Starting phenix.real_space_refine on Wed Jul 1 21:46:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d69_46590/07_2026/9d69_46590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d69_46590/07_2026/9d69_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_46590/07_2026/9d69_46590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d69_46590/07_2026/9d69_46590.map" model { file = "/net/cci-nas-00/data/ceres_data/9d69_46590/07_2026/9d69_46590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d69_46590/07_2026/9d69_46590.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.142 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' NA': 3, ' HG': 1} Chain breaks: 4 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: 0.91, per 1000 atoms: 0.29 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: 0.24 Conformation dependent library (CDL) restraints added in 74.5 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: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 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: 0.38 Time building geometry restraints manager: 0.31 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 3.210 nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.101 3.210 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.108 3.210 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.144 3.210 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.156 3.210 ... (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: 0.010 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.910 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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= 0.141 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.022 0.001 ARG A 445 TYR 0.011 0.001 TYR A 373 PHE 0.013 0.001 PHE A 341 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 3184) covalent geometry : angle 0.54914 / 0.29 ( 4321) hydrogen bonds : bond 0.23834 / 16.22 ( 249) hydrogen bonds : angle 8.47065 / 6.14 ( 744) *********************** 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 : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3095 time to fit residues: 17.1601 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 : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 296 HIS A 393 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.184858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136512 restraints weight = 1365.272| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.15 r_work: 0.3378 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3184 Z= 0.163 Angle : 0.569 8.441 4321 Z= 0.302 Chirality : 0.039 0.128 549 Planarity : 0.004 0.025 527 Dihedral : 3.744 12.939 433 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.65 % Allowed : 16.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.41), residues: 406 helix: 1.50 (0.28), residues: 324 sheet: -1.48 (1.08), residues: 18 loop : -0.05 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 447 TYR 0.012 0.002 TYR A 285 PHE 0.013 0.002 PHE A 341 TRP 0.003 0.001 TRP A 19 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3184) covalent geometry : angle 0.56853 / 0.30 ( 4321) hydrogen bonds : bond 0.04889 / 3.43 ( 249) hydrogen bonds : angle 5.39828 / 4.03 ( 744) *********************** 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 72 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.112 Fit side-chains REVERT: A 252 GLN cc_start: 0.7865 (mt0) cc_final: 0.7652 (mt0) REVERT: A 290 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7575 (mm) REVERT: A 329 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6085 (mpm) REVERT: A 445 ARG cc_start: 0.7058 (mpt180) cc_final: 0.6598 (mpt-90) REVERT: A 468 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7847 (mttt) outliers start: 16 outliers final: 5 residues processed: 65 average time/residue: 0.3728 time to fit residues: 25.0837 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 : 0.113 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4071 r_free = 0.4071 target = 0.190555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143367 restraints weight = 1342.300| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.15 r_work: 0.3399 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3184 Z= 0.135 Angle : 0.504 5.683 4321 Z= 0.269 Chirality : 0.039 0.132 549 Planarity : 0.004 0.024 527 Dihedral : 3.746 17.775 433 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.07 % Allowed : 16.57 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.41), residues: 406 helix: 1.70 (0.28), residues: 323 sheet: -1.14 (1.10), residues: 18 loop : 0.03 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 447 TYR 0.010 0.002 TYR A 285 PHE 0.010 0.001 PHE A 240 TRP 0.002 0.000 TRP A 256 HIS 0.001 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3184) covalent geometry : angle 0.50417 / 0.27 ( 4321) hydrogen bonds : bond 0.04198 / 2.98 ( 249) hydrogen bonds : angle 4.92056 / 3.67 ( 744) *********************** 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 : 0.123 Fit side-chains REVERT: A 252 GLN cc_start: 0.7780 (mt0) cc_final: 0.7577 (mt0) REVERT: A 290 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7589 (mm) REVERT: A 310 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7178 (tpp80) REVERT: A 342 ARG cc_start: 0.6546 (ttp-110) cc_final: 0.6057 (mtm110) REVERT: A 445 ARG cc_start: 0.6719 (mpt180) cc_final: 0.6218 (mpt-90) outliers start: 14 outliers final: 5 residues processed: 63 average time/residue: 0.3511 time to fit residues: 22.9023 Evaluate side-chains 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN 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 0 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 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 = 0.4015 r_free = 0.4015 target = 0.185449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136497 restraints weight = 1286.158| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.13 r_work: 0.3350 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3184 Z= 0.228 Angle : 0.586 7.306 4321 Z= 0.307 Chirality : 0.042 0.139 549 Planarity : 0.004 0.027 527 Dihedral : 4.008 27.168 433 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.36 % Allowed : 19.48 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.40), residues: 406 helix: 1.28 (0.28), residues: 329 sheet: -1.44 (1.11), residues: 18 loop : -0.47 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.010 0.002 TYR A 373 PHE 0.018 0.002 PHE A 240 TRP 0.002 0.001 TRP A 256 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 ( 3184) covalent geometry : angle 0.58647 / 0.31 ( 4321) hydrogen bonds : bond 0.04721 / 3.37 ( 249) hydrogen bonds : angle 5.07191 / 3.78 ( 744) *********************** 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 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.120 Fit side-chains REVERT: A 290 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7632 (mm) REVERT: A 310 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7213 (tpp80) REVERT: A 468 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7788 (mttm) outliers start: 15 outliers final: 6 residues processed: 62 average time/residue: 0.3724 time to fit residues: 23.9551 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 : 0.064 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 366 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.186852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138443 restraints weight = 1314.974| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.14 r_work: 0.3423 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2647 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= 0.140 Angle : 0.505 6.153 4321 Z= 0.269 Chirality : 0.039 0.130 549 Planarity : 0.004 0.025 527 Dihedral : 3.871 25.854 433 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.20 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.41), residues: 406 helix: 1.59 (0.28), residues: 324 sheet: -1.42 (1.14), residues: 18 loop : -0.04 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.011 0.001 TYR A 285 PHE 0.012 0.001 PHE A 240 TRP 0.002 0.000 TRP A 256 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 3184) covalent geometry : angle 0.50508 / 0.27 ( 4321) hydrogen bonds : bond 0.04001 / 2.83 ( 249) hydrogen bonds : angle 4.85183 / 3.62 ( 744) *********************** 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 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.121 Fit side-chains REVERT: A 290 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7625 (mm) REVERT: A 310 ARG cc_start: 0.7745 (mmt90) cc_final: 0.7213 (tpp80) REVERT: A 445 ARG cc_start: 0.6890 (mpt180) cc_final: 0.6412 (mpt-90) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.3618 time to fit residues: 23.6142 Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN 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 36 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4095 r_free = 0.4095 target = 0.192772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145519 restraints weight = 1284.004| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.13 r_work: 0.3417 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2775 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= 0.129 Angle : 0.500 5.632 4321 Z= 0.265 Chirality : 0.039 0.132 549 Planarity : 0.004 0.025 527 Dihedral : 3.832 26.226 433 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.20 % Allowed : 21.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.41), residues: 406 helix: 1.70 (0.28), residues: 326 sheet: -1.07 (1.16), residues: 18 loop : -0.16 (0.71), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.010 0.001 TYR A 285 PHE 0.010 0.001 PHE A 240 TRP 0.001 0.000 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 3184) covalent geometry : angle 0.50037 / 0.27 ( 4321) hydrogen bonds : bond 0.03823 / 2.72 ( 249) hydrogen bonds : angle 4.71359 / 3.51 ( 744) *********************** 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: 11 poor density : 58 time to evaluate : 0.121 Fit side-chains REVERT: A 138 THR cc_start: 0.7226 (OUTLIER) cc_final: 0.6868 (p) REVERT: A 290 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7587 (mm) REVERT: A 310 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7220 (tpp80) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.3499 time to fit residues: 23.6103 Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.068 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4033 r_free = 0.4033 target = 0.187513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139802 restraints weight = 1291.837| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.12 r_work: 0.3409 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3184 Z= 0.164 Angle : 0.544 6.115 4321 Z= 0.285 Chirality : 0.040 0.135 549 Planarity : 0.004 0.026 527 Dihedral : 3.941 28.999 433 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.65 % Allowed : 21.