Starting phenix.real_space_refine on Thu Jul 2 00:15:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvx_62603/07_2026/9kvx_62603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvx_62603/07_2026/9kvx_62603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kvx_62603/07_2026/9kvx_62603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvx_62603/07_2026/9kvx_62603.map" model { file = "/net/cci-nas-00/data/ceres_data/9kvx_62603/07_2026/9kvx_62603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvx_62603/07_2026/9kvx_62603.cif" } resolution = 2.79 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= 0.010 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 Mn 2 7.51 5 S 32 5.16 5 C 2892 2.51 5 N 720 2.21 5 O 790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4436 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2213 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: A Time building chain proxies: 1.53, per 1000 atoms: 0.34 Number of scatterers: 4436 At special positions: 0 Unit cell: (75.492, 60.58, 111.84, 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) Mn 2 24.99 S 32 16.00 O 790 8.00 N 720 7.00 C 2892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 404 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 404 " - pdb=" SG CYS A 409 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 146.9 milliseconds 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1088 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 59.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 14 through 32 removed outlier: 3.592A pdb=" N ALA B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 61 Processing helix chain 'B' and resid 76 through 106 removed outlier: 3.651A pdb=" N ALA B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 244 through 262 removed outlier: 3.845A pdb=" N ALA B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 307 removed outlier: 3.691A pdb=" N ILE B 279 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Proline residue: B 281 - end of helix removed outlier: 3.675A pdb=" N SER B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.955A pdb=" N ILE B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.511A pdb=" N SER B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.861A pdb=" N LYS B 411 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.593A pdb=" N ALA A 20 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 Processing helix chain 'A' and resid 76 through 106 removed outlier: 3.651A pdb=" N ALA A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 244 through 262 removed outlier: 3.845A pdb=" N ALA A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.691A pdb=" N ILE A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix removed outlier: 3.675A pdb=" N SER A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.955A pdb=" N ILE A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 removed outlier: 3.511A pdb=" N SER A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.861A pdb=" N LYS A 411 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 331 through 341 removed outlier: 3.686A pdb=" N SER B 331 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 335 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR B 348 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B 337 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 346 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU B 339 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS B 344 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 341 removed outlier: 5.785A pdb=" N VAL A 332 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS A 352 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU A 334 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A 350 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 738 1.32 - 1.45: 1128 1.45 - 1.59: 2596 1.59 - 1.72: 0 1.72 - 1.85: 46 Bond restraints: 4508 Sorted by residual: bond pdb=" CA SER B 39 " pdb=" CB SER B 39 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.65e+01 bond pdb=" CA SER A 39 " pdb=" CB SER A 39 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.63e+01 bond pdb=" C SER A 39 " pdb=" O SER A 39 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.15e-02 7.56e+03 1.44e+01 bond pdb=" C MET A 44 " pdb=" O MET A 44 " ideal model delta sigma weight residual 1.236 1.189 0.048 1.26e-02 6.30e+03 1.43e+01 bond pdb=" C SER B 39 " pdb=" O SER B 39 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.15e-02 7.56e+03 1.42e+01 ... (remaining 4503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 5962 1.78 - 3.55: 122 3.55 - 5.33: 38 5.33 - 7.11: 10 7.11 - 8.89: 2 Bond angle restraints: 6134 Sorted by residual: angle pdb=" CA SER B 39 " pdb=" C SER B 39 " pdb=" O SER B 39 " ideal model delta sigma weight residual 120.82 116.06 4.76 1.05e+00 9.07e-01 2.05e+01 angle pdb=" CA SER A 39 " pdb=" C SER A 39 " pdb=" O SER A 39 " ideal model delta sigma weight residual 120.82 116.07 4.75 1.05e+00 9.07e-01 2.05e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 112.80 108.36 4.44 1.15e+00 7.56e-01 1.49e+01 angle pdb=" N VAL B 264 " pdb=" CA VAL B 264 " pdb=" C VAL B 264 " ideal model delta sigma weight residual 112.80 108.37 4.43 1.15e+00 7.56e-01 1.49e+01 angle pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.28 104.57 5.71 1.55e+00 4.16e-01 1.36e+01 ... (remaining 6129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2342 17.56 - 35.12: 252 35.12 - 52.68: 76 52.68 - 70.24: 38 70.24 - 87.81: 6 Dihedral angle restraints: 2714 sinusoidal: 1036 harmonic: 1678 Sorted by residual: dihedral pdb=" CB CYS A 404 " pdb=" SG CYS A 404 " pdb=" SG CYS A 409 " pdb=" CB CYS A 409 " ideal model delta sinusoidal sigma weight residual -86.00 -14.18 -71.82 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS B 404 " pdb=" SG CYS B 404 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -14.20 -71.80 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CA GLY A 123 " pdb=" C GLY A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 457 0.033 - 0.065: 236 0.065 - 0.097: 47 0.097 - 0.130: 26 0.130 - 0.162: 2 Chirality restraints: 768 Sorted by residual: chirality pdb=" CA MET A 44 " pdb=" N MET A 44 " pdb=" C MET A 44 " pdb=" CB MET A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA MET B 44 " pdb=" N MET B 44 " pdb=" C MET B 44 " pdb=" CB MET B 44 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL B 332 " pdb=" N VAL B 332 " pdb=" C VAL B 332 " pdb=" CB VAL B 332 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 765 not shown) Planarity restraints: 752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 39 " 0.008 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C SER A 39 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 39 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 40 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 39 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C SER B 39 " 0.030 2.00e-02 2.50e+03 pdb=" O SER B 39 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 40 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 44 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C MET B 44 " -0.029 2.00e-02 2.50e+03 pdb=" O MET B 44 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 45 " 0.010 2.00e-02 2.50e+03 ... (remaining 749 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 107 2.69 - 3.24: 4279 3.24 - 3.80: 6956 3.80 - 4.35: 9503 4.35 - 4.90: 15186 Nonbonded interactions: 36031 Sorted by model distance: nonbonded pdb=" OD1 ASP B 248 " pdb="MN MN B 501 " model vdw 2.139 3.060 nonbonded pdb=" OD1 ASP A 248 " pdb="MN MN A 501 " model vdw 2.151 3.060 nonbonded pdb=" OG SER A 252 " pdb="MN MN A 501 " model vdw 2.152 3.060 nonbonded pdb=" OG SER B 252 " pdb="MN MN B 501 " model vdw 2.183 3.060 nonbonded pdb=" OD1 ASP B 40 " pdb="MN MN B 501 " model vdw 2.204 3.060 ... (remaining 36026 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.120 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.005 0.083 4512 Z= 0.248 Angle : 0.707 8.887 6142 Z= 0.379 Chirality : 0.042 0.162 768 Planarity : 0.004 0.029 752 Dihedral : 18.068 87.806 1614 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.21 % Allowed : 32.13 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.35), residues: 568 helix: -1.59 (0.26), residues: 328 sheet: -0.76 (0.79), residues: 50 loop : 0.08 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.015 0.001 TYR A 263 PHE 0.008 0.001 PHE B 382 TRP 0.007 0.002 TRP B 338 HIS 0.004 0.002 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.25 ( 4508) covalent geometry : angle 0.69983 / 0.38 ( 6134) SS BOND : bond 0.00686 / 0.35 ( 4) SS BOND : angle 2.82483 / 1.77 ( 8) hydrogen bonds : bond 0.23689 / 15.39 ( 262) hydrogen bonds : angle 9.34546 / 6.34 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 177 average time/residue: 0.4926 time to fit residues: 90.4264 Evaluate side-chains 130 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 415 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN B 308 GLN B 336 HIS B 401 ASN A 308 GLN A 384 ASN A 401 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085419 restraints weight = 7146.886| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.04 r_work: 0.2917 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4512 Z= 0.152 Angle : 0.683 9.739 6142 Z= 0.332 Chirality : 0.041 0.148 768 Planarity : 0.004 0.022 752 Dihedral : 5.332 41.115 614 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.02 % Allowed : 34.14 % Favored : 59.