Starting phenix.real_space_refine on Wed Jul 1 21:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d6a_46591/07_2026/9d6a_46591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d6a_46591/07_2026/9d6a_46591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d6a_46591/07_2026/9d6a_46591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d6a_46591/07_2026/9d6a_46591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d6a_46591/07_2026/9d6a_46591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d6a_46591/07_2026/9d6a_46591.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 S 21 5.16 5 Na 3 4.78 5 C 2028 2.51 5 N 493 2.21 5 O 559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 3105 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 9 Ad-hoc single atom residues: {' NA': 3, ' HG': 1} Classifications: {'water': 9} Link IDs: {None: 8} Chain breaks: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 31.053 23.676 22.775 1.00 66.55 S ATOM 2858 SG CYS A 441 30.136 24.991 25.191 1.00 58.20 S Time building chain proxies: 0.70, per 1000 atoms: 0.23 Number of scatterers: 3105 At special positions: 0 Unit cell: (60.225, 68.475, 70.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 S 21 16.00 Na 3 11.00 O 559 8.00 N 493 7.00 C 2028 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: 0.25 Conformation dependent library (CDL) restraints added in 110.8 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 85.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.516A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 86 through 117 removed outlier: 4.113A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.624A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.594A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.605A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.609A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.529A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.506A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.254A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.421A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.691A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.667A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.797A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.538A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 245 hydrogen bonds defined for protein. 726 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: 0.44 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 638 1.33 - 1.45: 609 1.45 - 1.57: 1852 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 3137 Sorted by residual: bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.32e-02 5.74e+03 6.71e+00 bond pdb=" N MET A 142 " pdb=" CA MET A 142 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.78e+00 bond pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.21e-02 6.83e+03 4.43e+00 bond pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 1.233 1.212 0.020 1.16e-02 7.43e+03 3.08e+00 bond pdb=" N GLN A 413 " pdb=" CA GLN A 413 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.77e-02 3.19e+03 2.91e+00 ... (remaining 3132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 4074 0.95 - 1.90: 135 1.90 - 2.85: 27 2.85 - 3.81: 14 3.81 - 4.76: 8 Bond angle restraints: 4258 Sorted by residual: angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.34 117.94 3.40 1.14e+00 7.69e-01 8.89e+00 angle pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" O LEU A 303 " ideal model delta sigma weight residual 120.55 117.42 3.13 1.06e+00 8.90e-01 8.71e+00 angle pdb=" N GLN A 413 " pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " ideal model delta sigma weight residual 114.27 109.51 4.76 1.64e+00 3.72e-01 8.41e+00 angle pdb=" CA VAL A 86 " pdb=" C VAL A 86 " pdb=" N SER A 87 " ideal model delta sigma weight residual 116.60 120.36 -3.76 1.45e+00 4.76e-01 6.73e+00 angle pdb=" N MET A 142 " pdb=" CA MET A 142 " pdb=" C MET A 142 " ideal model delta sigma weight residual 111.36 108.73 2.63 1.09e+00 8.42e-01 5.82e+00 ... (remaining 4253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1660 16.84 - 33.68: 147 33.68 - 50.53: 51 50.53 - 67.37: 12 67.37 - 84.21: 3 Dihedral angle restraints: 1873 sinusoidal: 708 harmonic: 1165 Sorted by residual: dihedral pdb=" CG ARG A 447 " pdb=" CD ARG A 447 " pdb=" NE ARG A 447 " pdb=" CZ ARG A 447 " ideal model delta sinusoidal sigma weight residual 180.00 135.23 44.77 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA LYS A 249 " pdb=" CB LYS A 249 " pdb=" CG LYS A 249 " pdb=" CD LYS A 249 " ideal model delta sinusoidal sigma weight residual -180.00 -120.77 -59.23 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 75 " pdb=" CG MET A 75 " pdb=" SD MET A 75 " pdb=" CE MET A 75 " ideal model delta sinusoidal sigma weight residual 180.00 124.22 55.78 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 374 0.032 - 0.064: 121 0.064 - 0.095: 34 0.095 - 0.127: 11 0.127 - 0.159: 2 Chirality restraints: 542 Sorted by residual: chirality pdb=" CA ILE A 365 " pdb=" N ILE A 365 " pdb=" C ILE A 365 " pdb=" CB