Starting phenix.real_space_refine on Mon Aug 25 01:20:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jm9_36410/08_2025/8jm9_36410_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jm9_36410/08_2025/8jm9_36410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jm9_36410/08_2025/8jm9_36410_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jm9_36410/08_2025/8jm9_36410_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jm9_36410/08_2025/8jm9_36410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jm9_36410/08_2025/8jm9_36410.map" } resolution = 2.6 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= 0.005 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7824 2.51 5 N 2056 2.21 5 O 2096 1.98 5 H 12472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24520 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 6.74, per 1000 atoms: 0.27 Number of scatterers: 24520 At special positions: 0 Unit cell: (110.67, 110.67, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2096 8.00 N 2056 7.00 C 7824 6.00 H 12472 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: 2.34 Conformation dependent library (CDL) restraints added in 961.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 85.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 369 Proline residue: A 347 - end of helix removed outlier: 3.753A pdb=" N THR A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE B 11 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 369 Proline residue: B 347 - end of helix removed outlier: 3.753A pdb=" N THR B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 369 Proline residue: C 347 - end of helix removed outlier: 3.753A pdb=" N THR C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 369 Proline residue: D 347 - end of helix removed outlier: 3.753A pdb=" N THR D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 3.18 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: 12440 1.03 - 1.22: 32 1.22 - 1.42: 5112 1.42 - 1.61: 7056 1.61 - 1.81: 112 Bond restraints: 24752 Sorted by residual: bond pdb=" CB LYS C 379 " pdb=" CG LYS C 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS D 379 " pdb=" CG LYS D 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS B 379 " pdb=" CG LYS B 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" C LYS B 357 " pdb=" O LYS B 357 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.31e-02 5.83e+03 6.00e-01 ... (remaining 24747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 41844 1.04 - 2.08: 2708 2.08 - 3.12: 116 3.12 - 4.16: 40 4.16 - 5.21: 12 Bond angle restraints: 44720 Sorted by residual: angle pdb=" N VAL D 69 " pdb=" CA VAL D 69 " pdb=" C VAL D 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL B 69 " pdb=" CA VAL B 69 " pdb=" C VAL B 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL C 69 " pdb=" CA VAL C 69 " pdb=" C VAL C 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" CA LYS A 379 " pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 114.10 118.99 -4.89 2.00e+00 2.50e-01 5.97e+00 ... (remaining 44715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 9532 11.72 - 23.45: 1192 23.45 - 35.17: 400 35.17 - 46.89: 220 46.89 - 58.62: 164 Dihedral angle restraints: 11508 sinusoidal: 6176 harmonic: 5332 Sorted by residual: dihedral pdb=" N GLN C 5 " pdb=" CA GLN C 5 " pdb=" CB GLN C 5 " pdb=" CG GLN C 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN B 5 " pdb=" CA GLN B 5 " pdb=" CB GLN B 5 " pdb=" CG GLN B 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN D 5 " pdb=" CA GLN D 5 " pdb=" CB GLN D 5 " pdb=" CG GLN D 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1516 0.036 - 0.071: 384 0.071 - 0.107: 80 0.107 - 0.142: 12 0.142 - 0.178: 4 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CB THR B 46 " pdb=" CA THR B 46 " pdb=" OG1 THR B 46 " pdb=" CG2 THR B 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 46 " pdb=" CA THR C 46 " pdb=" OG1 THR C 46 " pdb=" CG2 THR C 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 1993 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP C 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP C 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP C 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP D 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP D 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP D 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 83 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP B 83 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP B 83 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP B 83 " -0.006 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1060 2.18 - 2.78: 49068 2.78 - 3.39: 73844 3.39 - 3.99: 91204 3.99 - 4.60: 146036 Nonbonded interactions: 361212 Sorted by model distance: nonbonded pdb=" OD1 ASN C 207 " pdb=" HG1 THR C 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN D 207 " pdb=" HG1 THR D 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN A 207 " pdb=" HG1 THR A 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN B 207 " pdb=" HG1 THR B 358 " model vdw 1.569 2.450 nonbonded pdb=" OE2 GLU C 346 " pdb=" HE ARG C 402 " model vdw 1.622 2.450 ... (remaining 361207 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.140 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 28.100 Find NCS groups from input model: 0.170 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:9.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.003 0.026 12280 Z= 0.145 Angle : 0.466 5.206 16656 Z= 0.263 Chirality : 0.034 0.178 1996 Planarity : 0.002 0.017 2040 Dihedral : 15.463 58.615 4376 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 19.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.59 (0.21), residues: 1508 helix: 2.97 (0.14), residues: 1256 sheet: 0.61 (0.68), residues: 48 loop : -1.37 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 129 TYR 0.008 0.001 TYR D 56 PHE 0.013 0.001 PHE C 125 TRP 0.005 0.001 TRP A 38 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00292 (12280) covalent geometry : angle 0.46639 (16656) hydrogen bonds : bond 0.08186 ( 1080) hydrogen bonds : angle 4.11403 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5099 (tpp-160) REVERT: A 78 VAL cc_start: 0.7240 (t) cc_final: 0.6845 (p) REVERT: A 328 TRP cc_start: 0.5594 (m100) cc_final: 0.5281 (m-90) REVERT: A 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6965 (ttp80) REVERT: A 403 THR cc_start: 0.7874 (m) cc_final: 0.7644 (p) REVERT: B 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5100 (tpp-160) REVERT: B 78 VAL cc_start: 0.7241 (t) cc_final: 0.6846 (p) REVERT: B 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: B 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: B 403 THR cc_start: 0.7873 (m) cc_final: 0.7642 (p) REVERT: C 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: C 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: C 328 TRP cc_start: 0.5593 (m100) cc_final: 0.5280 (m-90) REVERT: C 399 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: C 403 THR cc_start: 0.7874 (m) cc_final: 0.7643 (p) REVERT: D 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: D 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: D 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: D 399 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6963 (ttp80) REVERT: D 403 THR cc_start: 0.7875 (m) cc_final: 0.7645 (p) outliers start: 8 outliers final: 8 residues processed: 196 average time/residue: 1.2102 time to fit residues: 256.4659 Evaluate side-chains 180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100734 restraints weight = 37778.654| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.92 r_work: 0.2998 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12280 Z= 0.128 Angle : 0.443 4.783 16656 Z= 0.244 Chirality : 0.033 0.128 1996 Planarity : 0.003 0.020 2040 Dihedral : 4.415 50.908 1676 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 17.02 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.63 (0.21), residues: 1508 helix: 3.03 (0.14), residues: 1256 sheet: 0.43 (0.71), residues: 48 loop : -1.56 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 129 TYR 0.006 0.001 TYR C 175 PHE 0.009 0.001 PHE A 125 TRP 0.005 0.001 TRP B 38 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00253 (12280) covalent geometry : angle 0.44263 (16656) hydrogen bonds : bond 0.04406 ( 1080) hydrogen bonds : angle 3.87128 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7387 (tpt170) cc_final: 0.6137 (tpp-160) REVERT: A 67 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 78 VAL cc_start: 0.8324 (t) cc_final: 0.7879 (p) REVERT: A 110 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 120 ASN cc_start: 0.7608 (p0) cc_final: 0.6778 (t160) REVERT: A 159 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5770 (mt0) REVERT: A 169 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: A 328 TRP cc_start: 0.6475 (m100) cc_final: 0.6134 (m-90) REVERT: A 399 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7594 (mtt90) REVERT: A 403 THR cc_start: 0.8981 (m) cc_final: 0.8719 (p) REVERT: B 57 ARG cc_start: 0.7395 (tpt170) cc_final: 0.6139 (tpp-160) REVERT: B 67 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 78 VAL cc_start: 0.8321 (t) cc_final: 0.7873 (p) REVERT: B 110 