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.36), residues: 568 helix: -0.06 (0.28), residues: 348 sheet: -0.51 (0.78), residues: 50 loop : 0.21 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 103 TYR 0.011 0.001 TYR B 263 PHE 0.008 0.001 PHE A 88 TRP 0.007 0.001 TRP A 338 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 4508) covalent geometry : angle 0.68187 / 0.33 ( 6134) SS BOND : bond 0.00470 / 0.24 ( 4) SS BOND : angle 1.41365 / 0.72 ( 8) hydrogen bonds : bond 0.05074 / 3.25 ( 262) hydrogen bonds : angle 5.02305 / 3.43 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 ARG cc_start: 0.4055 (pmt-80) cc_final: 0.3749 (pmt-80) REVERT: B 14 MET cc_start: 0.8158 (mmt) cc_final: 0.7900 (mmt) REVERT: B 103 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8592 (mtt180) REVERT: B 263 TYR cc_start: 0.8659 (t80) cc_final: 0.8371 (t80) REVERT: A 10 ARG cc_start: 0.4092 (pmt-80) cc_final: 0.3795 (pmt-80) REVERT: A 14 MET cc_start: 0.8142 (mmt) cc_final: 0.7929 (mmt) REVERT: A 43 ASN cc_start: 0.8742 (t0) cc_final: 0.8433 (t160) REVERT: A 263 TYR cc_start: 0.8645 (t80) cc_final: 0.8390 (t80) outliers start: 30 outliers final: 12 residues processed: 156 average time/residue: 0.5060 time to fit residues: 81.8171 Evaluate side-chains 147 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN B 401 ASN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.083882 restraints weight = 7062.232| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.07 r_work: 0.2921 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4512 Z= 0.149 Angle : 0.627 8.246 6142 Z= 0.302 Chirality : 0.041 0.137 768 Planarity : 0.003 0.022 752 Dihedral : 4.718 23.180 612 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.22 % Allowed : 34.54 % Favored : 60.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.37), residues: 568 helix: 0.74 (0.28), residues: 348 sheet: -0.04 (0.78), residues: 50 loop : 0.20 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.014 0.001 TYR B 359 PHE 0.008 0.001 PHE B 88 TRP 0.008 0.002 TRP A 338 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4508) covalent geometry : angle 0.62461 / 0.30 ( 6134) SS BOND : bond 0.00093 / 0.05 ( 4) SS BOND : angle 1.55763 / 0.81 ( 8) hydrogen bonds : bond 0.04273 / 2.72 ( 262) hydrogen bonds : angle 4.36444 / 3.00 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 280 ASP cc_start: 0.8618 (t0) cc_final: 0.8409 (t0) REVERT: B 365 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8203 (mttt) REVERT: A 43 ASN cc_start: 0.8715 (t0) cc_final: 0.8390 (t160) REVERT: A 280 ASP cc_start: 0.8646 (t0) cc_final: 0.8425 (t0) outliers start: 26 outliers final: 11 residues processed: 151 average time/residue: 0.5312 time to fit residues: 83.0034 Evaluate side-chains 136 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS B 401 ASN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080360 restraints weight = 7115.044| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.15 r_work: 0.2860 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4512 Z= 0.190 Angle : 0.625 6.098 6142 Z= 0.310 Chirality : 0.042 0.133 768 Planarity : 0.003 0.023 752 Dihedral : 4.534 20.221 610 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.82 % Allowed : 32.93 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.37), residues: 568 helix: 1.40 (0.29), residues: 344 sheet: 0.15 (0.78), residues: 50 loop : 0.40 (0.52), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 63 TYR 0.014 0.001 TYR B 359 PHE 0.009 0.001 PHE B 88 TRP 0.007 0.001 TRP A 338 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 4508) covalent geometry : angle 0.62309 / 0.31 ( 6134) SS BOND : bond 0.00297 / 0.15 ( 4) SS BOND : angle 1.56184 / 0.78 ( 8) hydrogen bonds : bond 0.04132 / 2.63 ( 262) hydrogen bonds : angle 4.08698 / 2.83 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8722 (t80) cc_final: 0.8234 (t80) REVERT: B 103 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8369 (mtt-85) REVERT: B 108 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7838 (pt0) REVERT: B 263 TYR cc_start: 0.8676 (t80) cc_final: 0.7960 (t80) REVERT: B 315 ASN cc_start: 0.8785 (t0) cc_final: 0.8285 (t0) REVERT: B 365 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8214 (mttt) REVERT: A 43 ASN cc_start: 0.8786 (t0) cc_final: 0.8453 (t0) REVERT: A 59 TYR cc_start: 0.8737 (t80) cc_final: 0.8442 (t80) REVERT: A 263 TYR cc_start: 0.8683 (t80) cc_final: 0.8132 (t80) REVERT: A 315 ASN cc_start: 0.8780 (t0) cc_final: 0.8276 (t0) REVERT: A 355 LYS cc_start: 0.9114 (tppp) cc_final: 0.8290 (tppp) REVERT: A 365 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8291 (mttt) REVERT: A 384 ASN cc_start: 0.8511 (m-40) cc_final: 0.8290 (m110) outliers start: 29 outliers final: 14 residues processed: 145 average time/residue: 0.5197 time to fit residues: 78.0469 Evaluate side-chains 145 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS B 401 ASN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.082966 restraints weight = 7054.924| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.11 r_work: 0.2903 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4512 Z= 0.130 Angle : 0.630 8.844 6142 Z= 0.301 Chirality : 0.041 0.130 768 Planarity : 0.004 0.037 752 Dihedral : 4.491 19.257 610 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.82 % Allowed : 33.94 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.37), residues: 568 helix: 1.72 (0.29), residues: 346 sheet: 0.40 (0.75), residues: 50 loop : 0.49 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.014 0.001 TYR A 359 PHE 0.008 0.001 PHE A 88 TRP 0.008 0.001 TRP A 338 HIS 0.002 0.000 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4508) covalent geometry : angle 0.62685 / 0.30 ( 6134) SS BOND : bond 0.00711 / 0.36 ( 4) SS BOND : angle 1.81571 / 0.94 ( 8) hydrogen bonds : bond 0.03697 / 2.34 ( 262) hydrogen bonds : angle 3.88981 / 2.70 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 103 ARG cc_start: 0.8365 (ttm170) cc_final: 0.8155 (mtt180) REVERT: B 315 ASN cc_start: 0.8729 (t0) cc_final: 0.8225 (t0) REVERT: B 365 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8215 (mttt) REVERT: A 43 ASN cc_start: 0.8734 (t0) cc_final: 0.8401 (t0) REVERT: A 59 TYR cc_start: 0.8749 (t80) cc_final: 0.8295 (t80) REVERT: A 99 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 315 ASN cc_start: 0.8727 (t0) cc_final: 0.8238 (t0) REVERT: A 355 LYS cc_start: 0.9156 (tppp) cc_final: 0.8721 (tppt) REVERT: A 365 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8286 (mttt) REVERT: A 384 ASN cc_start: 0.8559 (m-40) cc_final: 0.8348 (m-40) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.5612 time to fit residues: 80.0373 Evaluate side-chains 139 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.0040 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS B 384 ASN B 401 ASN A 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083493 restraints weight = 7174.810| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.11 r_work: 0.2896 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4512 Z= 0.127 Angle : 0.656 7.901 6142 Z= 0.313 Chirality : 0.042 0.139 768 Planarity : 0.003 0.031 752 Dihedral : 4.475 19.224 610 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.02 % Allowed : 35.14 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.37), residues: 568 helix: 1.91 (0.29), residues: 346 sheet: 0.62 (0.74), residues: 50 loop : 0.43 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.019 0.001 TYR B 59 PHE 0.006 0.001 PHE B 88 TRP 0.008 0.001 TRP A 338 HIS 0.002 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4508) covalent geometry : angle 0.65254 / 0.31 ( 6134) SS BOND : bond 0.00424 / 0.22 ( 4) SS BOND : angle 1.97273 / 1.01 ( 8) hydrogen bonds : bond 0.03587 / 2.28 ( 262) hydrogen bonds : angle 3.80899 / 2.64 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.166 Fit side-chains REVERT: B 99 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7995 (mm-30) REVERT: B 108 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7775 (pt0) REVERT: B 263 TYR cc_start: 0.8529 (t80) cc_final: 0.7807 (t80) REVERT: B 315 ASN cc_start: 0.8729 (t0) cc_final: 0.8215 (t0) REVERT: B 355 LYS cc_start: 0.8889 (tppt) cc_final: 0.8544 (tppt) REVERT: B 365 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8258 (mttt) REVERT: A 43 ASN cc_start: 0.8690 (t0) cc_final: 0.8345 (t0) REVERT: A 99 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 315 ASN cc_start: 0.8642 (t0) cc_final: 0.8115 (t0) REVERT: A 365 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8288 (mttt) outliers start: 20 outliers final: 10 residues processed: 134 average time/residue: 0.5654 time to fit residues: 78.3960 Evaluate side-chains 135 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS B 401 ASN A 384 ASN A 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.083972 