416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9of0_70416/07_2026/9of0_70416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2026/9of0_70416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2026/9of0_70416.map" model { file = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2026/9of0_70416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2026/9of0_70416.cif" } resolution = 3.6 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= 0.044 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 41 5.16 5 C 3380 2.51 5 N 988 2.21 5 O 1123 1.98 5 H 4664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10236 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 5035 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 3 Chain: "B" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4346 Classifications: {'peptide': 268} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 254} Chain breaks: 6 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Time building chain proxies: 1.87, per 1000 atoms: 0.18 Number of scatterers: 10236 At special positions: 0 Unit cell: (76.804, 79.336, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 40 15.00 O 1123 8.00 N 988 7.00 C 3380 6.00 H 4664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 324.2 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1118 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 5 sheets defined 43.6% alpha, 29.4% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.813A pdb=" N TYR A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.587A pdb=" N SER A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 4.346A pdb=" N LYS A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.946A pdb=" N PHE A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.897A pdb=" N LEU A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.815A pdb=" N TRP B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.742A pdb=" N LEU B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.761A pdb=" N VAL B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.562A pdb=" N MET A 108 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR A 103 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 110 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 219 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 257 removed outlier: 3.571A pdb=" N TYR A 256 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 246 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 336 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 257 removed outlier: 3.571A pdb=" N TYR A 256 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 246 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 336 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.481A pdb=" N ILE B 178 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 189 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 176 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 313 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 373 through 376 removed outlier: 4.321A pdb=" N PHE B 375 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 456 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 458 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 442 " --> pdb=" O THR B 460 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4644 1.03 - 1.23: 33 1.23 - 1.42: 2500 1.42 - 1.61: 3194 1.61 - 1.81: 62 Bond restraints: 10433 Sorted by residual: bond pdb=" C3' DT D 14 " pdb=" C2' DT D 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG D 9 " pdb=" C2' DG D 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC C 3 " pdb=" C2' DC C 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC C 6 " pdb=" C2' DC C 6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.30e+00 bond pdb=" C3' DC D 12 " pdb=" C2' DC D 12 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.33e+00 ... (remaining 10428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 18119 1.55 - 3.09: 384 3.09 - 4.64: 24 4.64 - 6.18: 3 6.18 - 7.73: 1 Bond angle restraints: 18531 Sorted by residual: angle pdb=" O4' DG C 20 " pdb=" C4' DG C 20 " pdb=" C3' DG C 20 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT C 12 " pdb=" C4 DT C 12 " pdb=" O4 DT C 12 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT D 14 " pdb=" C4 DT D 14 " pdb=" O4 DT D 14 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 ... (remaining 18526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 4637 35.29 - 70.59: 252 70.59 - 105.88: 12 105.88 - 141.18: 1 141.18 - 176.47: 1 Dihedral angle restraints: 4903 sinusoidal: 2871 harmonic: 2032 Sorted by residual: dihedral pdb=" C4' DC C 3 " pdb=" C3' DC C 3 " pdb=" O3' DC C 3 " pdb=" P DT C 4 " ideal model delta sinusoidal sigma weight residual 220.00 43.53 176.47 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC D 1 " pdb=" C3' DC D 1 " pdb=" O3' DC D 1 " pdb=" P DA D 2 " ideal model delta sinusoidal sigma weight residual -140.00 -16.80 -123.20 1 3.50e+01 8.16e-04 1.21e+01 dihedral pdb=" CA LEU A 319 " pdb=" C LEU A 319 " pdb=" N GLU A 320 " pdb=" CA GLU A 320 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 469 0.027 - 0.055: 276 0.055 - 0.082: 65 0.082 - 0.109: 48 0.109 - 0.136: 32 Chirality restraints: 890 Sorted by residual: chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL A 340 " pdb=" N VAL A 340 " pdb=" C VAL A 340 " pdb=" CB VAL A 340 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" C3' DG C 5 " pdb=" C4' DG C 5 " pdb=" O3' DG C 5 " pdb=" C2' DG C 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 887 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 328 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 329 