Starting phenix.real_space_refine on Wed Aug 5 14:15:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9of0_70416/08_2026/9of0_70416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9of0_70416/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9of0_70416/08_2026/9of0_70416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9of0_70416/08_2026/9of0_70416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9of0_70416/08_2026/9of0_70416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9of0_70416/08_2026/9of0_70416.map" } 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-2.2rc3-6140/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: 1.89, 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: 0.75 Conformation dependent library (CDL) restraints added in 144.2 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: 1.59 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: 1.96 Time building geometry restraints manager: 1.02 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: 5.800 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.030 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- 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 : 0.645 7.728 7956 Z= 0.456 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 0.64487 / 0.46 ( 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 : 0.161 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: 0.2009 time to fit residues: 17.4379 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 : 0.239 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.3840 r_free = 0.3840 target = 0.152533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118571 restraints weight = 17072.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122304 restraints weight = 9877.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124743 restraints weight = 6841.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126178 restraints weight = 5342.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127486 restraints weight = 4570.164| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5769 Z= 0.170 Angle : 0.588 8.733 7956 Z= 0.341 Chirality : 0.042 0.155 890 Planarity : 0.004 0.033 864 Dihedral : 22.341 177.147 1062 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.57 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: 0.55 (0.37), residues: 560 helix: 1.05 (0.41), residues: 193 sheet: -0.50 (0.39), residues: 156 loop : 0.70 (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 0.014 0.001 PHE A 244 TRP 0.004 0.001 TRP B 315 HIS 0.006 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 5769) covalent geometry : angle 0.58785 / 0.34 ( 7956) hydrogen bonds : bond 0.06423 / 4.25 ( 257) hydrogen bonds : angle 5.53869 / 4.26 ( 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 : 0.161 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: 0.1737 time to fit residues: 14.9918 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 : 0.216 ------------------------------------------------------------------------------- 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: 10.0000 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 overall best weight: 0.5280 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.153057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118750 restraints weight = 17209.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122543 restraints weight = 9911.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125076 restraints weight = 6842.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126500 restraints weight = 5322.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127820 restraints weight = 4542.421| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1161 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= 0.144 Angle : 0.530 7.852 7956 Z= 0.308 Chirality : 0.041 0.151 890 Planarity : 0.004 0.038 864 Dihedral : 22.374 174.876 1062 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.74 % Allowed : 10.91 % 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: 0.65 (0.37), residues: 560 helix: 1.12 (0.41), residues: 193 sheet: -0.42 (0.39), residues: 156 loop : 0.74 (0.46), residues: 211 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 0.012 0.001 PHE A 244 TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 5769) covalent geometry : angle 0.53029 / 0.31 ( 7956) hydrogen bonds : bond 0.05528 / 3.61 ( 257) hydrogen bonds : angle 5.19126 / 3.98 ( 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 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.1707 time to fit residues: 15.3083 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 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: 0.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116285 restraints weight = 17500.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119989 restraints weight = 10170.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122474 restraints weight = 7085.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123953 restraints weight = 5580.