restraints weight = 7136.215| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.13 r_work: 0.2917 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4512 Z= 0.135 Angle : 0.642 7.209 6142 Z= 0.309 Chirality : 0.042 0.122 768 Planarity : 0.004 0.052 752 Dihedral : 4.530 19.413 610 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.82 % Allowed : 34.74 % Favored : 61.45 % 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 are not related in a simple way. whole: 2.05 (0.37), residues: 568 helix: 2.02 (0.29), residues: 346 sheet: 0.79 (0.74), residues: 50 loop : 0.28 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 63 TYR 0.027 0.002 TYR A 59 PHE 0.007 0.001 PHE A 88 TRP 0.008 0.001 TRP A 338 HIS 0.002 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 4508) covalent geometry : angle 0.63656 / 0.31 ( 6134) SS BOND : bond 0.00582 / 0.30 ( 4) SS BOND : angle 2.29766 / 1.16 ( 8) hydrogen bonds : bond 0.03523 / 2.24 ( 262) hydrogen bonds : angle 3.76431 / 2.62 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.156 Fit side-chains REVERT: B 66 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7446 (mmm160) REVERT: B 99 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 315 ASN cc_start: 0.8783 (t0) cc_final: 0.8267 (t0) REVERT: B 365 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8300 (mttt) REVERT: A 43 ASN cc_start: 0.8738 (t0) cc_final: 0.8406 (t0) REVERT: A 99 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 315 ASN cc_start: 0.8747 (t0) cc_final: 0.8220 (t0) REVERT: A 339 GLU cc_start: 0.8983 (tt0) cc_final: 0.8743 (tt0) REVERT: A 365 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8312 (mttt) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.5289 time to fit residues: 75.4275 Evaluate side-chains 135 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS B 401 ASN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083563 restraints weight = 7138.251| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.14 r_work: 0.2894 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4512 Z= 0.150 Angle : 0.666 6.980 6142 Z= 0.326 Chirality : 0.043 0.126 768 Planarity : 0.004 0.057 752 Dihedral : 4.627 22.260 610 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.02 % Allowed : 32.73 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.37), residues: 568 helix: 2.08 (0.29), residues: 346 sheet: 0.70 (0.72), residues: 50 loop : 0.23 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 63 TYR 0.025 0.002 TYR A 59 PHE 0.007 0.001 PHE A 88 TRP 0.007 0.001 TRP A 338 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 4508) covalent geometry : angle 0.65945 / 0.32 ( 6134) SS BOND : bond 0.00552 / 0.28 ( 4) SS BOND : angle 2.58445 / 1.30 ( 8) hydrogen bonds : bond 0.03566 / 2.26 ( 262) hydrogen bonds : angle 3.73501 / 2.58 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.176 Fit side-chains REVERT: B 66 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7457 (mmm160) REVERT: B 99 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 263 TYR cc_start: 0.8531 (t80) cc_final: 0.7833 (t80) REVERT: B 315 ASN cc_start: 0.8749 (t0) cc_final: 0.8214 (t0) REVERT: B 365 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8305 (mttt) REVERT: A 43 ASN cc_start: 0.8695 (t0) cc_final: 0.8330 (t0) REVERT: A 66 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7278 (mmm160) REVERT: A 99 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7912 (mm-30) REVERT: A 315 ASN cc_start: 0.8700 (t0) cc_final: 0.8135 (t0) REVERT: A 339 GLU cc_start: 0.8970 (tt0) cc_final: 0.8714 (tt0) REVERT: A 365 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8280 (mttt) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.5695 time to fit residues: 79.4451 Evaluate side-chains 136 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS B 401 ASN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082423 restraints weight = 7166.824| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.17 r_work: 0.2884 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4512 Z= 0.162 Angle : 0.684 6.999 6142 Z= 0.334 Chirality : 0.043 0.132 768 Planarity : 0.004 0.042 752 Dihedral : 4.687 25.547 610 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.41 % Allowed : 34.54 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.38), residues: 568 helix: 2.12 (0.29), residues: 346 sheet: 0.50 (0.71), residues: 50 loop : 0.02 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.021 0.002 TYR A 59 PHE 0.008 0.001 PHE B 88 TRP 0.006 0.001 TRP A 338 HIS 0.009 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 