Starting phenix.real_space_refine on Fri Aug 22 13:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d6a_46591/08_2025/9d6a_46591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d6a_46591/08_2025/9d6a_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_46591/08_2025/9d6a_46591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d6a_46591/08_2025/9d6a_46591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d6a_46591/08_2025/9d6a_46591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d6a_46591/08_2025/9d6a_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-2.0-5787/lib/python3.9/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, 13 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4, 'water': 9} Link IDs: {None: 12} 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: 0.81, per 1000 atoms: 0.26 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: 0.27 Conformation dependent library (CDL) restraints added in 118.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.06 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: 0.32 Time building geometry restraints manager: 0.36 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 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.071 2.470 nonbonded pdb=" O ALA A 408 " pdb="NA NA A 602 " model vdw 2.099 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.151 2.470 nonbonded pdb=" O SER A 405 " pdb="NA NA A 602 " model vdw 2.154 2.470 ... (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: 1.820 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.420 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 aren 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 covalent geometry : bond 0.00316 ( 3137) covalent geometry : angle 0.48330 ( 4258) hydrogen bonds : bond 0.20355 ( 245) hydrogen bonds : angle 7.36062 ( 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 : 0.141 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.6553 time to fit residues: 38.8891 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 : 0.128 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.152532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119934 restraints weight = 849.913| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 0.74 r_work: 0.3199 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3137 Z= 0.159 Angle : 0.511 5.442 4258 Z= 0.274 Chirality : 0.040 0.158 542 Planarity : 0.004 0.029 518 Dihedral : 3.445 12.019 427 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.96 % Allowed : 16.27 % 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 aren not related in a simple way. whole: 1.79 (0.40), residues: 400 helix: 1.73 (0.28), residues: 306 sheet: 0.99 (1.25), residues: 18 loop : -0.94 (0.62), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.007 0.001 TYR A 97 PHE 0.009 0.001 PHE A 218 TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3137) covalent geometry : angle 0.51149 ( 4258) hydrogen bonds : bond 0.05442 ( 245) hydrogen bonds : angle 4.99542 ( 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 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.128 Fit side-chains REVERT: A 281 LYS cc_start: 0.7886 (tttt) cc_final: 0.7600 (ptmt) REVERT: A 346 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: A 421 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (mp) outliers start: 10 outliers final: 2 residues processed: 66 average time/residue: 0.5296 time to fit residues: 35.8596 Evaluate side-chains 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121942 restraints weight = 759.532| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 0.69 r_work: 0.3202 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1683 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= 0.138 Angle : 0.476 4.909 4258 Z= 0.254 Chirality : 0.039 0.150 542 Planarity : 0.004 0.027 518 Dihedral : 3.450 13.097 427 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 17.46 % Favored : 79.88 % 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: 1.95 (0.40), residues: 400 helix: 1.85 (0.28), residues: 309 sheet: 0.69 (1.23), residues: 18 loop : -0.93 (0.63), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.010 0.001 TYR A 373 PHE 0.010 0.001 PHE A 218 TRP 0.005 0.001 TRP A 256 HIS 0.000 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3137) covalent geometry : angle 0.47573 ( 4258) hydrogen bonds : bond 0.04789 ( 245) hydrogen bonds : angle 4.67833 ( 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 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.119 Fit side-chains REVERT: A 142 MET cc_start: 0.8176 (tpp) cc_final: 0.7959 (mmp) REVERT: A 205 MET cc_start: 0.8106 (ttt) cc_final: 0.7493 (tmt) REVERT: A 281 LYS cc_start: 0.7956 (tttt) cc_final: 0.7666 (ptmt) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.5915 time to fit residues: 38.8136 Evaluate side-chains 59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124020 restraints weight = 734.860| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.68 r_work: 0.3237 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1888 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= 0.118 Angle : 0.454 4.866 4258 Z= 0.240 Chirality : 0.038 0.146 542 Planarity : 0.003 0.029 518 Dihedral : 3.341 11.610 427 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.37 % Allowed : 18.34 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.41), residues: 400 helix: 1.94 (0.29), residues: 311 sheet: 0.57 (1.22), residues: 18 loop : -0.80 (0.65), 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 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3137) covalent geometry : angle 0.45434 ( 4258) hydrogen bonds : bond 0.04324 ( 245) hydrogen bonds : angle 4.50316 ( 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 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.095 Fit side-chains REVERT: A 142 MET cc_start: 0.8102 (tpp) cc_final: 0.7876 (mmp) REVERT: A 205 MET cc_start: 0.8093 (ttt) cc_final: 0.7480 (tmt) REVERT: A 281 LYS cc_start: 0.7902 (tttt) cc_final: 0.7638 (ptmt) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.4934 time to fit residues: 32.4958 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 10 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124312 restraints weight = 744.525| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 0.68 r_work: 0.3257 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1997 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= 0.117 Angle : 0.444 4.911 4258 Z= 0.236 Chirality : 0.038 0.144 542 Planarity : 0.003 0.029 518 Dihedral : 3.291 11.757 427 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 18.64 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.41), residues: 400 helix: 1.94 (0.29), residues: 313 sheet: 0.48 (1.22), residues: 18 loop : -0.77 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.009 0.001 TYR A 373 PHE 0.009 0.001 PHE A 218 TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3137) covalent geometry : angle 0.44421 ( 4258) hydrogen bonds : bond 0.04263 ( 245) hydrogen bonds : angle 4.45293 ( 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: 9 poor density : 61 time to evaluate : 0.122 Fit side-chains REVERT: A 205 MET cc_start: 0.8030 (ttt) cc_final: 0.7434 (tmt) REVERT: A 281 LYS cc_start: 0.7900 (tttt) cc_final: 0.7625 (ptmt) REVERT: A 419 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8263 (ttp) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.5419 time to fit residues: 37.2378 Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.154674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123438 restraints weight = 748.553| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.68 r_work: 0.3235 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3137 Z= 0.128 Angle : 0.469 5.342 4258 Z= 0.246 Chirality : 0.038 0.145 542 Planarity : 0.004 0.031 518 Dihedral : 3.299 11.914 427 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.25 % Allowed : 18.05 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.41), residues: 400 helix: 1.92 (0.29), residues: 312 sheet: 0.48 (1.22), residues: 18 loop : -0.63 (0.69), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.006 0.001 TYR A 97 PHE 0.010 0.001 PHE A 218 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3137) covalent geometry : angle 0.46865 ( 4258) hydrogen bonds : bond 0.04389 ( 245) hydrogen bonds : angle 4.48546 ( 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 71 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.138 Fit side-chains REVERT: A 205 MET cc_start: 0.8013 (ttt) cc_final: 0.7408 (tmt) REVERT: A 281 LYS cc_start: 0.7896 (tttt) cc_final: 0.7593 (ptmt) REVERT: A 311 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7333 (mtpm) REVERT: A 354 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7272 (pp) REVERT: A 419 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8260 (ttp) outliers start: 11 outliers final: 3 residues processed: 65 average time/residue: 0.5782 time to fit residues: 38.5476 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 : 0.114 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 34 optimal weight: 0.0020 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.0040 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.1600 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.158995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128388 restraints weight = 765.029| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.70 r_work: 0.3301 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3137 Z= 0.105 Angle : 0.440 4.782 4258 Z= 0.232 Chirality : 0.037 0.139 542 Planarity : 0.003 0.030 518 Dihedral : 3.180 11.235 427 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.48 % Allowed : 20.41 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.42), residues: 400 helix: 2.10 (0.29), residues: 318 sheet: 0.45 (1.21), residues: 18 loop : -0.42 (0.74), residues: 64 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 0.007 0.001 PHE A 218 TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 3137) covalent geometry : angle 0.44008 ( 4258) hydrogen bonds : bond 0.03806 ( 245) hydrogen bonds : angle 4.29679 ( 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 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.100 Fit side-chains REVERT: A 92 LEU cc_start: 0.7070 (tp) cc_final: 0.6610 (tm) REVERT: A 205 MET cc_start: 0.8071 (ttt) cc_final: 0.7470 (tmt) REVERT: A 281 LYS cc_start: 0.7827 (tttt) cc_final: 0.7542 (ptmt) REVERT: A 311 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7174 (mtpm) REVERT: A 352 LYS cc_start: 0.7525 (mttm) cc_final: 0.7280 (mtpm) REVERT: A 419 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8282 (ttp) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.4912 time to fit residues: 35.8515 Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.155641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124113 restraints weight = 