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124909 restraints weight = 4749.278| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5769 Z= 0.192 Angle : 0.555 7.169 7956 Z= 0.317 Chirality : 0.042 0.149 890 Planarity : 0.004 0.042 864 Dihedral : 22.609 172.681 1062 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.29 % Allowed : 11.28 % Favored : 87.43 % 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: 0.44 (0.37), residues: 560 helix: 1.00 (0.40), residues: 193 sheet: -0.41 (0.40), residues: 147 loop : 0.39 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.013 0.002 TYR A 202 PHE 0.015 0.002 PHE B 363 TRP 0.006 0.001 TRP B 436 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 ( 5769) covalent geometry : angle 0.55519 / 0.32 ( 7956) hydrogen bonds : bond 0.05443 / 3.68 ( 257) hydrogen bonds : angle 5.02775 / 3.84 ( 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 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 HIS cc_start: 0.6941 (t-90) cc_final: 0.6300 (t-90) outliers start: 7 outliers final: 6 residues processed: 71 average time/residue: 0.1707 time to fit residues: 15.8195 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER 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 B residue 181 CYS Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 46 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119871 restraints weight = 16756.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123627 restraints weight = 9766.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126136 restraints weight = 6775.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127649 restraints weight = 5300.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128827 restraints weight = 4490.103| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.002 0.034 5769 Z= 0.118 Angle : 0.510 7.448 7956 Z= 0.291 Chirality : 0.040 0.150 890 Planarity : 0.003 0.042 864 Dihedral : 22.643 172.740 1062 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 0.65 (0.37), residues: 560 helix: 1.19 (0.41), residues: 193 sheet: -0.38 (0.39), residues: 148 loop : 0.59 (0.45), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 14 TYR 0.012 0.001 TYR A 202 PHE 0.012 0.001 PHE A 244 TRP 0.003 0.001 TRP B 315 HIS 0.007 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 5769) covalent geometry : angle 0.51030 / 0.29 ( 7956) hydrogen bonds : bond 0.04794 / 3.21 ( 257) hydrogen bonds : angle 4.81568 / 3.69 ( 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 : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 HIS cc_start: 0.6940 (t-90) cc_final: 0.6310 (t-90) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.1726 time to fit residues: 15.3628 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 LEU 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: 0.8980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.152778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117917 restraints weight = 17059.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121687 restraints weight = 10023.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124093 restraints weight = 6954.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125640 restraints weight = 5446.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126790 restraints weight = 4615.607| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5769 Z= 0.174 Angle : 0.533 6.846 7956 Z= 0.301 Chirality : 0.040 0.147 890 Planarity : 0.004 0.042 864 Dihedral : 22.795 172.264 1062 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.11 % Allowed : 12.01 % Favored : 86.88 % 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: 1.19 (0.41), residues: 193 sheet: -0.53 (0.39), residues: 146 loop : 0.52 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 14 TYR 0.011 0.002 TYR A 202 PHE 0.013 0.002 PHE B 363 TRP 0.005 0.001 TRP B 204 HIS 0.006 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 5769) covalent geometry : angle 0.53306 / 0.30 ( 7956) hydrogen bonds : bond 0.04910 / 3.33 ( 257) hydrogen bonds : angle 4.76262 / 3.64 ( 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 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.1589 time to fit residues: 14.5965 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 : 0.266 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 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 = 0.3855 r_free = 0.3855 target = 0.153837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118828 restraints weight = 16781.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122658 restraints weight = 9915.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125094 restraints weight = 6868.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126645 restraints weight = 5374.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127389 restraints weight = 4560.025| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5769 Z= 0.139 Angle : 0.506 6.604 7956 Z= 0.287 Chirality : 0.040 0.149 890 Planarity : 0.004 0.042 864 Dihedral : 22.819 171.701 1062 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.92 % Allowed : 12.01 % 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: 0.61 (0.37), residues: 560 helix: 1.21 (0.41), residues: 194 sheet: -0.49 (0.40), residues: 146 loop : 0.56 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 14 TYR 0.011 0.001 TYR A 202 PHE 0.016 0.001 PHE B 444 TRP 0.004 0.001 TRP B 204 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 5769) covalent geometry : angle 0.50609 / 0.29 ( 7956) hydrogen bonds : bond 0.04731 / 3.21 ( 257) hydrogen bonds : angle 4.64502 / 3.56 ( 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 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 THR cc_start: 0.8914 (m) cc_final: 0.8468 (p) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1716 time to fit residues: 15.8188 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 : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 LEU 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: 0.5980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.154538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119409 restraints weight = 16700.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123218 restraints weight = 9870.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125690 restraints weight = 6846.