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: B 120 ASN cc_start: 0.7626 (p0) cc_final: 0.6799 (t160) REVERT: B 159 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5772 (mt0) REVERT: B 169 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: B 276 ASP cc_start: 0.8167 (t0) cc_final: 0.7956 (m-30) REVERT: B 328 TRP cc_start: 0.6494 (m100) cc_final: 0.6152 (m-90) REVERT: B 399 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7608 (mtt90) REVERT: B 403 THR cc_start: 0.8977 (m) cc_final: 0.8718 (p) REVERT: C 57 ARG cc_start: 0.7390 (tpt170) cc_final: 0.6141 (tpp-160) REVERT: C 67 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7663 (tt) REVERT: C 78 VAL cc_start: 0.8327 (t) cc_final: 0.7880 (p) REVERT: C 110 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: C 120 ASN cc_start: 0.7597 (p0) cc_final: 0.6761 (t160) REVERT: C 159 GLN cc_start: 0.6220 (OUTLIER) cc_final: 0.5778 (mt0) REVERT: C 169 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: C 276 ASP cc_start: 0.8173 (t0) cc_final: 0.7961 (m-30) REVERT: C 328 TRP cc_start: 0.6493 (m100) cc_final: 0.6152 (m-90) REVERT: C 399 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7608 (mtt90) REVERT: C 403 THR cc_start: 0.8980 (m) cc_final: 0.8719 (p) REVERT: D 57 ARG cc_start: 0.7393 (tpt170) cc_final: 0.6139 (tpp-160) REVERT: D 67 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7664 (tt) REVERT: D 78 VAL cc_start: 0.8321 (t) cc_final: 0.7880 (p) REVERT: D 110 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: D 120 ASN cc_start: 0.7616 (p0) cc_final: 0.6788 (t160) REVERT: D 159 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5768 (mt0) REVERT: D 169 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: D 328 TRP cc_start: 0.6483 (m100) cc_final: 0.6144 (m-90) REVERT: D 399 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7594 (mtt90) REVERT: D 403 THR cc_start: 0.8976 (m) cc_final: 0.8721 (p) outliers start: 16 outliers final: 0 residues processed: 200 average time/residue: 1.3413 time to fit residues: 290.8674 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095429 restraints weight = 37996.666| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.91 r_work: 0.2877 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12280 Z= 0.288 Angle : 0.538 5.782 16656 Z= 0.300 Chirality : 0.038 0.141 1996 Planarity : 0.004 0.025 2040 Dihedral : 3.577 12.592 1660 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.43 % Allowed : 13.98 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.20), residues: 1508 helix: 2.28 (0.13), residues: 1256 sheet: 0.11 (0.67), residues: 48 loop : -1.95 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 111 TYR 0.013 0.002 TYR C 56 PHE 0.028 0.003 PHE C 422 TRP 0.007 0.002 TRP C 154 HIS 0.004 0.002 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00657 (12280) covalent geometry : angle 0.53849 (16656) hydrogen bonds : bond 0.05459 ( 1080) hydrogen bonds : angle 4.19970 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.687 Fit side-chains REVERT: A 57 ARG cc_start: 0.7469 (tpt170) cc_final: 0.6188 (tpp-160) REVERT: A 78 VAL cc_start: 0.8274 (t) cc_final: 0.7846 (p) REVERT: A 110 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: A 120 ASN cc_start: 0.7584 (p0) cc_final: 0.6704 (t0) REVERT: A 169 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: A 328 TRP cc_start: 0.6559 (m100) cc_final: 0.6192 (m-90) REVERT: A 399 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7866 (mtt90) REVERT: B 57 ARG cc_start: 0.7475 (tpt170) cc_final: 0.6190 (tpp-160) REVERT: B 78 VAL cc_start: 0.8274 (t) cc_final: 0.7844 (p) REVERT: B 110 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: B 120 ASN cc_start: 0.7598 (p0) cc_final: 0.6710 (t0) REVERT: B 169 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: B 328 TRP cc_start: 0.6553 (m100) cc_final: 0.6185 (m-90) REVERT: B 399 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7853 (mtt90) REVERT: C 57 ARG cc_start: 0.7472 (tpt170) cc_final: 0.6191 (tpp-160) REVERT: C 78 VAL cc_start: 0.8288 (t) cc_final: 0.7858 (p) REVERT: C 110 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: C 120 ASN cc_start: 0.7582 (p0) cc_final: 0.6689 (t0) REVERT: C 169 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: C 328 TRP cc_start: 0.6546 (m100) cc_final: 0.6180 (m-90) REVERT: C 399 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7856 (mtt90) REVERT: D 57 ARG cc_start: 0.7481 (tpt170) cc_final: 0.6197 (tpp-160) REVERT: D 78 VAL cc_start: 0.8268 (t) cc_final: 0.7837 (p) REVERT: D 110 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: D 120 ASN cc_start: 0.7597 (p0) cc_final: 0.6709 (t0) REVERT: D 169 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: D 328 TRP cc_start: 0.6552 (m100) cc_final: 0.6187 (m-90) REVERT: D 399 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7864 (mtt90) outliers start: 32 outliers final: 4 residues processed: 204 average time/residue: 1.4495 time to fit residues: 319.0213 Evaluate side-chains 192 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097078 restraints weight = 37789.920| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.91 r_work: 0.2903 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12280 Z= 0.181 Angle : 0.479 5.164 16656 Z= 0.264 Chirality : 0.035 0.131 1996 Planarity : 0.003 0.038 2040 Dihedral : 3.493 12.576 1660 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.22 % Allowed : 15.50 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.21), residues: 1508 helix: 2.43 (0.13), residues: 1260 sheet: 0.23 (0.70), residues: 48 loop : -1.71 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.008 0.001 TYR C 56 PHE 0.017 0.002 PHE A 422 TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00391 (12280) covalent geometry : angle 0.47856 (16656) hydrogen bonds : bond 0.04832 ( 1080) hydrogen bonds : angle 4.03631 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.707 Fit side-chains REVERT: A 57 ARG cc_start: 0.7459 (tpt170) cc_final: 0.6156 (tpp-160) REVERT: A 78 VAL cc_start: 0.8276 (t) cc_final: 0.7852 (p) REVERT: A 110 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: A 120 ASN cc_start: 0.7577 (p0) cc_final: 0.6701 (t0) REVERT: A 159 GLN cc_start: 0.6146 (pt0) cc_final: 0.5732 (mt0) REVERT: A 328 TRP cc_start: 0.6512 (m100) cc_final: 0.6165 (m-90) REVERT: A 399 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7866 (mtt90) REVERT: B 57 ARG cc_start: 0.7459 (tpt170) cc_final: 0.6155 (tpp-160) REVERT: B 78 VAL cc_start: 0.8274 (t) cc_final: 0.7850 (p) REVERT: B 110 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: B 120 ASN cc_start: 0.7588 (p0) cc_final: 0.6714 (t0) REVERT: B 159 GLN cc_start: 0.6149 (pt0) cc_final: 0.5734 (mt0) REVERT: B 328 TRP cc_start: 0.6506 (m100) cc_final: 0.6159 (m-90) REVERT: B 399 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7858 (mtt90) REVERT: C 57 ARG cc_start: 0.7451 (tpt170) cc_final: 0.6150 (tpp-160) REVERT: C 78 VAL cc_start: 0.8276 (t) cc_final: 0.7849 (p) REVERT: C 110 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: C 120 ASN cc_start: 0.7565 (p0) cc_final: 0.6684 (t0) REVERT: C 159 GLN cc_start: 0.6147 (pt0) cc_final: 0.5729 (mt0) REVERT: C 328 TRP cc_start: 0.6498 (m100) cc_final: 0.6151 (m-90) REVERT: C 399 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7854 (mtt90) REVERT: D 57 ARG cc_start: 0.7470 (tpt170) cc_final: 0.6169 (tpp-160) REVERT: D 78 VAL cc_start: 0.8265 (t) cc_final: 0.7840 (p) REVERT: D 110 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: D 120 ASN cc_start: 0.7584 (p0) cc_final: 0.6713 (t0) REVERT: D 159 GLN cc_start: 0.6150 (pt0) cc_final: 0.5735 (mt0) REVERT: D 328 TRP cc_start: 0.6505 (m100) cc_final: 0.6159 (m-90) REVERT: D 399 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7858 (mtt90) outliers start: 16 outliers final: 8 residues processed: 192 average time/residue: 1.4796 time to fit residues: 309.3303 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097996 restraints weight = 37445.391| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.91 r_work: 0.2921 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12280 Z= 0.155 Angle : 0.450 4.491 16656 Z= 0.249 Chirality : 0.034 0.130 1996 Planarity : 0.003 0.028 2040 Dihedral : 3.403 11.720 1660 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.52 % Allowed : 15.81 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.21), residues: 1508 helix: 2.59 (0.14), residues: 1260 sheet: 0.21 (0.71), residues: 48 loop : -1.61 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.008 0.001 TYR A 56 PHE 0.015 0.001 PHE A 422 TRP 0.006 0.001 TRP C 154 HIS 0.002 0.001 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00326 (12280) covalent geometry : angle 0.45010 (16656) hydrogen bonds : bond 0.04570 ( 1080) hydrogen bonds : angle 3.92222 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.722 Fit side-chains REVERT: A 57 ARG cc_start: 0.7480 (tpt170) cc_final: 0.6097 (tpp-160) REVERT: A 78 VAL cc_start: 0.8268 (t) cc_final: 0.7840 (p) REVERT: A 110 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: A 120 ASN cc_start: 0.7551 (p0) cc_final: 0.6618 (t0) REVERT: A 159 GLN cc_start: 0.6148 (pt0) cc_final: 0.5819 (mt0) REVERT: A 328 TRP cc_start: 0.6513 (m100) cc_final: 0.6105 (m-90) REVERT: A 399 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7822 (mtt90) REVERT: B 57 ARG cc_start: 0.7488 (tpt170) cc_final: 0.6102 (tpp-160) REVERT: B 78 VAL cc_start: 0.8267 (t) cc_final: 0.7840 (p) REVERT: B 110 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: B 120 ASN cc_start: 0.7565 (p0) cc_final: 0.6632 (t0) REVERT: B 159 GLN cc_start: 0.6149 (pt0) cc_final: 0.5818 (mt0) REVERT: B 328 TRP cc_start: 0.6500 (m100) cc_final: 0.6093 (m-90) REVERT: B 399 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7823 (mtt90) REVERT: C 57 ARG cc_start: 0.7488 (tpt170) cc_final: 0.6102 (tpp-160) REVERT: C 78 VAL cc_start: 0.8270 (t) cc_final: 0.7840 (p) REVERT: C 110 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: C 120 ASN cc_start: 0.7538 (p0) cc_final: 0.6600 (t0) REVERT: C 159 GLN cc_start: 0.6146 (pt0) cc_final: 0.5817 (mt0) REVERT: C 328 TRP cc_start: 0.6493 (m100) cc_final: 0.6087 (m-90) REVERT: C 399 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7815 (mtt90) REVERT: D 57 ARG cc_start: 0.7490 (tpt170) cc_final: 0.6109 (tpp-160) REVERT: D 78 VAL cc_start: 0.8259 (t) cc_final: 0.7830 (p) REVERT: D 110 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: D 120 ASN cc_start: 0.7559 (p0) cc_final: 0.6630 (t0) REVERT: D 159 GLN cc_start: 0.6149 (pt0) cc_final: 0.5820 (mt0) REVERT: D 328 TRP cc_start: 0.6505 (m100) cc_final: 0.6099 (m-90) REVERT: D 399 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7825 (mtt90) outliers start: 20 outliers final: 8 residues processed: 200 average time/residue: 1.4703 time to fit residues: 319.0275 Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096799 restraints weight = 37657.443| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.91 r_work: 0.2899 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12280 Z= 0.200 Angle : 0.482 5.646 16656 Z= 0.267 Chirality : 0.035 0.131 1996 Planarity : 0.003 0.024 2040 Dihedral : 3.505 12.326 1660 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.43 % Allowed : 14.59 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.21), residues: 1508 helix: 2.46 (0.13), residues: 1260 sheet: 0.20 (0.71), residues: 48 loop : -1.62 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.008 0.001 TYR B 56 PHE 0.023 0.002 PHE C 422 TRP 0.006 0.001 TRP D 154 HIS 0.003 0.001 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00440 (12280) covalent geometry : angle 0.48182 (16656) hydrogen bonds : bond 0.04860 ( 1080) hydrogen bonds : angle 4.00479 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.728 Fit side-chains REVERT: A 26 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7135 (ttm170) REVERT: A 57 ARG cc_start: 0.7505 (tpt170) cc_final: 0.6085 (tpp-160) REVERT: A 59 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 78 VAL cc_start: 0.8260 (t) cc_final: 0.7834 (p) REVERT: A 110 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: A 120 ASN cc_start: 0.7578 (p0) cc_final: 0.6651 (t0) REVERT: A 159 GLN cc_start: 0.6168 (pt0) cc_final: 0.5830 (mt0) REVERT: A 328 TRP cc_start: 0.6501 (m100) cc_final: 0.6083 (m-90) REVERT: B 26 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7203 (ttm170) REVERT: B 57 ARG cc_start: 0.7510 (tpt170) cc_final: 0.6094 (tpp-160) REVERT: B 59 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7264 (mp) REVERT: B 78 VAL cc_start: 0.8257 (t) cc_final: 0.7831 (p) REVERT: B 110 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 120 ASN cc_start: 0.7593 (p0) cc_final: 0.6665 (t0) REVERT: B 159 GLN cc_start: 0.6171 (pt0) cc_final: 0.5828 (mt0) REVERT: B 328 TRP cc_start: 0.6497 (m100) cc_final: 0.6081 (m-90) REVERT: C 26 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7206 (ttm170) REVERT: C 57 ARG cc_start: 0.7503 (tpt170) cc_final: 0.6085 (tpp-160) REVERT: C 59 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7254 (mp) REVERT: C 78 VAL cc_start: 0.8265 (t) cc_final: 0.7839 (p) REVERT: C 110 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: C 120 ASN cc_start: 0.7562 (p0) cc_final: 0.6626 (t0) REVERT: C 159 GLN cc_start: 0.6169 (pt0) cc_final: 0.5827 (mt0) REVERT: C 328 TRP cc_start: 0.6496 (m100) cc_final: 0.6079 (m-90) REVERT: D 26 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7210 (ttm170) REVERT: D 57 ARG cc_start: 0.7521 (tpt170) cc_final: 0.6104 (tpp-160) REVERT: D 59 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7263 (mp) REVERT: D 78 VAL cc_start: 0.8253 (t) cc_final: 0.7827 (p) REVERT: D 110 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: D 120 ASN cc_start: 0.7588 (p0) cc_final: 0.6659 (t0) REVERT: D 159 GLN cc_start: 0.6174 (pt0) cc_final: 0.5831 (mt0) REVERT: D 328 TRP cc_start: 0.6509 (m100) cc_final: 0.6093 (m-90) outliers