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 316 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 317 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC D 18 " -0.015 2.00e-02 2.50e+03 8.12e-03 1.48e+00 pdb=" N1 DC D 18 " 0.018 2.00e-02 2.50e+03 pdb=" C2 DC D 18 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DC D 18 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC D 18 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC D 18 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC D 18 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC D 18 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC D 18 " 0.001 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 144 2.08 - 2.71: 15103 2.71 - 3.34: 26644 3.34 - 3.97: 34604 3.97 - 4.60: 54249 Nonbonded interactions: 130744 Sorted by model distance: nonbonded pdb=" OE1 GLU B 403 " pdb=" H GLU B 403 " model vdw 1.448 2.450 nonbonded pdb=" HZ1 LYS B 220 " pdb=" O ILE B 264 " model vdw 1.628 2.450 nonbonded pdb="HH11 ARG A 58 " pdb=" O THR A 127 " model vdw 1.648 2.450 nonbonded pdb=" O SER A 163 " pdb="HH12 ARG A 166 " model vdw 1.667 2.450 nonbonded pdb=" H GLN B 387 " pdb=" OE1 GLU B 390 " model vdw 1.679 2.450 ... (remaining 130739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.750 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5769 Z= 0.324 Angle : 0.643 7.728 7956 Z= 0.454 Chirality : 0.044 0.136 890 Planarity : 0.004 0.060 864 Dihedral : 20.146 176.472 2237 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.43 (0.37), residues: 560 helix: 0.98 (0.42), residues: 192 sheet: -0.59 (0.40), residues: 151 loop : 0.59 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 14 TYR 0.014 0.001 TYR A 202 PHE 0.009 0.001 PHE B 363 TRP 0.003 0.001 TRP B 315 HIS 0.008 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.32 ( 5769) covalent geometry : angle 0.64348 / 0.45 ( 7956) hydrogen bonds : bond 0.20695 / 13.47 ( 257) hydrogen bonds : angle 8.01804 / 6.18 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2057 time to fit residues: 17.8405 Evaluate side-chains 60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120278 restraints weight = 16745.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123962 restraints weight = 9760.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126506 restraints weight = 6808.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128207 restraints weight = 5297.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129203 restraints weight = 4492.530| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5769 Z= 0.169 Angle : 0.582 8.776 7956 Z= 0.339 Chirality : 0.041 0.154 890 Planarity : 0.004 0.034 864 Dihedral : 22.357 177.802 1062 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.55 % Allowed : 11.09 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.56 (0.37), residues: 560 helix: 1.05 (0.41), residues: 193 sheet: -0.47 (0.39), residues: 156 loop : 0.69 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 14 TYR 0.015 0.001 TYR A 202 PHE 0.015 0.002 PHE A 244 TRP 0.004 0.001 TRP B 315 HIS 0.012 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 5769) covalent geometry : angle 0.58173 / 0.34 ( 7956) hydrogen bonds : bond 0.06500 / 4.30 ( 257) hydrogen bonds : angle 5.56645 / 4.28 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.2036 time to fit residues: 17.6243 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain B residue 181 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** 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 = 0.3826 r_free = 0.3826 target = 0.151216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116898 restraints weight = 17329.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120685 restraints weight = 10153.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123128 restraints weight = 7013.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124808 restraints weight = 5466.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125802 restraints weight = 4635.496| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5769 Z= 0.188 Angle : 0.555 7.920 7956 Z= 0.322 Chirality : 0.042 0.151 890 Planarity : 0.004 0.039 864 Dihedral : 22.493 174.449 1062 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 10.91 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.46 (0.37), residues: 560 helix: 0.99 (0.41), residues: 193 sheet: -0.52 (0.39), residues: 156 loop : 0.60 (0.46), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 428 TYR 0.014 0.002 TYR A 202 PHE 0.015 0.002 PHE B 363 TRP 0.013 0.001 TRP B 436 HIS 0.006 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 5769) covalent geometry : angle 0.55460 / 0.32 ( 7956) hydrogen bonds : bond 0.05905 / 3.89 ( 257) hydrogen bonds : angle 5.22771 / 4.01 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.1892 time to fit residues: 17.0618 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 181 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.154022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119185 restraints weight = 16911.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123003 restraints weight = 9992.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125478 restraints weight = 6916.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127091 restraints weight = 5392.