776.574| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.72 r_work: 0.3223 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2208 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= 0.125 Angle : 0.479 5.885 4258 Z= 0.251 Chirality : 0.038 0.142 542 Planarity : 0.003 0.030 518 Dihedral : 3.228 11.862 427 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.48 % Allowed : 21.60 % 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 aren not related in a simple way. whole: 2.34 (0.41), residues: 400 helix: 2.05 (0.28), residues: 314 sheet: 0.36 (1.19), residues: 18 loop : -0.43 (0.74), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.006 0.001 TYR A 97 PHE 0.010 0.001 PHE A 218 TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3137) covalent geometry : angle 0.47857 ( 4258) hydrogen bonds : bond 0.04253 ( 245) hydrogen bonds : angle 4.40276 ( 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 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.077 Fit side-chains REVERT: A 281 LYS cc_start: 0.7822 (tttt) cc_final: 0.7509 (ptmt) REVERT: A 352 LYS cc_start: 0.7529 (mttm) cc_final: 0.7254 (mtpm) REVERT: A 419 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8282 (ttp) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 0.5614 time to fit residues: 38.6045 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 0.0060 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.0010 chunk 28 optimal weight: 0.8980 overall best weight: 0.5002 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.156704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125581 restraints weight = 779.426| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 0.70 r_work: 0.3280 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3137 Z= 0.118 Angle : 0.463 5.014 4258 Z= 0.244 Chirality : 0.038 0.144 542 Planarity : 0.003 0.029 518 Dihedral : 3.244 12.013 427 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 22.49 % 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 aren not related in a simple way. whole: 2.32 (0.41), residues: 400 helix: 2.04 (0.28), residues: 314 sheet: 0.32 (1.18), residues: 18 loop : -0.45 (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 0.009 0.001 PHE A 218 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3137) covalent geometry : angle 0.46256 ( 4258) hydrogen bonds : bond 0.04181 ( 245) hydrogen bonds : angle 4.41113 ( 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 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.072 Fit side-chains REVERT: A 92 LEU cc_start: 0.7104 (tp) cc_final: 0.6646 (tm) REVERT: A 281 LYS cc_start: 0.7840 (tttt) cc_final: 0.7526 (ptmt) REVERT: A 352 LYS cc_start: 0.7546 (mttm) cc_final: 0.7271 (mtpm) REVERT: A 419 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8312 (ttp) outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.5124 time to fit residues: 34.6795 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.154638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123561 restraints weight = 760.254| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 0.69 r_work: 0.3242 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2191 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= 0.127 Angle : 0.483 5.717 4258 Z= 0.253 Chirality : 0.039 0.145 542 Planarity : 0.003 0.030 518 Dihedral : 3.273 12.087 427 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.27 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 aren not related in a simple way. whole: 2.27 (0.41), residues: 400 helix: 2.00 (0.28), residues: 314 sheet: 0.19 (1.17), residues: 18 loop : -0.43 (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 0.010 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 covalent geometry : bond 0.00287 ( 3137) covalent geometry : angle 0.48328 ( 4258) hydrogen bonds : bond 0.04318 ( 245) hydrogen bonds : angle 4.46012 ( 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: 3 poor density : 63 time to evaluate : 0.076 Fit side-chains REVERT: A 281 LYS cc_start: 0.7833 (tttt) cc_final: 0.7516 (ptmt) REVERT: A 352 LYS cc_start: 0.7561 (mttm) cc_final: 0.7284 (mtpm) REVERT: A 419 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8296 (ttp) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.5172 time to fit residues: 33.9258 Evaluate side-chains 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- 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: 0.1980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.155417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124283 restraints weight = 779.393| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.70 r_work: 0.3275 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3137 Z= 0.116 Angle : 0.460 5.019 4258 Z= 0.243 Chirality : 0.038 0.144 542 Planarity : 0.003 0.030 518 Dihedral : 3.257 11.913 427 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.48 % Allowed : 23.08 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.41), residues: 400 helix: 2.05 (0.28), residues: 314 sheet: 0.17 (1.17), residues: 18 loop : -0.43 (0.74), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.010 0.001 TYR A 373 PHE 0.009 0.001 PHE A 218 TRP 0.007 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3137) covalent geometry : angle 0.46014 ( 4258) hydrogen bonds : bond 0.04146 ( 245) hydrogen bonds : angle 4.41932 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.03 seconds wall clock time: 23 minutes 49.52 seconds (1429.52 seconds total)