start: 32 outliers final: 8 residues processed: 196 average time/residue: 1.4937 time to fit residues: 316.9562 Evaluate side-chains 204 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098778 restraints weight = 37417.110| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.90 r_work: 0.2926 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12280 Z= 0.141 Angle : 0.442 5.059 16656 Z= 0.244 Chirality : 0.033 0.130 1996 Planarity : 0.003 0.021 2040 Dihedral : 3.381 11.074 1660 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.82 % Allowed : 15.73 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.21), residues: 1508 helix: 2.68 (0.14), residues: 1260 sheet: 0.21 (0.73), residues: 48 loop : -1.34 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.006 0.001 TYR C 56 PHE 0.025 0.001 PHE C 422 TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00289 (12280) covalent geometry : angle 0.44195 (16656) hydrogen bonds : bond 0.04448 ( 1080) hydrogen bonds : angle 3.86727 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.681 Fit side-chains REVERT: A 26 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7157 (ttm170) REVERT: A 57 ARG cc_start: 0.7424 (tpt170) cc_final: 0.5997 (tpp-160) REVERT: A 59 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A 67 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 78 VAL cc_start: 0.8201 (t) cc_final: 0.7771 (p) REVERT: A 120 ASN cc_start: 0.7472 (p0) cc_final: 0.6548 (t0) REVERT: A 159 GLN cc_start: 0.6112 (pt0) cc_final: 0.5813 (mt0) REVERT: A 328 TRP cc_start: 0.6436 (m100) cc_final: 0.5685 (m-10) REVERT: A 399 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7668 (mtt90) REVERT: B 26 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7125 (ttm170) REVERT: B 57 ARG cc_start: 0.7428 (tpt170) cc_final: 0.6001 (tpp-160) REVERT: B 59 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7121 (mp) REVERT: B 67 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7714 (tt) REVERT: B 78 VAL cc_start: 0.8194 (t) cc_final: 0.7764 (p) REVERT: B 120 ASN cc_start: 0.7487 (p0) cc_final: 0.6562 (t0) REVERT: B 159 GLN cc_start: 0.6123 (pt0) cc_final: 0.5820 (mt0) REVERT: B 328 TRP cc_start: 0.6434 (m100) cc_final: 0.5687 (m-10) REVERT: B 399 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7657 (mtt90) REVERT: C 26 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7130 (ttm170) REVERT: C 57 ARG cc_start: 0.7419 (tpt170) cc_final: 0.5993 (tpp-160) REVERT: C 59 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7104 (mp) REVERT: C 67 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7728 (tt) REVERT: C 78 VAL cc_start: 0.8198 (t) cc_final: 0.7765 (p) REVERT: C 120 ASN cc_start: 0.7459 (p0) cc_final: 0.6528 (t0) REVERT: C 159 GLN cc_start: 0.6122 (pt0) cc_final: 0.5822 (mt0) REVERT: C 328 TRP cc_start: 0.6427 (m100) cc_final: 0.5681 (m-10) REVERT: C 399 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7665 (mtt90) REVERT: D 57 ARG cc_start: 0.7430 (tpt170) cc_final: 0.6005 (tpp-160) REVERT: D 59 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7106 (mp) REVERT: D 67 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7727 (tt) REVERT: D 78 VAL cc_start: 0.8190 (t) cc_final: 0.7761 (p) REVERT: D 120 ASN cc_start: 0.7478 (p0) cc_final: 0.6555 (t0) REVERT: D 159 GLN cc_start: 0.6114 (pt0) cc_final: 0.5815 (mt0) REVERT: D 328 TRP cc_start: 0.6441 (m100) cc_final: 0.5691 (m-10) REVERT: D 399 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7675 (mtt90) outliers start: 24 outliers final: 4 residues processed: 208 average time/residue: 1.4166 time to fit residues: 320.6705 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097184 restraints weight = 37888.965| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.93 r_work: 0.2881 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12280 Z= 0.189 Angle : 0.470 4.621 16656 Z= 0.261 Chirality : 0.034 0.128 1996 Planarity : 0.003 0.021 2040 Dihedral : 3.465 11.331 1660 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.90 % Allowed : 15.20 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.21), residues: 1508 helix: 2.53 (0.14), residues: 1260 sheet: 0.21 (0.71), residues: 48 loop : -1.46 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 111 TYR 0.008 0.001 TYR B 56 PHE 0.041 0.002 PHE B 422 TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00413 (12280) covalent geometry : angle 0.47021 (16656) hydrogen bonds : bond 0.04756 ( 1080) hydrogen bonds : angle 3.95718 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.726 Fit side-chains REVERT: A 26 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7174 (ttm170) REVERT: A 57 ARG