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127381 restraints weight = 5342.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128244 restraints weight = 4491.176| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5769 Z= 0.127 Angle : 0.495 5.891 7956 Z= 0.279 Chirality : 0.039 0.150 890 Planarity : 0.004 0.041 864 Dihedral : 22.872 171.900 1062 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.74 % Allowed : 12.38 % Favored : 86.88 % 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: 0.83 (0.37), residues: 560 helix: 1.42 (0.41), residues: 194 sheet: -0.38 (0.40), residues: 146 loop : 0.67 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 14 TYR 0.011 0.001 TYR A 202 PHE 0.011 0.001 PHE A 244 TRP 0.003 0.001 TRP B 315 HIS 0.002 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5769) covalent geometry : angle 0.49523 / 0.28 ( 7956) hydrogen bonds : bond 0.04236 / 2.89 ( 257) hydrogen bonds : angle 4.50312 / 3.46 ( 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 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 THR cc_start: 0.8976 (m) cc_final: 0.8529 (p) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.1764 time to fit residues: 16.2833 Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118350 restraints weight = 16935.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122090 restraints weight = 9912.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124571 restraints weight = 6911.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126079 restraints weight = 5416.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127285 restraints weight = 4595.967| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2257 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= 0.146 Angle : 0.499 5.830 7956 Z= 0.282 Chirality : 0.039 0.148 890 Planarity : 0.005 0.076 864 Dihedral : 22.835 170.913 1062 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 0.76 (0.37), residues: 560 helix: 1.40 (0.41), residues: 194 sheet: -0.39 (0.40), residues: 146 loop : 0.56 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 14 TYR 0.010 0.001 TYR A 202 PHE 0.016 0.001 PHE B 444 TRP 0.004 0.001 TRP B 204 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 5769) covalent geometry : angle 0.49932 / 0.28 ( 7956) hydrogen bonds : bond 0.04459 / 3.06 ( 257) hydrogen bonds : angle 4.48937 / 3.44 ( 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 : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 THR cc_start: 0.8916 (m) cc_final: 0.8483 (p) outliers start: 5 outliers final: 5 residues processed: 73 average time/residue: 0.1691 time to fit residues: 16.0786 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 : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=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: 0.2980 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.155603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120273 restraints weight = 16786.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124083 restraints weight = 9826.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126539 restraints weight = 6813.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128258 restraints weight = 5333.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129106 restraints weight = 4519.542| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5769 Z= 0.107 Angle : 0.490 6.772 7956 Z= 0.274 Chirality : 0.039 0.147 890 Planarity : 0.004 0.039 864 Dihedral : 22.762 170.865 1062 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.74 % Allowed : 12.94 % 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: 0.99 (0.38), residues: 560 helix: 1.54 (0.41), residues: 194 sheet: -0.29 (0.40), residues: 146 loop : 0.77 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 14 TYR 0.011 0.001 TYR A 202 PHE 0.011 0.001 PHE A 244 TRP 0.003 0.000 TRP A 190 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 5769) covalent geometry : angle 0.49015 / 0.27 ( 7956) hydrogen bonds : bond 0.03959 / 2.72 ( 257) hydrogen bonds : angle 4.37627 / 3.36 ( 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 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 LYS cc_start: 0.8522 (mttt) cc_final: 0.8254 (mttp) REVERT: B 462 THR cc_start: 0.8947 (m) cc_final: 0.8534 (p) outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 0.1829 time to fit residues: 17.0467 Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.153597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118205 restraints weight = 16967.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121937 restraints weight = 10025.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124422 restraints weight = 7019.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126083 restraints weight = 5492.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126999 restraints weight = 4645.211| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5769 Z= 0.166 Angle : 0.508 6.072 7956 Z= 0.285 Chirality : 0.040 0.149 890 Planarity : 0.004 0.038 864 Dihedral : 22.834 170.202 1062 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 13.12 % Favored : 85.77 % 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: 0.80 (0.37), residues: 560 helix: 1.47 (0.41), residues: 194 sheet: -0.39 (0.40), residues: 146 loop : 0.56 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 14 TYR 0.009 0.002 TYR A 316 PHE 0.016 0.002 PHE B 444 TRP 0.027 0.002 TRP B 436 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 5769) covalent geometry : angle 0.50759 / 0.29 ( 7956) hydrogen bonds : bond 0.04467 / 3.09 ( 257) hydrogen bonds : angle 4.44574 / 3.39 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.68 seconds wall clock time: 36 minutes 28.74 seconds (2188.74 seconds total)