Starting phenix.real_space_refine on Mon Feb 10 22:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d6a_46591/02_2025/9d6a_46591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d6a_46591/02_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_46591/02_2025/9d6a_46591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d6a_46591/02_2025/9d6a_46591.map" model { file = "/net/cci-nas-00/data/ceres_data/9d6a_46591/02_2025/9d6a_46591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d6a_46591/02_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-5592/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: 3.18, per 1000 atoms: 1.02 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: 0.84 Conformation dependent library (CDL) restraints added in 380.1 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: 0.31 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: 0.90 Time building geometry restraints manager: 0.90 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: 1.150 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.030 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- 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 : 0.348 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.4217 time to fit residues: 84.5066 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 : 0.369 ------------------------------------------------------------------------------- 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: 0.3980 chunk 11 optimal weight: 0.7980 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 A 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.153133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121400 restraints weight = 781.100| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.70 r_work: 0.3221 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1406 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= 0.222 Angle : 0.506 5.383 4258 Z= 0.269 Chirality : 0.040 0.159 542 Planarity : 0.004 0.030 518 Dihedral : 3.461 13.005 427 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.55 % Allowed : 15.38 % 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: 1.82 (0.40), residues: 400 helix: 1.76 (0.28), residues: 306 sheet: 0.97 (1.25), residues: 18 loop : -0.97 (0.62), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.001 0.001 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.007 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 77 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.333 Fit side-chains REVERT: A 281 LYS cc_start: 0.7909 (tttt) cc_final: 0.7617 (ptmt) REVERT: A 421 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7465 (mp) outliers start: 12 outliers final: 3 residues processed: 70 average time/residue: 1.1648 time to fit residues: 83.9117 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 : 0.363 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.152489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121614 restraints weight = 714.097| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.65 r_work: 0.3204 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1651 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= 0.219 Angle : 0.484 5.038 4258 Z= 0.258 Chirality : 0.039 0.155 542 Planarity : 0.004 0.028 518 Dihedral : 3.456 12.946 427 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 17.75 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.29), residues: 309 sheet: 0.71 (1.22), residues: 18 loop : -0.96 (0.63), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 256 HIS 0.000 0.000 HIS A 41 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: 9 poor density : 58 time to evaluate : 0.332 Fit side-chains REVERT: A 205 MET cc_start: 0.8097 (ttt) cc_final: 0.7481 (tmt) REVERT: A 281 LYS cc_start: 0.7950 (tttt) cc_final: 0.7660 (ptmt) outliers start: 9 outliers final: 3 residues processed: 62 average time/residue: 1.3381 time to fit residues: 85.1859 Evaluate side-chains 57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.153014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121574 restraints weight = 727.811| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 0.68 r_work: 0.3192 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1693 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= 0.223 Angle : 0.481 4.981 4258 Z= 0.255 Chirality : 0.039 0.151 542 Planarity : 0.004 0.030 518 Dihedral : 3.446 12.011 427 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.25 % Allowed : 17.75 % 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: 1.87 (0.40), residues: 400 helix: 1.79 (0.28), residues: 309 sheet: 0.56 (1.20), residues: 18 loop : -0.91 (0.64), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.366 Fit side-chains REVERT: A 205 MET cc_start: 0.8117 (ttt) cc_final: 0.7500 (tmt) REVERT: A 281 LYS cc_start: 0.7903 (tttt) cc_final: 0.7598 (ptmt) REVERT: A 354 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7397 (pp) outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 1.2549 time to fit residues: 77.4703 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 : 0.383 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.154265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123013 restraints weight = 723.310| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.67 r_work: 0.3219 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1910 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= 0.187 Angle : 0.456 4.943 4258 Z= 0.243 Chirality : 0.038 0.148 542 Planarity : 0.004 0.030 518 Dihedral : 3.365 11.728 427 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 19.53 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.41), residues: 400 helix: 1.82 (0.29), residues: 313 sheet: 0.50 (1.20), residues: 18 loop : -0.86 (0.66), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.001 0.000 HIS A 296 PHE 0.009 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 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.354 Fit side-chains REVERT: A 205 MET cc_start: 0.8063 (ttt) cc_final: 0.7461 (tmt) REVERT: A 281 LYS cc_start: 0.7887 (tttt) cc_final: 0.7563 (ptmt) REVERT: A 354 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7288 (pp) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 1.1403 time to fit residues: 77.5219 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 : 0.355 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.155208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124037 restraints weight = 742.880| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.68 r_work: 0.3187 