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128286 restraints weight = 4562.792| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5769 Z= 0.146 Angle : 0.520 7.474 7956 Z= 0.300 Chirality : 0.041 0.149 890 Planarity : 0.004 0.040 864 Dihedral : 22.566 173.591 1062 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.92 % Allowed : 11.09 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.37), residues: 560 helix: 1.09 (0.41), residues: 193 sheet: -0.55 (0.38), residues: 157 loop : 0.68 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 14 TYR 0.013 0.001 TYR A 202 PHE 0.013 0.001 PHE A 244 TRP 0.004 0.001 TRP B 315 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 5769) covalent geometry : angle 0.51974 / 0.30 ( 7956) hydrogen bonds : bond 0.05128 / 3.44 ( 257) hydrogen bonds : angle 4.97299 / 3.82 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.1798 time to fit residues: 16.7780 Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118354 restraints weight = 16920.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122044 restraints weight = 9923.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124506 restraints weight = 6925.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125974 restraints weight = 5450.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127259 restraints weight = 4636.409| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5769 Z= 0.161 Angle : 0.522 7.153 7956 Z= 0.298 Chirality : 0.040 0.148 890 Planarity : 0.005 0.099 864 Dihedral : 22.719 173.168 1062 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.92 % Allowed : 11.46 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.46 (0.37), residues: 560 helix: 1.10 (0.41), residues: 193 sheet: -0.74 (0.38), residues: 155 loop : 0.67 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 14 TYR 0.012 0.001 TYR A 202 PHE 0.013 0.002 PHE B 363 TRP 0.018 0.001 TRP B 438 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 5769) covalent geometry : angle 0.52172 / 0.30 ( 7956) hydrogen bonds : bond 0.05117 / 3.43 ( 257) hydrogen bonds : angle 4.86486 / 3.73 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1855 time to fit residues: 17.0317 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 378 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117834 restraints weight = 17147.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121560 restraints weight = 10019.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124078 restraints weight = 6972.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125592 restraints weight = 5455.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126443 restraints weight = 4644.517| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5769 Z= 0.170 Angle : 0.522 6.386 7956 Z= 0.298 Chirality : 0.040 0.150 890 Planarity : 0.004 0.041 864 Dihedral : 22.881 172.032 1062 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 11.46 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.41 (0.37), residues: 560 helix: 1.07 (0.41), residues: 193 sheet: -0.65 (0.39), residues: 146 loop : 0.45 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 14 TYR 0.012 0.002 TYR A 202 PHE 0.024 0.002 PHE B 444 TRP 0.007 0.001 TRP B 438 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 5769) covalent geometry : angle 0.52225 / 0.30 ( 7956) hydrogen bonds : bond 0.05095 / 3.48 ( 257) hydrogen bonds : angle 4.77684 / 3.66 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8429 (tppp) cc_final: 0.7941 (ttpp) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.1845 time to fit residues: 17.7721 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.4980 chunk 51 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 59 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 378 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.154747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119689 restraints weight = 16752.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123451 restraints weight = 9825.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125972 restraints weight = 6875.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127648 restraints weight = 5368.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128609 restraints weight = 4561.271| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5769 Z= 0.116 Angle : 0.494 6.952 7956 Z= 0.280 Chirality : 0.039 0.148 890 Planarity : 0.004 0.071 864 Dihedral : 22.876 172.530 1062 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.92 % Allowed : 12.38 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.66 (0.37), residues: 560 helix: 1.23 (0.41), residues: 194 sheet: -0.41 (0.40), residues: 148 loop : 0.58 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 14 TYR 0.012 0.001 TYR A 202 PHE 0.012 0.001 PHE A 244 TRP 0.007 0.001 TRP B 438 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 ( 5769) covalent geometry : angle 0.49407 / 0.28 ( 7956) hydrogen bonds : bond 0.04483 / 3.04 ( 257) hydrogen bonds : angle 4.58957 / 3.53 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8410 (tppp) cc_final: 0.7839 (ttpp) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1801 time to fit residues: 16.5299 Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 181 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 37 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 378 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.154164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119011 restraints weight = 16717.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122752 restraints weight = 9793.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125304 restraints weight = 6837.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126947 restraints weight = 5318.