Starting phenix.real_space_refine on Wed Mar 5 17:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d69_46590/03_2025/9d69_46590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d69_46590/03_2025/9d69_46590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d69_46590/03_2025/9d69_46590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d69_46590/03_2025/9d69_46590.map" model { file = "/net/cci-nas-00/data/ceres_data/9d69_46590/03_2025/9d69_46590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d69_46590/03_2025/9d69_46590.cif" } resolution = 2.99 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= 0.142 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 22 5.16 5 Na 3 4.78 5 C 2055 2.51 5 N 500 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3132 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 11, 'TRANS': 400} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 30.766 23.748 24.903 1.00 69.67 S Time building chain proxies: 2.95, per 1000 atoms: 0.94 Number of scatterers: 3143 At special positions: 0 Unit cell: (59.4, 69.3, 77.55, 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 22 16.00 Na 3 11.00 O 562 8.00 N 500 7.00 C 2055 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: 0.81 Conformation dependent library (CDL) restraints added in 377.6 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 86.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 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 82 removed outlier: 3.517A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.734A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 removed outlier: 4.257A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.641A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.567A 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 230 removed outlier: 3.832A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.662A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.601A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.510A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.644A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.861A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.337A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 466 removed outlier: 4.002A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 removed outlier: 4.025A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 249 hydrogen bonds defined for protein. 744 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: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 938 1.34 - 1.45: 359 1.45 - 1.57: 1847 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3184 Sorted by residual: bond pdb=" N GLN A 413 " pdb=" CA GLN A 413 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.32e-02 5.74e+03 5.42e+00 bond pdb=" N ARG A 342 " pdb=" CA ARG A 342 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.72e+00 bond pdb=" N ALA A 414 " pdb=" CA ALA A 414 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.25e-02 6.40e+03 3.60e+00 bond pdb=" C VAL A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.34e-02 5.57e+03 3.00e+00 bond pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 1.233 1.216 0.017 1.19e-02 7.06e+03 2.01e+00 ... (remaining 3179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 4228 1.55 - 3.10: 68 3.10 - 4.64: 20 4.64 - 6.19: 4 6.19 - 7.74: 1 Bond angle restraints: 4321 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 121.56 118.09 3.47 1.16e+00 7.43e-01 8.94e+00 angle pdb=" CA ARG A 342 " pdb=" C ARG A 342 " pdb=" O ARG A 342 " ideal model delta sigma weight residual 120.82 118.10 2.72 1.05e+00 9.07e-01 6.72e+00 angle pdb=" CB MET A 255 " pdb=" CG MET A 255 " pdb=" SD MET A 255 " ideal model delta sigma weight residual 112.70 120.44 -7.74 3.00e+00 1.11e-01 6.66e+00 angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 111.71 108.77 2.94 1.15e+00 7.56e-01 6.52e+00 angle pdb=" CA MET A 255 " pdb=" CB MET A 255 " pdb=" CG MET A 255 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.66e+00 ... (remaining 4316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 1716 17.66 - 35.32: 127 35.32 - 52.97: 45 52.97 - 70.63: 10 70.63 - 88.29: 6 Dihedral angle restraints: 1904 sinusoidal: 721 harmonic: 1183 Sorted by residual: dihedral pdb=" CB GLU A 345 " pdb=" CG GLU A 345 " pdb=" CD GLU A 345 " pdb=" OE1 GLU A 345 " ideal model delta sinusoidal sigma weight residual 0.00 -88.29 88.29 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 469 " pdb=" CG GLU A 469 " pdb=" CD GLU A 469 " pdb=" OE1 GLU A 469 " ideal model delta sinusoidal sigma weight residual 0.00 -87.68 87.68 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB MET A 449 " pdb=" CG MET A 449 " pdb=" SD MET A 449 " pdb=" CE MET A 449 " ideal model delta sinusoidal sigma weight residual 60.00 119.52 -59.52 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 306 0.022 - 0.044: 126 0.044 - 0.067: 73 0.067 - 0.089: 36 0.089 - 0.111: 8 Chirality restraints: 549 Sorted by residual: chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.08e-01 chirality pdb=" CA VAL A 203 " pdb=" N VAL A 203 " pdb=" C VAL A 203 " pdb=" CB VAL A 203 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA ILE A 202 " pdb=" N ILE A 202 " pdb=" C ILE A 202 " pdb=" CB ILE A 202 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 546 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 445 " 0.256 9.50e-02 1.11e+02 1.15e-01 9.64e+00 pdb=" NE ARG A 445 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 445 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 445 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 445 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 342 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.29e+00 pdb=" NE ARG A 342 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 342 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 342 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 342 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 302 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.015 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 48 2.66 - 3.22: 3322 3.22 - 3.78: 4828 3.78 - 4.34: 6992 4.34 - 4.90: 11326 Nonbonded interactions: 26516 Sorted by model distance: nonbonded pdb=" O SER A 405 " pdb="NA NA A 602 " model vdw 2.096 2.470 nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.101 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.108 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.144 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.156 2.470 ... (remaining 26511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:11.870 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: 0.7988 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 0.048 3184 Z= 0.195 Angle : 0.549 7.740 4321 Z= 0.291 Chirality : 0.035 0.111 549 Planarity : 0.008 0.116 527 Dihedral : 15.992 88.291 1140 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 19.48 % Favored : 80.52 % 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: 0.78 (0.42), residues: 406 helix: 1.02 (0.30), residues: 318 sheet: -1.66 (1.10), residues: 18 loop : -0.87 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR A 373 ARG 0.022 0.001 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.8125 time to fit residues: 44.9248 Evaluate side-chains 44 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.184039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135459 restraints weight = 1342.414| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.15 r_work: 0.3407 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3184 Z= 0.245 Angle : 0.560 8.496 4321 Z= 0.297 Chirality : 0.039 0.131 549 Planarity : 0.004 0.025 527 Dihedral : 3.625 12.787 433 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.36 % Allowed : 16.57 % Favored : 79.07 % 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: 1.67 (0.41), residues: 406 helix: 1.54 (0.28), residues: 324 sheet: -1.51 (1.08), residues: 18 loop : -0.03 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.012 0.002 TYR A 285 ARG 0.003 0.001 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.357 Fit side-chains REVERT: A 252 GLN cc_start: 0.7878 (mt0) cc_final: 0.7665 (mt0) REVERT: A 290 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7604 (mm) REVERT: A 329 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.6148 (mpm) REVERT: A 445 ARG cc_start: 0.7420 (mpt180) cc_final: 0.7058 (mpt-90) REVERT: A 468 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7821 (mttt) outliers start: 15 outliers final: 5 residues processed: 65 average time/residue: 0.9858 time to fit residues: 66.2926 Evaluate side-chains 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 364 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.187732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139850 restraints weight = 1412.801| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.19 r_work: 0.3395 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3184 Z= 0.201 Angle : 0.507 5.626 4321 Z= 0.268 Chirality : 0.038 0.137 549 Planarity : 0.003 0.024 527 Dihedral : 3.619 17.173 433 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.07 % Allowed : 16.28 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.41), residues: 406 helix: 1.74 (0.28), residues: 323 sheet: -1.14 (1.11), residues: 18 loop : 0.08 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 19 HIS 0.002 0.001 HIS A 296 PHE 0.010 0.001 PHE A 240 TYR 0.010 0.002 TYR A 285 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.339 Fit side-chains REVERT: A 252 GLN cc_start: 0.7784 (mt0) cc_final: 0.7582 (mt0) REVERT: A 290 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7600 (mm) REVERT: A 310 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7189 (tpp80) REVERT: A 342 ARG cc_start: 0.6547 (ttp-110) cc_final: 0.6058 (mtm110) REVERT: A 