ILE A 365 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA MET A 142 " pdb=" N MET A 142 " pdb=" C MET A 142 " pdb=" CB MET A 142 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA VAL A 309 " pdb=" N VAL A 309 " pdb=" C VAL A 309 " pdb=" CB VAL A 309 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 539 not shown) Planarity restraints: 518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 302 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " 0.005 2.00e-02 2.50e+03 9.28e-03 8.61e-01 pdb=" C THR A 364 " -0.016 2.00e-02 2.50e+03 pdb=" O THR A 364 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE A 365 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 412 " 0.004 2.00e-02 2.50e+03 8.21e-03 6.74e-01 pdb=" C PRO A 412 " -0.014 2.00e-02 2.50e+03 pdb=" O PRO A 412 " 0.005 2.00e-02 2.50e+03 pdb=" N GLN A 413 " 0.005 2.00e-02 2.50e+03 ... (remaining 515 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 39 2.63 - 3.19: 2952 3.19 - 3.76: 5083 3.76 - 4.33: 7241 4.33 - 4.90: 11528 Nonbonded interactions: 26843 Sorted by model distance: nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.057 3.210 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.071 3.210 nonbonded pdb=" O ALA A 408 " pdb="NA NA A 602 " model vdw 2.099 3.210 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.151 3.210 nonbonded pdb=" O SER A 405 " pdb="NA NA A 602 " model vdw 2.154 3.210 ... (remaining 26838 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 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: 1.600 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.820 Find NCS groups from input model: 0.010 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3137 Z= 0.154 Angle : 0.483 4.756 4258 Z= 0.274 Chirality : 0.036 0.159 542 Planarity : 0.003 0.035 518 Dihedral : 15.562 84.209 1121 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 17.46 % Favored : 82.54 % 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: 1.00 (0.40), residues: 400 helix: 1.19 (0.29), residues: 298 sheet: 1.00 (1.23), residues: 18 loop : -1.17 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.009 0.001 TYR A 373 PHE 0.006 0.001 PHE A 218 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 3137) covalent geometry : angle 0.48330 / 0.27 ( 4258) hydrogen bonds : bond 0.20355 / 14.01 ( 245) hydrogen bonds : angle 7.36062 / 5.50 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.5102 time to fit residues: 30.3122 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 ASN A 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118264 restraints weight = 945.593| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.76 r_work: 0.3189 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3137 Z= 0.164 Angle : 0.527 5.463 4258 Z= 0.284 Chirality : 0.041 0.160 542 Planarity : 0.004 0.030 518 Dihedral : 3.525 11.963 427 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.25 % Allowed : 15.98 % Favored : 80.77 % 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: 1.65 (0.40), residues: 400 helix: 1.63 (0.28), residues: 306 sheet: 0.95 (1.25), residues: 18 loop : -0.97 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.006 0.001 TYR A 97 PHE 0.011 0.002 PHE A 218 TRP 0.005 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 3137) covalent geometry : angle 0.52697 / 0.28 ( 4258) hydrogen bonds : bond 0.05396 / 3.66 ( 245) hydrogen bonds : angle 5.00986 / 3.79 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.070 Fit side-chains REVERT: A 281 LYS cc_start: 0.7905 (tttt) cc_final: 0.7613 (ptmt) REVERT: A 346 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: A 421 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7510 (mp) outliers start: 11 outliers final: 2 residues processed: 69 average time/residue: 0.3671 time to fit residues: 26.0658 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 421 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122102 restraints weight = 1001.986| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.81 r_work: 0.3179 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3137 Z= 0.142 Angle : 0.492 4.963 4258 Z= 0.264 Chirality : 0.039 0.150 542 Planarity : 0.004 0.028 518 Dihedral : 3.522 11.948 427 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 17.75 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.40), residues: 400 helix: 1.76 (0.28), residues: 309 sheet: 0.66 (1.22), residues: 18 loop : -1.03 (0.65), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.010 0.001 TYR A 373 PHE 0.010 0.001 PHE A 218 TRP 0.006 0.001 TRP A 256 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 3137) covalent geometry : angle 0.49201 / 0.26 ( 4258) hydrogen bonds : bond 0.04858 / 3.28 ( 245) hydrogen bonds : angle 4.71042 / 3.55 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.072 Fit side-chains REVERT: A 142 MET cc_start: 0.8189 (tpp) cc_final: 0.7988 (mmp) REVERT: A 205 MET cc_start: 0.8205 (ttt) cc_final: 0.7589 (tmt) REVERT: A 281 LYS cc_start: 0.7949 (tttt) cc_final: 0.7651 (ptmt) REVERT: A 354 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7428 (pp) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.4794 time to fit residues: 32.4242 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122403 restraints weight = 921.827| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.75 r_work: 0.3243 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3137 Z= 0.116 Angle : 0.460 5.005 4258 Z= 0.242 Chirality : 0.038 0.145 542 Planarity : 0.003 0.028 518 Dihedral : 3.432 12.102 427 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.85 % Allowed : 17.16 % Favored : 78.99 % 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: 2.06 (0.41), residues: 400 helix: 1.92 (0.28), residues: 311 sheet: 0.62 (1.20), residues: 18 loop : -0.91 (0.67), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.006 0.001 TYR A 97 PHE 0.008 0.001 PHE A 218 TRP 0.007 0.001 TRP A 256 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 3137) covalent geometry : angle 0.45986 / 0.24 ( 4258) hydrogen bonds : bond 0.04236 / 2.84 ( 245) hydrogen bonds : angle 4.51328 / 3.39 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.084 Fit side-chains REVERT: A 142 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7823 (mmp) REVERT: A 205 MET cc_start: 0.8167 (ttt) cc_final: 0.7547 (tmt) REVERT: A 281 LYS cc_start: 0.7895 (tttt) cc_final: 0.7612 (ptmt) outliers start: 13 outliers final: 4 residues processed: 71 average time/residue: 0.4246 time to fit residues: 30.9615 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122254 restraints weight = 881.508| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.75 r_work: 0.3190 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3137 Z= 0.147 Angle : 0.490 4.979 4258 Z= 0.261 Chirality : 0.039 0.148 542 Planarity : 0.004 0.032 518 Dihedral : 3.500 12.364 427 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.25 % Allowed : 18.93 % Favored : 77.81 % 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: 1.84 (0.41), residues: 400 helix: 1.75 (0.29), residues: 312 sheet: 0.48 (1.21), residues: 18 loop : -0.92 (0.68), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.011 0.001 TYR A 373 PHE 0.011 0.002 PHE A 218 TRP 0.004 0.001 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3137) covalent geometry : angle 0.48969 / 0.26 ( 4258) hydrogen bonds : bond 0.04720 / 3.18 ( 245) hydrogen bonds : angle 4.60974 / 3.46 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.100 Fit side-chains REVERT: A 205 MET cc_start: 0.8155 (ttt) cc_final: 0.7546 (tmt) REVERT: A 346 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: A 354 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7397 (pp) REVERT: A 419 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8260 (ttp) outliers start: 11 outliers final: 3 residues processed: 65 average time/residue: 0.4398 time to fit residues: 29.3931 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122990 restraints weight = 895.363| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.73 r_work: 0.3223 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3137 Z= 0.119 Angle : 0.477 6.639 4258 Z= 0.249 Chirality : 0.038 0.147 542 Planarity : 0.004 0.030 518 Dihedral : 3.415 12.444 427 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.96 % Allowed : 19.53 % Favored : 77.51 % 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 (0.41), residues: 400 helix: 1.86 (0.29), residues: 314 sheet: 0.41 (1.17), residues: 18 loop : -0.82 (0.70), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 315 TYR 0.006 0.001 TYR A 97 PHE 0.009 0.001 PHE A 218 TRP 0.006 0.001 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3137) covalent geometry : angle 0.47674 / 0.25 ( 4258) hydrogen bonds : bond 0.04272 / 2.86 ( 245) hydrogen bonds : angle 4.46069 / 3.34 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.075 Fit side-chains REVERT: A 281 LYS cc_start: 0.7866 (tttt) cc_final: 0.7555 (ptmt) REVERT: A 311 LYS cc_start: 0.7534 (mtpt) cc_final: 0.7317 (mtpm) REVERT: A 419 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8278 (ttp) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.4827 time to fit residues: 33.1085 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.0000 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124158 restraints weight = 919.632| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 0.77 r_work: 0.3205 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3137 Z= 0.126 Angle : 0.483 5.415 4258 Z= 0.254 Chirality : 0.038 0.148 542 Planarity : 0.004 0.031 518 Dihedral : 3.411 12.223 427 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 20.71 % Favored : 77.51 % 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: 2.02 (0.41), residues: 400 helix: 1.87 (0.29), residues: 312 sheet: 0.26 (1.14), residues: 18 loop : -0.71 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.010 0.001 TYR A 373 PHE 0.016 0.001 PHE A 99 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 3137) covalent geometry : angle 0.48329 / 0.25 ( 4258) hydrogen bonds : bond 0.04358 / 2.91 ( 245) hydrogen bonds : angle 4.47227 / 3.34 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.115 