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127773 restraints weight = 4533.602| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5769 Z= 0.126 Angle : 0.495 6.376 7956 Z= 0.281 Chirality : 0.039 0.147 890 Planarity : 0.004 0.040 864 Dihedral : 22.894 172.083 1062 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.92 % Allowed : 12.75 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.78 (0.37), residues: 560 helix: 1.33 (0.41), residues: 194 sheet: -0.34 (0.40), residues: 148 loop : 0.64 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 14 TYR 0.011 0.001 TYR A 202 PHE 0.017 0.001 PHE B 444 TRP 0.005 0.001 TRP B 438 HIS 0.009 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 5769) covalent geometry : angle 0.49506 / 0.28 ( 7956) hydrogen bonds : bond 0.04353 / 2.97 ( 257) hydrogen bonds : angle 4.51485 / 3.47 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8383 (tppp) cc_final: 0.7831 (ttpp) REVERT: B 462 THR cc_start: 0.8956 (m) cc_final: 0.8491 (p) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.1622 time to fit residues: 15.2489 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 181 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 378 HIS ** 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 = 0.3849 r_free = 0.3849 target = 0.153697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118592 restraints weight = 16923.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122353 restraints weight = 9915.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124851 restraints weight = 6906.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126559 restraints weight = 5386.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127182 restraints weight = 4549.023| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5769 Z= 0.144 Angle : 0.511 6.580 7956 Z= 0.290 Chirality : 0.040 0.148 890 Planarity : 0.004 0.040 864 Dihedral : 22.916 171.407 1062 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.92 % Allowed : 13.12 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.74 (0.37), residues: 560 helix: 1.37 (0.41), residues: 194 sheet: -0.43 (0.40), residues: 146 loop : 0.58 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 14 TYR 0.010 0.001 TYR A 202 PHE 0.012 0.001 PHE A 244 TRP 0.005 0.001 TRP B 438 HIS 0.008 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5769) covalent geometry : angle 0.51083 / 0.29 ( 7956) hydrogen bonds : bond 0.04510 / 3.08 ( 257) hydrogen bonds : angle 4.50969 / 3.46 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8356 (tppp) cc_final: 0.7797 (ttpp) outliers start: 5 outliers final: 5 residues processed: 73 average time/residue: 0.1611 time to fit residues: 15.2210 Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 181 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.0770 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 378 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.154131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118934 restraints weight = 16833.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122700 restraints weight = 9876.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125213 restraints weight = 6888.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126735 restraints weight = 5390.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127932 restraints weight = 4568.611| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5769 Z= 0.129 Angle : 0.504 6.478 7956 Z= 0.285 Chirality : 0.039 0.148 890 Planarity : 0.004 0.038 864 Dihedral : 22.861 171.230 1062 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.92 % Allowed : 13.68 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.79 (0.37), residues: 560 helix: 1.43 (0.41), residues: 194 sheet: -0.41 (0.40), residues: 146 loop : 0.60 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 14 TYR 0.010 0.001 TYR A 202 PHE 0.017 0.001 PHE B 444 TRP 0.024 0.002 TRP B 436 HIS 0.005 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 5769) covalent geometry : angle 0.50370 / 0.29 ( 7956) hydrogen bonds : bond 0.04323 / 2.97 ( 257) hydrogen bonds : angle 4.44923 / 3.41 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8370 (tppp) cc_final: 0.7817 (ttpp) REVERT: B 394 LYS cc_start: 0.8541 (mttt) cc_final: 0.8254 (mttp) outliers start: 5 outliers final: 5 residues processed: 70 average time/residue: 0.1528 time to fit residues: 13.8219 Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 181 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 378 HIS ** 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 = 0.3840 r_free = 0.3840 target = 0.152934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117793 restraints weight = 16962.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121509 restraints weight = 9993.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124005 restraints weight = 7009.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125663 restraints weight = 5475.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126487 restraints weight = 4644.278| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5769 Z= 0.162 Angle : 0.521 6.126 7956 Z= 0.294 Chirality : 0.040 0.150 890 Planarity : 0.004 0.038 864 Dihedral : 22.906 170.725 1062 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 13.68 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.70 (0.37), residues: 560 helix: 1.36 (0.41), residues: 194 sheet: -0.36 (0.40), residues: 148 loop : 0.48 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.009 0.002 TYR A 202 PHE 0.013 0.002 PHE B 363 TRP 0.018 0.001 TRP B 436 HIS 0.007 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 5769) covalent geometry : angle 0.52076 / 0.29 ( 7956) hydrogen bonds : bond 0.04611 / 3.18 ( 257) hydrogen bonds : angle 4.49389 / 3.43 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.07 seconds wall clock time: 37 minutes 35.36 seconds (2255.36 seconds total)