445 ARG cc_start: 0.7250 (mpt180) cc_final: 0.6836 (mpt-90) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 1.0048 time to fit residues: 65.5502 Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.188954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140489 restraints weight = 1450.369| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.21 r_work: 0.3398 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3184 Z= 0.206 Angle : 0.503 5.970 4321 Z= 0.264 Chirality : 0.038 0.134 549 Planarity : 0.003 0.024 527 Dihedral : 3.636 20.551 433 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 19.48 % Favored : 77.03 % 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: 406 helix: 1.84 (0.28), residues: 324 sheet: -1.23 (1.12), residues: 18 loop : 0.04 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 19 HIS 0.002 0.001 HIS A 296 PHE 0.012 0.001 PHE A 240 TYR 0.010 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.369 Fit side-chains REVERT: A 290 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7611 (mm) REVERT: A 310 ARG cc_start: 0.7735 (mmt90) cc_final: 0.7187 (tpp80) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 0.8264 time to fit residues: 57.8257 Evaluate side-chains 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.0270 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.186145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136981 restraints weight = 1487.199| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.22 r_work: 0.3399 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3184 Z= 0.196 Angle : 0.497 5.368 4321 Z= 0.261 Chirality : 0.038 0.133 549 Planarity : 0.003 0.024 527 Dihedral : 3.627 21.844 433 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 21.22 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.41), residues: 406 helix: 1.86 (0.28), residues: 325 sheet: -1.15 (1.13), residues: 18 loop : 0.02 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.010 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.362 Fit side-chains REVERT: A 290 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 310 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7200 (tpp80) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.9044 time to fit residues: 57.4184 Evaluate side-chains 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.188328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138848 restraints weight = 1557.484| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.26 r_work: 0.3392 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3184 Z= 0.186 Angle : 0.493 5.199 4321 Z= 0.260 Chirality : 0.038 0.133 549 Planarity : 0.003 0.023 527 Dihedral : 3.627 23.159 433 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 21.51 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.41), residues: 406 helix: 1.91 (0.28), residues: 326 sheet: -1.03 (1.13), residues: 18 loop : 0.16 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.010 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.355 Fit side-chains REVERT: A 138 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6789 (p) REVERT: A 248 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7774 (mmm) REVERT: A 286 MET cc_start: 0.7258 (mtp) cc_final: 0.6957 (mtp) REVERT: A 290 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7633 (mm) REVERT: A 310 ARG cc_start: 0.7760 (mmt90) cc_final: 0.7219 (tpp80) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.8130 time to fit residues: 54.3167 Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.191811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143929 restraints weight = 1527.255| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.23 r_work: 0.3396 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3184 Z= 0.212 Angle : 0.513 5.861 4321 Z= 0.267 Chirality : 0.039 0.135 549 Planarity : 0.003 0.024 527 Dihedral : 3.680 25.114 433 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 21.51 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.20 (0.41), residues: 406 helix: 1.89 (0.28), residues: 326 sheet: -0.98 (1.12), residues: 18 loop : 0.08 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.013 0.001 PHE A 240 TYR 0.009 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.321 Fit side-chains REVERT: A 138 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6878 (p) REVERT: A 252 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: A 290 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7637 (mm) REVERT: A 310 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7209 (tpp80) REVERT: A 342 ARG cc_start: 0.6479 (ttp-110) cc_final: 0.6209 (mtm110) outliers start: 12 outliers final: 4 residues processed: 61 average time/residue: 0.8326 time to fit residues: 52.9240 Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.191448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.143419 restraints weight = 1616.454| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.28 