Starting phenix.real_space_refine on Wed Mar 5 17:33:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d6a_46591/03_2025/9d6a_46591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d6a_46591/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d6a_46591/03_2025/9d6a_46591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d6a_46591/03_2025/9d6a_46591.map" model { file = "/net/cci-nas-00/data/ceres_data/9d6a_46591/03_2025/9d6a_46591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d6a_46591/03_2025/9d6a_46591.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.76, per 1000 atoms: 0.89 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: 0.86 Conformation dependent library (CDL) restraints added in 331.0 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: 0.29 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: 0.92 Time building geometry restraints manager: 0.98 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: 1.490 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.610 Find NCS groups from input model: 0.040 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- 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= 0.206 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.006 0.001 PHE A 218 TYR 0.009 0.001 TYR A 373 ARG 0.002 0.000 ARG A 61 *********************** 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 : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.4002 time to fit residues: 83.3062 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.151869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119929 restraints weight = 820.256| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 0.71 r_work: 0.3215 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1386 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= 0.219 Angle : 0.502 5.393 4258 Z= 0.268 Chirality : 0.040 0.157 542 Planarity : 0.004 0.029 518 Dihedral : 3.446 13.043 427 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.25 % Allowed : 15.68 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.40), residues: 400 helix: 1.78 (0.28), residues: 306 sheet: 0.98 (1.25), residues: 18 loop : -0.94 (0.62), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.001 0.001 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** 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 75 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.316 Fit side-chains REVERT: A 281 LYS cc_start: 0.7912 (tttt) cc_final: 0.7615 (ptmt) REVERT: A 421 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7473 (mp) outliers start: 11 outliers final: 3 residues processed: 68 average time/residue: 1.3771 time to fit residues: 96.1557 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 : 0.352 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 overall best weight: 0.7544 ------------------------------------------------------------------------------- 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 = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122080 restraints weight = 730.195| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 0.68 r_work: 0.3199 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3137 Z= 0.217 Angle : 0.480 4.942 4258 Z= 0.256 Chirality : 0.039 0.155 542 Planarity : 0.004 0.027 518 Dihedral : 3.451 12.955 427 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.37 % Allowed : 17.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.40), residues: 400 helix: 1.79 (0.28), residues: 311 sheet: 0.69 (1.22), residues: 18 loop : -0.88 (0.64), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 256 HIS 0.000 0.000 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.010 0.001 TYR A 373 ARG 0.001 0.000 ARG A 447 *********************** 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.361 Fit side-chains REVERT: A 142 MET cc_start: 0.8204 (tpp) cc_final: 0.7987 (mmp) REVERT: A 205 MET cc_start: 0.8115 (ttt) cc_final: 0.7499 (tmt) REVERT: A 281 LYS cc_start: 0.7951 (tttt) cc_final: 0.7662 (ptmt) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 1.3413 time to fit residues: 86.8022 Evaluate side-chains 58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.152479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120833 restraints weight = 742.450| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 0.69 r_work: 0.3199 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3137 Z= 0.226 Angle : 0.483 5.011 4258 Z= 0.257 Chirality : 0.039 0.151 542 Planarity : 0.004 0.030 518 Dihedral : 3.448 12.050 427 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.96 % Allowed : 18.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.40), residues: 400 helix: 1.81 (0.29), residues: 309 sheet: 0.51 (1.21), residues: 18 loop : -0.90 (0.64), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** 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 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.324 Fit side-chains REVERT: A 205 MET cc_start: 0.8117 (ttt) cc_final: 0.7495 (tmt) REVERT: A 281 LYS cc_start: 0.7894 (tttt) cc_final: 0.7586 (ptmt) REVERT: A 354 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7406 (pp) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 1.1977 time to fit residues: 73.9382 Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 309 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.0040 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124272 restraints weight = 738.379| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.69 r_work: 0.3281 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1952 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= 0.169 Angle : 0.447 4.925 4258 Z= 0.238 Chirality : 0.038 0.146 542 Planarity : 0.003 0.030 518 Dihedral : 3.331 11.517 427 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.96 % Allowed : 18.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.41), residues: 400 helix: 1.90 (0.29), residues: 313 sheet: 0.40 (1.19), residues: 18 loop : -0.84 (0.66), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.010 0.001 TYR A 373 ARG 0.001 0.000 ARG A 315 *********************** 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 71 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.351 Fit side-chains REVERT: A 205 MET cc_start: 0.8057 (ttt) cc_final: 0.7438 (tmt) REVERT: A 281 LYS cc_start: 0.7916 (tttt) cc_final: 0.7612 (ptmt) REVERT: A 419 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8196 (ttp) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 1.2222 time to fit residues: 81.7029 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 : 0.351 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.153933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122665 restraints weight = 750.911| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.68 r_work: 0.3194 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1870 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= 0.230 