Starting phenix.real_space_refine on Fri Aug 22 15:00:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afx_15411/08_2025/8afx_15411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afx_15411/08_2025/8afx_15411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8afx_15411/08_2025/8afx_15411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afx_15411/08_2025/8afx_15411.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8afx_15411/08_2025/8afx_15411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afx_15411/08_2025/8afx_15411.map" } resolution = 4.8 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2498 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1603 2.51 5 N 406 2.21 5 O 472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 2498 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2498 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 4 Time building chain proxies: 0.87, per 1000 atoms: 0.35 Number of scatterers: 2498 At special positions: 0 Unit cell: (68.7898, 65.4342, 69.6287, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 472 8.00 N 406 7.00 C 1603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 82.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 4.119A pdb=" N PHE A 10 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 23 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 12 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 40 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASN A 32 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 38 " --> pdb=" O ASN A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.755A pdb=" N VAL A 62 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 50 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 60 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 75 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU A 88 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 77 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 84 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 108 removed outlier: 7.134A pdb=" N ILE A 113 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 126 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 115 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.556A pdb=" N TYR A 150 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLY A 225 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU A 242 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 227 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 240 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 229 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 236 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.211A pdb=" N ALA A 263 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET A 251 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 261 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 253 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 259 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 271 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 264 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 269 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 282 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP A 274 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS A 280 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 298 removed outlier: 6.991A pdb=" N THR A 308 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 296 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 306 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE A 298 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR A 304 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 309 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 316 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 413 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.571A pdb=" N ARG A 468 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 462 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 437 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 431 removed outlier: 3.571A pdb=" N ARG A 468 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A 478 " --> pdb=" O LEU A 492 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 165 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: 0.28 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 784 1.34 - 1.46: 559 1.46 - 1.58: 1170 1.58 - 1.70: 2 1.70 - 1.81: 30 Bond restraints: 2545 Sorted by residual: bond pdb=" CB PRO A 483 " pdb=" CG PRO A 483 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.03e+01 bond pdb=" N PRO A 483 " pdb=" CA PRO A 483 " ideal model delta sigma weight residual 1.470 1.446 0.025 1.01e-02 9.80e+03 5.90e+00 bond pdb=" CB PRO A 141 " pdb=" CG PRO A 141 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.86e+00 bond pdb=" N PRO A 483 " pdb=" CD PRO A 483 " ideal model delta sigma weight residual 1.473 1.499 -0.026 1.40e-02 5.10e+03 3.58e+00 bond pdb=" CG PRO A 483 " pdb=" CD PRO A 483 " ideal model delta sigma weight residual 1.503 1.446 