r_work: 0.3452 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3184 Z= 0.149 Angle : 0.482 5.687 4321 Z= 0.253 Chirality : 0.038 0.134 549 Planarity : 0.003 0.023 527 Dihedral : 3.576 23.742 433 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.62 % Allowed : 22.97 % Favored : 74.42 % 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: 2.36 (0.41), residues: 406 helix: 2.07 (0.29), residues: 322 sheet: -0.86 (1.12), residues: 18 loop : -0.14 (0.69), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 256 HIS 0.001 0.001 HIS A 296 PHE 0.009 0.001 PHE A 218 TYR 0.009 0.001 TYR A 285 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.331 Fit side-chains REVERT: A 138 THR cc_start: 0.7260 (OUTLIER) cc_final: 0.6915 (p) REVERT: A 252 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7561 (mm-40) REVERT: A 290 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7561 (mm) REVERT: A 297 SER cc_start: 0.8937 (m) cc_final: 0.8707 (p) REVERT: A 310 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7237 (tpp80) REVERT: A 342 ARG cc_start: 0.6455 (ttp-110) cc_final: 0.6173 (mtm110) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.8497 time to fit residues: 53.9363 Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.194958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147579 restraints weight = 1565.344| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.25 r_work: 0.3428 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3184 Z= 0.211 Angle : 0.536 7.268 4321 Z= 0.274 Chirality : 0.039 0.131 549 Planarity : 0.003 0.024 527 Dihedral : 3.667 25.800 433 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.78 % Allowed : 22.67 % Favored : 73.55 % 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: 2.26 (0.41), residues: 406 helix: 1.98 (0.28), residues: 322 sheet: -0.81 (1.13), residues: 18 loop : -0.16 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.013 0.001 PHE A 240 TYR 0.008 0.001 TYR A 285 ARG 0.004 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.310 Fit side-chains REVERT: A 138 THR cc_start: 0.7260 (OUTLIER) cc_final: 0.6929 (p) REVERT: A 252 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7569 (mm-40) REVERT: A 290 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7636 (mm) REVERT: A 310 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7234 (tpp80) REVERT: A 342 ARG cc_start: 0.6552 (ttp-110) cc_final: 0.6262 (mtm110) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.8405 time to fit residues: 56.8489 Evaluate side-chains 65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.188626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139286 restraints weight = 1613.282| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.26 r_work: 0.3410 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3184 Z= 0.190 Angle : 0.556 11.483 4321 Z= 0.284 Chirality : 0.039 0.133 549 Planarity : 0.003 0.024 527 Dihedral : 3.723 25.924 433 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.91 % Allowed : 23.26 % Favored : 73.84 % 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: 2.06 (0.41), residues: 406 helix: 1.87 (0.29), residues: 323 sheet: -0.79 (1.14), residues: 18 loop : -0.43 (0.67), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.009 0.001 TYR A 285 ARG 0.003 0.000 ARG A 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.315 Fit side-chains REVERT: A 138 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6924 (p) REVERT: A 252 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7580 (mm-40) REVERT: A 290 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7612 (mm) REVERT: A 310 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7241 (tpp80) REVERT: A 342 ARG cc_start: 0.6436 (ttp-110) cc_final: 0.6137 (mtm110) REVERT: A 439 VAL cc_start: 0.7791 (t) cc_final: 0.7477 (p) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.9248 time to fit residues: 58.5629 Evaluate side-chains 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.0050 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.191061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142278 restraints weight = 1642.245| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.29 r_work: 0.3405 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3184 Z= 0.183 Angle : 0.543 9.337 4321 Z= 0.278 Chirality : 0.039 0.152 549 Planarity : 0.003 0.024 527 Dihedral : 3.693 26.253 433 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.33 % Allowed : 23.26 % Favored : 74.42 % 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: 2.13 (0.41), residues: 406 helix: 1.90 (0.29), residues: 322 sheet: -0.81 (1.14), residues: 18 loop : -0.25 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 PHE 0.011 0.001 PHE A 240 TYR 0.010 0.001 TYR A 285 ARG 0.002 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.91 seconds wall clock time: 48 minutes 42.12 seconds (2922.12 seconds total)