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1825 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= 0.228 Angle : 0.487 5.074 4258 Z= 0.257 Chirality : 0.039 0.149 542 Planarity : 0.004 0.033 518 Dihedral : 3.409 12.181 427 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.37 % Allowed : 20.41 % 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: 1.87 (0.41), residues: 400 helix: 1.75 (0.29), residues: 312 sheet: 0.45 (1.19), residues: 18 loop : -0.76 (0.67), residues: 70 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 0.011 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 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.344 Fit side-chains REVERT: A 205 MET cc_start: 0.8105 (ttt) cc_final: 0.7499 (tmt) REVERT: A 281 LYS cc_start: 0.7890 (tttt) cc_final: 0.7558 (ptmt) REVERT: A 354 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7394 (pp) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 1.3315 time to fit residues: 86.1399 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 : 0.335 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.0040 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.155387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124356 restraints weight = 753.290| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.69 r_work: 0.3260 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2111 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= 0.168 Angle : 0.460 4.993 4258 Z= 0.244 Chirality : 0.038 0.147 542 Planarity : 0.003 0.030 518 Dihedral : 3.301 11.840 427 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 21.30 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.07 (0.41), residues: 400 helix: 1.89 (0.29), residues: 314 sheet: 0.37 (1.17), residues: 18 loop : -0.72 (0.68), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 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 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.368 Fit side-chains REVERT: A 281 LYS cc_start: 0.7866 (tttt) cc_final: 0.7562 (ptmt) REVERT: A 419 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8268 (ttp) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 1.2636 time to fit residues: 85.7011 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.152885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121254 restraints weight = 760.665| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 0.70 r_work: 0.3196 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1976 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= 0.222 Angle : 0.498 5.941 4258 Z= 0.261 Chirality : 0.039 0.148 542 Planarity : 0.004 0.032 518 Dihedral : 3.372 12.346 427 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 21.60 % 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: 1.93 (0.41), residues: 400 helix: 1.77 (0.29), residues: 314 sheet: 0.29 (1.16), residues: 18 loop : -0.66 (0.70), 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 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.002 0.000 ARG A 445 *********************** 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 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.370 Fit side-chains REVERT: A 354 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7333 (pp) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 1.2900 time to fit residues: 83.4617 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 : 0.363 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.152935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121719 restraints weight = 767.704| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.69 r_work: 0.3257 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2049 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 : 0.485 5.087 4258 Z= 0.257 Chirality : 0.039 0.149 542 Planarity : 0.004 0.031 518 Dihedral : 3.368 12.192 427 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 21.60 % 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: 1.93 (0.41), residues: 400 helix: 1.78 (0.29), residues: 314 sheet: 0.22 (1.15), residues: 18 loop : -0.66 (0.69), 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 0.011 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 65 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.389 Fit side-chains REVERT: A 281 LYS cc_start: 0.7876 (tttt) cc_final: 0.7554 (ptmt) REVERT: A 419 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8229 (ttp) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 1.2600 time to fit residues: 80.3225 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 : 0.362 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.153151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122311 restraints weight = 748.082| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.67 r_work: 0.3211 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2016 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= 0.211 Angle : 0.502 7.692 4258 Z= 0.261 Chirality : 0.039 0.149 542 Planarity : 0.004 0.031 518 Dihedral : 3.368 12.211 427 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 22.19 % 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: 1.91 (0.41), residues: 400 helix: 1.76 (0.29), residues: 314 sheet: 0.24 (1.14), residues: 18 loop : -0.66 (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 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 ********************** REFINEMENT MACRO_CYCLE 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 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.360 Fit side-chains REVERT: A 281 LYS cc_start: 0.7862 (tttt) cc_final: 0.7541 (ptmt) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 1.2088 time to fit residues: 75.8750 Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.154153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123322 restraints weight = 783.817| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.69 r_work: 0.3237 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2198 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 : 0.469 5.025 4258 Z= 0.248 Chirality : 0.038 0.145 542 Planarity : 0.004 0.030 518 Dihedral : 3.303 11.907 427 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.12 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 (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: 1.86 (0.29), residues: 314 sheet: 0.30 (1.15), residues: 18 loop : -0.59 (0.70), 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 0.010 0.001 TYR A 373 ARG 0.002 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.19 seconds wall clock time: 51 minutes 55.47 seconds (3115.47 seconds total)