0.057 3.40e-02 8.65e+02 2.81e+00 ... (remaining 2540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 3411 3.35 - 6.71: 22 6.71 - 10.06: 7 10.06 - 13.41: 1 13.41 - 16.76: 1 Bond angle restraints: 3442 Sorted by residual: angle pdb=" CA PRO A 483 " pdb=" N PRO A 483 " pdb=" CD PRO A 483 " ideal model delta sigma weight residual 112.00 95.24 16.76 1.40e+00 5.10e-01 1.43e+02 angle pdb=" N PRO A 483 " pdb=" CD PRO A 483 " pdb=" CG PRO A 483 " ideal model delta sigma weight residual 103.20 95.59 7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C PRO A 483 " pdb=" CA PRO A 483 " pdb=" CB PRO A 483 " ideal model delta sigma weight residual 110.00 114.53 -4.53 1.12e+00 7.97e-01 1.64e+01 angle pdb=" CA PRO A 141 " pdb=" N PRO A 141 " pdb=" CD PRO A 141 " ideal model delta sigma weight residual 112.00 106.66 5.34 1.40e+00 5.10e-01 1.46e+01 angle pdb=" CA LEU A 417 " pdb=" CB LEU A 417 " pdb=" CG LEU A 417 " ideal model delta sigma weight residual 116.30 128.37 -12.07 3.50e+00 8.16e-02 1.19e+01 ... (remaining 3437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1315 16.68 - 33.36: 178 33.36 - 50.04: 38 50.04 - 66.72: 6 66.72 - 83.40: 3 Dihedral angle restraints: 1540 sinusoidal: 610 harmonic: 930 Sorted by residual: dihedral pdb=" CA MET A 462 " pdb=" C MET A 462 " pdb=" N LYS A 463 " pdb=" CA LYS A 463 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 98 " pdb=" C VAL A 98 " pdb=" N LYS A 99 " pdb=" CA LYS A 99 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 284 0.047 - 0.094: 85 0.094 - 0.141: 36 0.141 - 0.188: 0 0.188 - 0.235: 1 Chirality restraints: 406 Sorted by residual: chirality pdb=" CA PRO A 483 " pdb=" N PRO A 483 " pdb=" C PRO A 483 " pdb=" CB PRO A 483 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR A 56 " pdb=" N THR A 56 " pdb=" C THR A 56 " pdb=" CB THR A 56 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 403 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " -0.084 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 483 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 417 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 418 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 140 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 141 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 141 " -0.022 5.00e-02 4.00e+02 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 123 2.71 - 3.26: 2430 3.26 - 3.80: 3814 3.80 - 4.35: 4506 4.35 - 4.90: 7520 Nonbonded interactions: 18393 Sorted by model distance: nonbonded pdb=" OG SER A 471 " pdb=" OD1 ASP A 473 " model vdw 2.159 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OD1 ASN A 79 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN A 101 " pdb=" N SER A 103 " model vdw 2.234 3.120 nonbonded pdb=" OG SER A 44 " pdb=" OH TYR A 47 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" N GLY A 17 " model vdw 2.238 3.120 ... (remaining 18388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.940 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 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 0.160 2545 Z= 0.190 Angle : 0.901 16.763 3442 Z= 0.482 Chirality : 0.051 0.235 406 Planarity : 0.007 0.114 430 Dihedral : 16.079 83.399 940 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.05 % Allowed : 28.22 % Favored : 70.73 % 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: -0.47 (0.46), residues: 311 helix: None (None), residues: 0 sheet: 1.07 (0.45), residues: 121 loop : -1.34 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 286 TYR 0.018 0.002 TYR A 116 PHE 0.019 0.002 PHE A 317 HIS 0.002 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 2545) covalent geometry : angle 0.90111 ( 3442) hydrogen bonds : bond 0.26110 ( 57) hydrogen bonds : angle 11.12507 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.103 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.0424 time to fit residues: 3.8083 Evaluate side-chains 64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.122452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111598 restraints weight = 6181.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.113273 restraints weight = 4378.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114577 restraints weight = 3339.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115565 restraints weight = 2674.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116300 restraints weight = 2217.858| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2545 Z= 0.127 Angle : 0.637 6.709 3442 Z= 0.324 Chirality : 0.051 0.163 406 Planarity : 0.004 0.045 430 Dihedral : 5.171 19.805 342 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: -0.38 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 1.19 (0.45), residues: 121 loop : -1.33 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 292 TYR 0.010 0.001 TYR A 116 PHE 0.020 0.002 PHE A 412 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2545) covalent geometry : angle 0.63667 ( 3442) hydrogen bonds : bond 0.04400 ( 57) hydrogen bonds : angle 7.45486 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.061 Fit side-chains REVERT: A 148 LEU cc_start: 0.8823 (tp) cc_final: 0.8615 (tp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0498 time to fit residues: 4.9956 Evaluate side-chains 64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.0030 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.119375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.108609 restraints weight = 6376.