Angle : 0.487 5.222 4258 Z= 0.256 Chirality : 0.039 0.150 542 Planarity : 0.004 0.033 518 Dihedral : 3.385 12.153 427 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.66 % Allowed : 18.93 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.41), residues: 400 helix: 1.80 (0.29), residues: 312 sheet: 0.26 (1.16), residues: 18 loop : -0.70 (0.67), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** 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 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.317 Fit side-chains REVERT: A 281 LYS cc_start: 0.7905 (tttt) cc_final: 0.7575 (ptmt) REVERT: A 354 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7376 (pp) REVERT: A 419 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8199 (ttp) outliers start: 9 outliers final: 3 residues processed: 64 average time/residue: 1.2365 time to fit residues: 81.2858 Evaluate side-chains 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 overall best weight: 0.3884 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.155709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124693 restraints weight = 753.607| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 0.70 r_work: 0.3262 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2115 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= 0.165 Angle : 0.458 4.985 4258 Z= 0.243 Chirality : 0.038 0.147 542 Planarity : 0.003 0.030 518 Dihedral : 3.278 11.824 427 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.07 % Allowed : 20.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.41), residues: 400 helix: 1.93 (0.29), residues: 314 sheet: 0.19 (1.14), residues: 18 loop : -0.62 (0.70), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.008 0.001 PHE A 218 TYR 0.011 0.001 TYR A 373 ARG 0.001 0.000 ARG A 315 *********************** 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 71 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.328 Fit side-chains REVERT: A 281 LYS cc_start: 0.7864 (tttt) cc_final: 0.7558 (ptmt) REVERT: A 419 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8264 (ttp) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 1.2103 time to fit residues: 84.5378 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 : 0.320 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.153921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122717 restraints weight = 761.160| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 0.69 r_work: 0.3229 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2107 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= 0.187 Angle : 0.481 6.042 4258 Z= 0.251 Chirality : 0.038 0.145 542 Planarity : 0.004 0.031 518 Dihedral : 3.284 12.102 427 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 21.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.41), residues: 400 helix: 1.90 (0.29), residues: 314 sheet: 0.17 (1.14), residues: 18 loop : -0.55 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 447 *********************** 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.315 Fit side-chains REVERT: A 281 LYS cc_start: 0.7890 (tttt) cc_final: 0.7575 (ptmt) REVERT: A 354 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7233 (pp) REVERT: A 419 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8271 (ttp) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 1.1907 time to fit residues: 78.3303 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 : 0.356 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.0030 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.155218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124011 restraints weight = 778.638| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 0.74 r_work: 0.3229 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2160 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= 0.175 Angle : 0.466 5.019 4258 Z= 0.247 Chirality : 0.038 0.145 542 Planarity : 0.003 0.030 518 Dihedral : 3.271 12.053 427 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.48 % Allowed : 21.89 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.41), residues: 400 helix: 1.94 (0.29), residues: 314 sheet: 0.09 (1.14), residues: 18 loop : -0.53 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.012 0.001 TYR A 373 ARG 0.001 0.000 ARG A 447 *********************** 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: 5 poor density : 63 time to evaluate : 0.352 Fit side-chains REVERT: A 281 LYS cc_start: 0.7821 (tttt) cc_final: 0.7493 (ptmt) REVERT: A 419 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8211 (ttp) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 1.2074 time to fit residues: 80.6502 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 : 0.316 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.0020 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.153347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122181 restraints weight = 754.786| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.69 r_work: 0.3222 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2064 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= 0.210 Angle : 0.493 5.628 4258 Z= 0.258 Chirality : 0.039 0.148 542 Planarity : 0.004 0.031 518 Dihedral : 3.332 12.397 427 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 22.78 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.41), residues: 400 helix: 1.82 (0.29), residues: 314 sheet: 0.11 (1.13), residues: 18 loop : -0.55 (0.71), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 ********************** 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: 4 poor density : 62 time to evaluate : 0.460 Fit side-chains REVERT: A 419 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8250 (ttp) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 1.2458 time to fit residues: 80.6234 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 : 0.313 ------------------------------------------------------------------------------- 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 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.155649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124544 restraints weight = 778.653| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.70 r_work: 0.3275 rms_B_bonded: 1.33 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: 0.2203 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= 0.170 Angle : 0.463 5.014 4258 Z= 0.245 Chirality : 0.038 0.144 542 Planarity : 0.003 0.030 518 Dihedral : 3.273 11.982 427 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 22.78 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.41), residues: 400 helix: 1.93 (0.28), residues: 314 sheet: 0.14 (1.14), residues: 18 loop : -0.51 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.011 0.001 TYR A 373 ARG 0.001 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.30 seconds wall clock time: 52 minutes 40.77 seconds (3160.77 seconds total)