Fit side-chains REVERT: A 311 LYS cc_start: 0.7586 (mtpt) cc_final: 0.7371 (mtpm) REVERT: A 419 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8296 (ttp) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.4897 time to fit residues: 33.1378 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121759 restraints weight = 972.891| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 0.79 r_work: 0.3210 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3137 Z= 0.122 Angle : 0.486 5.054 4258 Z= 0.253 Chirality : 0.038 0.147 542 Planarity : 0.004 0.030 518 Dihedral : 3.407 12.115 427 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.48 % Allowed : 21.30 % Favored : 77.22 % 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: 2.02 (0.41), residues: 400 helix: 1.84 (0.28), residues: 316 sheet: 0.19 (1.14), residues: 18 loop : -0.68 (0.74), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.006 0.001 TYR A 97 PHE 0.009 0.001 PHE A 218 TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3137) covalent geometry : angle 0.48584 / 0.25 ( 4258) hydrogen bonds : bond 0.04280 / 2.86 ( 245) hydrogen bonds : angle 4.44330 / 3.32 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.113 Fit side-chains REVERT: A 205 MET cc_start: 0.8118 (ttm) cc_final: 0.7836 (ttt) REVERT: A 419 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8292 (ttp) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.4465 time to fit residues: 29.8257 Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.0070 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.151504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121167 restraints weight = 979.311| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 0.79 r_work: 0.3202 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3137 Z= 0.128 Angle : 0.485 5.043 4258 Z= 0.255 Chirality : 0.038 0.146 542 Planarity : 0.004 0.031 518 Dihedral : 3.425 12.229 427 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.78 % Allowed : 21.30 % Favored : 76.92 % 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: 1.99 (0.41), residues: 400 helix: 1.83 (0.29), residues: 314 sheet: 0.15 (1.13), residues: 18 loop : -0.65 (0.74), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.010 0.001 TYR A 373 PHE 0.018 0.001 PHE A 99 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3137) covalent geometry : angle 0.48535 / 0.25 ( 4258) hydrogen bonds : bond 0.04373 / 2.93 ( 245) hydrogen bonds : angle 4.47699 / 3.34 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.071 Fit side-chains REVERT: A 354 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7240 (pp) REVERT: A 419 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8286 (ttp) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.4251 time to fit residues: 27.4723 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122106 restraints weight = 934.996| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.77 r_work: 0.3227 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3137 Z= 0.122 Angle : 0.496 6.721 4258 Z= 0.257 Chirality : 0.039 0.146 542 Planarity : 0.004 0.030 518 Dihedral : 3.408 12.248 427 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.48 % Allowed : 21.30 % Favored : 77.22 % 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 (0.41), residues: 400 helix: 1.86 (0.28), residues: 314 sheet: 0.21 (1.13), residues: 18 loop : -0.63 (0.74), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.006 0.001 TYR A 97 PHE 0.009 0.001 PHE A 218 TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3137) covalent geometry : angle 0.49622 / 0.26 ( 4258) hydrogen bonds : bond 0.04279 / 2.86 ( 245) hydrogen bonds : angle 4.45048 / 3.32 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.122 Fit side-chains REVERT: A 205 MET cc_start: 0.8138 (ttm) cc_final: 0.7829 (ttt) REVERT: A 419 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8283 (ttp) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.5023 time to fit residues: 32.5349 Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 0.0270 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123637 restraints weight = 933.552| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 0.77 r_work: 0.3243 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3137 Z= 0.114 Angle : 0.472 5.031 4258 Z= 0.246 Chirality : 0.038 0.144 542 Planarity : 0.003 0.030 518 Dihedral : 3.376 12.601 427 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.89 % Allowed : 22.78 % Favored : 76.33 % 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: 2.09 (0.41), residues: 400 helix: 1.87 (0.28), residues: 316 sheet: 0.26 (1.13), residues: 18 loop : -0.61 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.012 0.001 TYR A 373 PHE 0.019 0.001 PHE A 99 TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 3137) covalent geometry : angle 0.47166 / 0.25 ( 4258) hydrogen bonds : bond 0.04136 / 2.76 ( 245) hydrogen bonds : angle 4.41539 / 3.28 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.04 seconds wall clock time: 20 minutes 33.54 seconds (1233.54 seconds total)