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.110253 restraints weight = 4549.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.111529 restraints weight = 3476.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.112388 restraints weight = 2785.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.113171 restraints weight = 2359.263| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2545 Z= 0.137 Angle : 0.669 7.524 3442 Z= 0.330 Chirality : 0.051 0.180 406 Planarity : 0.003 0.034 430 Dihedral : 5.263 21.960 342 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -0.70 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.71 (0.43), residues: 123 loop : -1.35 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.017 0.001 TYR A 47 PHE 0.014 0.002 PHE A 31 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2545) covalent geometry : angle 0.66854 ( 3442) hydrogen bonds : bond 0.04158 ( 57) hydrogen bonds : angle 7.20094 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.076 Fit side-chains REVERT: A 296 ILE cc_start: 0.9118 (mm) cc_final: 0.8528 (pt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0412 time to fit residues: 4.0668 Evaluate side-chains 63 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.103478 restraints weight = 6109.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.105517 restraints weight = 4009.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107018 restraints weight = 2900.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108096 restraints weight = 2224.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108883 restraints weight = 1792.352| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2545 Z= 0.125 Angle : 0.657 7.508 3442 Z= 0.322 Chirality : 0.050 0.153 406 Planarity : 0.003 0.033 430 Dihedral : 5.188 21.571 342 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -0.75 (0.44), residues: 311 helix: None (None), residues: 0 sheet: 0.86 (0.44), residues: 117 loop : -1.47 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.009 0.001 TYR A 116 PHE 0.026 0.002 PHE A 13 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2545) covalent geometry : angle 0.65719 ( 3442) hydrogen bonds : bond 0.03686 ( 57) hydrogen bonds : angle 7.00947 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.097 Fit side-chains REVERT: A 34 GLU cc_start: 0.8706 (tp30) cc_final: 0.8069 (tm-30) REVERT: A 273 PHE cc_start: 0.7538 (m-80) cc_final: 0.7091 (m-10) REVERT: A 296 ILE cc_start: 0.9163 (mm) cc_final: 0.8604 (pt) REVERT: A 298 PHE cc_start: 0.8742 (m-80) cc_final: 0.8475 (m-10) REVERT: A 412 PHE cc_start: 0.7832 (t80) cc_final: 0.7560 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0466 time to fit residues: 4.6229 Evaluate side-chains 62 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.115939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.105627 restraints weight = 6164.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.107484 restraints weight = 4154.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.108882 restraints weight = 3016.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109946 restraints weight = 2333.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.110829 restraints weight = 1857.415| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2545 Z= 0.115 Angle : 0.643 8.031 3442 Z= 0.314 Chirality : 0.051 0.145 406 Planarity : 0.004 0.045 430 Dihedral : 5.126 20.614 342 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.77 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 1.03 (0.46), residues: 111 loop : -1.54 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.025 0.002 TYR A 442 PHE 0.017 0.002 PHE A 13 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 2545) covalent geometry : angle 0.64288 ( 3442) hydrogen bonds : bond 0.03376 ( 57) hydrogen bonds : angle 6.80427 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.097 Fit side-chains REVERT: A 33 CYS cc_start: 0.8199 (m) cc_final: 0.7834 (m) REVERT: A 273 PHE cc_start: 0.7497 (m-80) cc_final: 0.7131 (m-10) REVERT: A 296 ILE cc_start: 0.9143 (mm) cc_final: 0.8490 (pt) REVERT: A 298 PHE cc_start: 0.8742 (m-80) cc_final: 0.8508 (m-10) REVERT: A 492 LEU cc_start: 0.9134 (tp) cc_final: 0.8768 (tp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0412 time to fit residues: 4.0626 Evaluate side-chains 60 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.0000 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.112318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101129 restraints weight = 6155.