4508) covalent geometry : angle 0.67369 / 0.33 ( 6134) SS BOND : bond 0.00478 / 0.24 ( 4) SS BOND : angle 3.27777 / 1.65 ( 8) hydrogen bonds : bond 0.03569 / 2.27 ( 262) hydrogen bonds : angle 3.74774 / 2.59 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.171 Fit side-chains REVERT: B 44 MET cc_start: 0.8475 (mtm) cc_final: 0.8227 (mtm) REVERT: B 66 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7435 (mmm160) REVERT: B 99 GLU cc_start: 0.8221 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 315 ASN cc_start: 0.8757 (t0) cc_final: 0.8212 (t0) REVERT: B 365 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (mttt) REVERT: A 43 ASN cc_start: 0.8672 (t0) cc_final: 0.8334 (t0) REVERT: A 66 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7331 (mmm160) REVERT: A 99 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8014 (mm-30) REVERT: A 315 ASN cc_start: 0.8700 (t0) cc_final: 0.8134 (t0) REVERT: A 339 GLU cc_start: 0.8927 (tt0) cc_final: 0.8666 (tt0) REVERT: A 355 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8663 (mmmm) REVERT: A 365 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8273 (mttt) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.5012 time to fit residues: 69.4783 Evaluate side-chains 134 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 333 HIS A 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083248 restraints weight = 7101.582| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.17 r_work: 0.2880 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4512 Z= 0.151 Angle : 0.714 8.748 6142 Z= 0.349 Chirality : 0.043 0.125 768 Planarity : 0.004 0.047 752 Dihedral : 4.740 27.553 610 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.21 % Allowed : 35.14 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.38), residues: 568 helix: 2.14 (0.29), residues: 346 sheet: 0.37 (0.72), residues: 50 loop : -0.11 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.023 0.002 TYR A 59 PHE 0.007 0.001 PHE B 88 TRP 0.007 0.001 TRP A 338 HIS 0.007 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 4508) covalent geometry : angle 0.70239 / 0.34 ( 6134) SS BOND : bond 0.00147 / 0.08 ( 4) SS BOND : angle 3.60009 / 1.81 ( 8) hydrogen bonds : bond 0.03503 / 2.24 ( 262) hydrogen bonds : angle 3.70600 / 2.56 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1136 Ramachandran restraints generated. 568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.251 Fit side-chains REVERT: B 44 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: B 66 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7416 (mmm160) REVERT: B 99 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 263 TYR cc_start: 0.8525 (t80) cc_final: 0.7811 (t80) REVERT: B 315 ASN cc_start: 0.8762 (t0) cc_final: 0.8214 (t0) REVERT: B 365 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (mttt) REVERT: A 43 ASN cc_start: 0.8657 (t0) cc_final: 0.8299 (t0) REVERT: A 66 ARG cc_start: 0.7689 (mmm160) cc_final: 0.7333 (mmm160) REVERT: A 99 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 315 ASN cc_start: 0.8721 (t0) cc_final: 0.8179 (t0) REVERT: A 339 GLU cc_start: 0.8922 (tt0) cc_final: 0.8667 (tt0) REVERT: A 365 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8282 (mttt) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.5545 time to fit residues: 74.5039 Evaluate side-chains 128 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.0270 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083666 restraints weight = 7131.637| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.22 r_work: 0.2909 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4512 Z= 0.145 Angle : 0.720 7.659 6142 Z= 0.354 Chirality : 0.044 0.133 768 Planarity : 0.004 0.043 752 Dihedral : 4.781 29.129 610 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.81 % Allowed : 36.55 % Favored : 60.64 % 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 are not related in a simple way. whole: 1.90 (0.37), residues: 568 helix: 2.10 (0.29), residues: 346 sheet: 0.31 (0.72), residues: 50 loop : -0.12 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.021 0.002 TYR A 59 PHE 0.007 0.001 PHE B 88 TRP 0.007 0.001 TRP A 338 HIS 0.005 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 4508) covalent geometry : angle 0.70640 / 0.35 ( 6134) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 3.92023 / 1.97 ( 8) hydrogen bonds : bond 0.03437 / 2.19 ( 262) hydrogen bonds : angle 3.73829 / 2.58 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.65 seconds wall clock time: 31 minutes 38.31 seconds (1898.31 seconds total)