cc_start: 0.7447 (tpt170) cc_final: 0.6017 (tpp-160) REVERT: A 59 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7116 (mp) REVERT: A 78 VAL cc_start: 0.8211 (t) cc_final: 0.7783 (p) REVERT: A 120 ASN cc_start: 0.7475 (p0) cc_final: 0.6532 (t0) REVERT: A 159 GLN cc_start: 0.6150 (pt0) cc_final: 0.5822 (mt0) REVERT: A 328 TRP cc_start: 0.6405 (m100) cc_final: 0.5711 (m-10) REVERT: A 399 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7687 (mtt90) REVERT: B 26 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7157 (ttm170) REVERT: B 57 ARG cc_start: 0.7449 (tpt170) cc_final: 0.6016 (tpp-160) REVERT: B 59 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7107 (mp) REVERT: B 78 VAL cc_start: 0.8205 (t) cc_final: 0.7778 (p) REVERT: B 120 ASN cc_start: 0.7486 (p0) cc_final: 0.6542 (t0) REVERT: B 159 GLN cc_start: 0.6161 (pt0) cc_final: 0.5828 (mt0) REVERT: B 328 TRP cc_start: 0.6409 (m100) cc_final: 0.5717 (m-10) REVERT: B 399 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7673 (mtt90) REVERT: C 26 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: C 57 ARG cc_start: 0.7449 (tpt170) cc_final: 0.6015 (tpp-160) REVERT: C 59 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7111 (mp) REVERT: C 78 VAL cc_start: 0.8191 (t) cc_final: 0.7760 (p) REVERT: C 120 ASN cc_start: 0.7460 (p0) cc_final: 0.6511 (t0) REVERT: C 159 GLN cc_start: 0.6161 (pt0) cc_final: 0.5827 (mt0) REVERT: C 328 TRP cc_start: 0.6408 (m100) cc_final: 0.5716 (m-10) REVERT: C 399 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7678 (mtt90) REVERT: D 57 ARG cc_start: 0.7456 (tpt170) cc_final: 0.6027 (tpp-160) REVERT: D 59 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7171 (mp) REVERT: D 78 VAL cc_start: 0.8206 (t) cc_final: 0.7778 (p) REVERT: D 120 ASN cc_start: 0.7481 (p0) cc_final: 0.6536 (t0) REVERT: D 159 GLN cc_start: 0.6155 (pt0) cc_final: 0.5823 (mt0) REVERT: D 328 TRP cc_start: 0.6410 (m100) cc_final: 0.5716 (m-10) REVERT: D 399 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7691 (mtt90) outliers start: 25 outliers final: 6 residues processed: 197 average time/residue: 1.4997 time to fit residues: 319.8301 Evaluate side-chains 191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 141 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098124 restraints weight = 37609.527| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.93 r_work: 0.2952 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12280 Z= 0.156 Angle : 0.452 4.301 16656 Z= 0.250 Chirality : 0.033 0.128 1996 Planarity : 0.003 0.064 2040 Dihedral : 3.422 11.033 1660 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.29 % Allowed : 15.43 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.21), residues: 1508 helix: 2.63 (0.14), residues: 1260 sheet: 0.23 (0.73), residues: 48 loop : -1.37 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 129 TYR 0.006 0.001 TYR A 56 PHE 0.041 0.002 PHE D 422 TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00330 (12280) covalent geometry : angle 0.45182 (16656) hydrogen bonds : bond 0.04560 ( 1080) hydrogen bonds : angle 3.89006 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.680 Fit side-chains REVERT: A 26 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7204 (ttm170) REVERT: A 57 ARG cc_start: 0.7515 (tpt170) cc_final: 0.6077 (tpp-160) REVERT: A 59 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7208 (mp) REVERT: A 67 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7718 (tt) REVERT: A 78 VAL cc_start: 0.8248 (t) cc_final: 0.7818 (p) REVERT: A 120 ASN cc_start: 0.7489 (p0) cc_final: 0.6547 (t0) REVERT: A 159 GLN cc_start: 0.6259 (pt0) cc_final: 0.5909 (mt0) REVERT: A 328 TRP cc_start: 0.6462 (m100) cc_final: 0.5779 (m-10) REVERT: A 399 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7712 (mtt90) REVERT: B 26 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7149 (ttm170) REVERT: B 57 ARG cc_start: 0.7518 (tpt170) cc_final: 0.6077 (tpp-160) REVERT: B 59 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7201 (mp) REVERT: B 67 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7720 (tt) REVERT: B 78 VAL cc_start: 0.8245 (t) cc_final: 0.7815 (p) REVERT: B 120 ASN cc_start: 0.7517 (p0) cc_final: 0.6583 (t0) REVERT: B 159 GLN cc_start: 0.6264 (pt0) cc_final: 0.5914 (mt0) REVERT: B 328 TRP cc_start: 0.6462 (m100) cc_final: 0.5783 (m-10) REVERT: B 399 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7702 (mtt90) REVERT: C 26 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7171 (ttm170) REVERT: C 57 ARG cc_start: 0.7514 (tpt170) cc_final: 0.6072 (tpp-160) REVERT: C 59 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7189 (mp) REVERT: C 67 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7719 (tt) REVERT: C 78 VAL cc_start: 0.8243 (t) cc_final: 0.7812 (p) REVERT: C 120 ASN cc_start: 0.7475 (p0) cc_final: 0.6525 (t0) REVERT: C 159 GLN cc_start: 0.6269 (pt0) cc_final: 0.5916 (mt0) REVERT: C 328 TRP cc_start: 0.6458 (m100) cc_final: 0.5779 (m-10) REVERT: C 399 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7708 (mtt90) REVERT: D 57 ARG cc_start: 0.7513 (tpt170) cc_final: 0.6075 (tpp-160) REVERT: D 59 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7194 (mp) REVERT: D 67 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7718 (tt) REVERT: D 78 VAL cc_start: 0.8240 (t) cc_final: 0.7812 (p) REVERT: D 120 ASN cc_start: 0.7494 (p0) cc_final: 0.6551 (t0) REVERT: D 159 GLN cc_start: 0.6262 (pt0) cc_final: 0.5910 (mt0) REVERT: D 328 TRP cc_start: 0.6462 (m100) cc_final: 0.5780 (m-10) REVERT: D 399 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7720 (mtt90) outliers start: 17 outliers final: 2 residues processed: 189 average time/residue: 1.4711 time to fit residues: 300.8426 Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100538 restraints weight = 37471.115| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.93 r_work: 0.2987 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12280 Z= 0.117 Angle : 0.434 5.802 16656 Z= 0.238 Chirality : 0.032 0.129 1996 Planarity : 0.003 0.056 2040 Dihedral : 3.259 10.667 1660 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.46 % Allowed : 16.26 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (0.21), residues: 1508 helix: 2.89 (0.14), residues: 1260 sheet: 0.24 (0.74), residues: 48 loop : -1.21 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 129 TYR 0.005 0.001 TYR C 182 PHE 0.033 0.001 PHE D 422 TRP 0.007 0.001 TRP C 154 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00231 (12280) covalent geometry : angle 0.43365 (16656) hydrogen bonds : bond 0.04195 ( 1080) hydrogen bonds : angle 3.75773 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.427 Fit side-chains REVERT: A 57 ARG cc_start: 0.7482 (tpt170) cc_final: 0.6067 (tpp-160) REVERT: A 67 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7729 (tt) REVERT: A 78 VAL cc_start: 0.8220 (t) cc_final: 0.7779 (p) REVERT: A 159 GLN cc_start: 0.6248 (pt0) cc_final: 0.5908 (mt0) REVERT: A 399 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7680 (mtt90) REVERT: B 57 ARG cc_start: 0.7481 (tpt170) cc_final: 0.6063 (tpp-160) REVERT: B 67 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 78 VAL cc_start: 0.8210 (t) cc_final: 0.7770 (p) REVERT: B 159 GLN cc_start: 0.6256 (pt0) cc_final: 0.5914 (mt0) REVERT: B 399 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7674 (mtt90) REVERT: C 57 ARG cc_start: 0.7480 (tpt170) cc_final: 0.6061 (tpp-160) REVERT: C 67 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7724 (tt) REVERT: C 78 VAL cc_start: 0.8203 (t) cc_final: 0.7762 (p) REVERT: C 159 GLN cc_start: 0.6259 (pt0) cc_final: 0.5914 (mt0) REVERT: C 399 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7672 (mtt90) REVERT: D 57 ARG cc_start: 0.7475 (tpt170) cc_final: 0.6054 (tpp-160) REVERT: D 67 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7730 (tt) REVERT: D 78 VAL cc_start: 0.8206 (t) cc_final: 0.7767 (p) REVERT: D 159 GLN cc_start: 0.6250 (pt0) cc_final: 0.5907 (mt0) REVERT: D 399 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7688 (mtt90) outliers start: 6 outliers final: 1 residues processed: 183 average time/residue: 1.1950 time to fit residues: 237.6402 Evaluate side-chains 184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain D residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097202 restraints weight = 37672.439| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.93 r_work: 0.2928 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12280 Z= 0.200 Angle : 0.483 5.757 16656 Z= 0.267 Chirality : 0.035 0.127 1996 Planarity : 0.004 0.057 2040 Dihedral : 3.450 11.381 1660 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.06 % Allowed : 15.35 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.21), residues: 1508 helix: 2.60 (0.14), residues: 1260 sheet: 0.16 (0.72), residues: 48 loop : -1.25 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 129 TYR 0.016 0.001 TYR D 182 PHE 0.043 0.002 PHE A 422 TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00440 (12280) covalent geometry : angle 0.48285 (16656) hydrogen bonds : bond 0.04792 ( 1080) hydrogen bonds : angle 3.93100 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8981.05 seconds wall clock time: 152 minutes 49.38 seconds (9169.38 seconds total)