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103188 restraints weight = 4068.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104736 restraints weight = 2934.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.105871 restraints weight = 2252.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106604 restraints weight = 1798.182| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2545 Z= 0.118 Angle : 0.647 7.933 3442 Z= 0.316 Chirality : 0.051 0.148 406 Planarity : 0.003 0.019 430 Dihedral : 5.142 20.852 342 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 aren not related in a simple way. whole: -0.89 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.85 (0.45), residues: 117 loop : -1.63 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.020 0.002 TYR A 47 PHE 0.018 0.002 PHE A 13 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2545) covalent geometry : angle 0.64726 ( 3442) hydrogen bonds : bond 0.03368 ( 57) hydrogen bonds : angle 6.91082 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.132 Fit side-chains REVERT: A 33 CYS cc_start: 0.8164 (m) cc_final: 0.7797 (m) REVERT: A 137 MET cc_start: 0.8475 (mpp) cc_final: 0.8266 (mpp) REVERT: A 273 PHE cc_start: 0.7519 (m-80) cc_final: 0.6544 (m-10) REVERT: A 296 ILE cc_start: 0.9161 (mm) cc_final: 0.8624 (pt) REVERT: A 298 PHE cc_start: 0.8785 (m-80) cc_final: 0.8489 (m-10) REVERT: A 319 LEU cc_start: 0.8918 (mt) cc_final: 0.8681 (mt) REVERT: A 492 LEU cc_start: 0.9016 (tp) cc_final: 0.8633 (tp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0444 time to fit residues: 3.9907 Evaluate side-chains 58 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.0000 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.3182 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.124347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.113328 restraints weight = 5961.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.115179 restraints weight = 4083.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116709 restraints weight = 3030.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117863 restraints weight = 2348.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118718 restraints weight = 1884.935| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2545 Z= 0.105 Angle : 0.626 8.181 3442 Z= 0.305 Chirality : 0.050 0.155 406 Planarity : 0.003 0.019 430 Dihedral : 4.838 21.491 342 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.86 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.74 (0.45), residues: 118 loop : -1.53 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.017 0.001 TYR A 47 PHE 0.019 0.002 PHE A 13 HIS 0.001 0.000 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2545) covalent geometry : angle 0.62598 ( 3442) hydrogen bonds : bond 0.03341 ( 57) hydrogen bonds : angle 6.66414 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.098 Fit side-chains REVERT: A 33 CYS cc_start: 0.7971 (m) cc_final: 0.7580 (m) REVERT: A 75 LEU cc_start: 0.8939 (tt) cc_final: 0.8667 (tt) REVERT: A 273 PHE cc_start: 0.7350 (m-80) cc_final: 0.6452 (m-10) REVERT: A 296 ILE cc_start: 0.9078 (mm) cc_final: 0.8489 (pt) REVERT: A 298 PHE cc_start: 0.8691 (m-80) cc_final: 0.8489 (m-10) REVERT: A 492 LEU cc_start: 0.9002 (tp) cc_final: 0.8584 (tp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0398 time to fit residues: 3.9215 Evaluate side-chains 62 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 0.0370 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.121558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109426 restraints weight = 6176.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.111676 restraints weight = 4031.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.113366 restraints weight = 2877.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114626 restraints weight = 2198.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.115476 restraints weight = 1751.189| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2545 Z= 0.123 Angle : 0.652 7.871 3442 Z= 0.316 Chirality : 0.051 0.189 406 Planarity : 0.003 0.019 430 Dihedral : 4.990 22.208 342 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 aren not related in a simple way. whole: -0.88 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.78 (0.44), residues: 118 loop : -1.59 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 286 TYR 0.017 0.002 TYR A 47 PHE 0.010 0.002 PHE A 39 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2545) covalent geometry : angle 0.65249 ( 3442) hydrogen bonds : bond 0.03328 ( 57) hydrogen bonds : angle 6.87660 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.075 Fit side-chains REVERT: A 33 CYS cc_start: 0.8045 (m) cc_final: 0.7770 (m) REVERT: A 75 LEU cc_start: 0.8889 (tt) cc_final: 0.8675 (tt) REVERT: A 273 PHE cc_start: 0.7548 (m-80) cc_final: 0.6677 (m-10) REVERT: A 296 ILE cc_start: 0.9166 (mm) cc_final: 0.8656 (pt) REVERT: A 298 PHE cc_start: 0.8717 (m-80) cc_final: 0.8434 (m-10) REVERT: A 319 LEU cc_start: 0.8887 (mt) cc_final: 0.8651 (mt) REVERT: A 481 MET cc_start: 0.7239 (ttp) cc_final: 0.7013 (ttm) REVERT: A 492 LEU cc_start: 0.9062 (tp) cc_final: 0.8673 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0452 time to fit residues: 4.1857 Evaluate side-chains 57 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.126063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.115057 restraints weight = 6055.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.117021 restraints weight = 4136.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118283 restraints weight = 3052.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119400 restraints weight = 2441.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120222 restraints weight = 1989.070| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2545 Z= 0.114 Angle : 0.652 8.423 3442 Z= 0.316 Chirality : 0.050 0.173 406 Planarity : 0.003 0.019 430 Dihedral : 5.032 22.946 342 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.93 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.77 (0.45), residues: 118 loop : -1.63 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.015 0.001 TYR A 47 PHE 0.022 0.002 PHE A 13 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2545) covalent geometry : angle 0.65191 ( 3442) hydrogen bonds : bond 0.03311 ( 57) hydrogen bonds : angle 7.01581 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.096 Fit side-chains REVERT: A 28 PHE cc_start: 0.8569 (p90) cc_final: 0.8323 (p90) REVERT: A 33 CYS cc_start: 0.7886 (m) cc_final: 0.7440 (m) REVERT: A 273 PHE cc_start: 0.7478 (m-80) cc_final: 0.6738 (m-10) REVERT: A 296 ILE cc_start: 0.9166 (mm) cc_final: 0.8622 (pt) REVERT: A 298 PHE cc_start: 0.8742 (m-80) cc_final: 0.8456 (m-10) REVERT: A 319 LEU cc_start: 0.8896 (mt) cc_final: 0.8678 (mt) REVERT: A 492 LEU cc_start: 0.9070 (tp) cc_final: 0.8674 (tp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0476 time to fit residues: 4.2298 Evaluate side-chains 64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 27 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102770 restraints weight = 6228.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.104575 restraints weight = 4193.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106125 restraints weight = 3110.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107238 restraints weight = 2391.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108072 restraints weight = 1916.705| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2545 Z= 0.116 Angle : 0.666 8.870 3442 Z= 0.318 Chirality : 0.050 0.174 406 Planarity : 0.003 0.019 430 Dihedral : 5.043 24.736 342 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.93 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.81 (0.46), residues: 116 loop : -1.64 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.014 0.001 TYR A 47 PHE 0.020 0.002 PHE A 13 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2545) covalent geometry : angle 0.66623 ( 3442) hydrogen bonds : bond 0.03281 ( 57) hydrogen bonds : angle 7.04318 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 622 Ramachandran restraints generated. 311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.101 Fit side-chains REVERT: A 33 CYS cc_start: 0.8046 (m) cc_final: 0.7522 (m) REVERT: A 273 PHE cc_start: 0.7418 (m-80) cc_final: 0.6609 (m-10) REVERT: A 296 ILE cc_start: 0.9143 (mm) cc_final: 0.8666 (pt) REVERT: A 298 PHE cc_start: 0.8735 (m-80) cc_final: 0.8412 (m-10) REVERT: A 319 LEU cc_start: 0.8923 (mt) cc_final: 0.8693 (mt) REVERT: A 431 ILE cc_start: 0.9446 (mt) cc_final: 0.9201 (mm) REVERT: A 492 LEU cc_start: 0.9077 (tp) cc_final: 0.8668 (tp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0455 time to fit residues: 4.1330 Evaluate side-chains 56 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8118 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.112782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102111 restraints weight = 6290.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.103985 restraints weight = 4284.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.105590 restraints weight = 3130.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.106618 restraints weight = 2396.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107447 restraints weight = 1924.369| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2545 Z= 0.126 Angle : 0.674 8.439 3442 Z= 0.326 Chirality : 0.050 0.190 406 Planarity : 0.003 0.019 430 Dihedral : 5.042 23.787 342 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.05 (0.45), residues: 311 helix: None (None), residues: 0 sheet: 0.68 (0.45), residues: 116 loop : -1.68 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.012 0.002 TYR A 47 PHE 0.024 0.002 PHE A 412 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2545) covalent geometry : angle 0.67379 ( 3442) hydrogen bonds : bond 0.03396 ( 57) hydrogen bonds : angle 7.04246 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 612.91 seconds wall clock time: 11 minutes 9.49 seconds (669.49 seconds total)