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.41), residues: 406 helix: 1.63 (0.28), residues: 325 sheet: -1.09 (1.13), residues: 18 loop : 0.06 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.010 0.001 TYR A 285 PHE 0.015 0.002 PHE A 240 TRP 0.002 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 3184) covalent geometry : angle 0.54435 / 0.28 ( 4321) hydrogen bonds : bond 0.04053 / 2.88 ( 249) hydrogen bonds : angle 4.78011 / 3.56 ( 744) *********************** 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 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.068 Fit side-chains REVERT: A 138 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6909 (p) REVERT: A 248 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7632 (mmm) REVERT: A 290 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7569 (mm) REVERT: A 310 ARG cc_start: 0.7753 (mmt90) cc_final: 0.7199 (tpp80) outliers start: 16 outliers final: 6 residues processed: 64 average time/residue: 0.3032 time to fit residues: 20.1354 Evaluate side-chains 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 103 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4118 r_free = 0.4118 target = 0.194751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148301 restraints weight = 1292.184| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.13 r_work: 0.3408 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2811 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= 0.139 Angle : 0.517 5.606 4321 Z= 0.273 Chirality : 0.039 0.132 549 Planarity : 0.004 0.025 527 Dihedral : 3.878 28.822 433 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.07 % Allowed : 22.67 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.41), residues: 406 helix: 1.66 (0.28), residues: 326 sheet: -1.02 (1.14), residues: 18 loop : -0.24 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.012 0.001 PHE A 240 TRP 0.002 0.000 TRP A 256 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3184) covalent geometry : angle 0.51743 / 0.27 ( 4321) hydrogen bonds : bond 0.03866 / 2.75 ( 249) hydrogen bonds : angle 4.70938 / 3.50 ( 744) *********************** 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 69 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.112 Fit side-chains REVERT: A 138 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6931 (p) REVERT: A 248 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7606 (mmm) REVERT: A 252 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 290 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 310 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7199 (tpp80) REVERT: A 439 VAL cc_start: 0.7756 (m) cc_final: 0.7552 (p) outliers start: 14 outliers final: 6 residues processed: 64 average time/residue: 0.3516 time to fit residues: 23.2897 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 : 0.096 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain A residue 248 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4099 r_free = 0.4099 target = 0.193238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146344 restraints weight = 1294.709| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.13 r_work: 0.3460 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3184 Z= 0.119 Angle : 0.508 5.214 4321 Z= 0.268 Chirality : 0.038 0.131 549 Planarity : 0.003 0.025 527 Dihedral : 3.814 27.456 433 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.49 % Allowed : 23.26 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.41), residues: 406 helix: 1.81 (0.29), residues: 323 sheet: -0.89 (1.13), residues: 18 loop : -0.36 (0.68), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.009 0.001 PHE A 218 TRP 0.005 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 3184) covalent geometry : angle 0.50757 / 0.27 ( 4321) hydrogen bonds : bond 0.03638 / 2.58 ( 249) hydrogen bonds : angle 4.60152 / 3.41 ( 744) *********************** 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: 12 poor density : 58 time to evaluate : 0.071 Fit side-chains REVERT: A 138 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6930 (p) REVERT: A 248 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7417 (mmm) REVERT: A 252 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7478 (mm-40) REVERT: A 290 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 310 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7190 (tpp80) REVERT: A 439 VAL cc_start: 0.7615 (m) cc_final: 0.7388 (p) outliers start: 12 outliers final: 4 residues processed: 66 average time/residue: 0.3280 time to fit residues: 22.4767 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 : 0.110 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain A residue 248 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.0870 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4129 r_free = 0.4129 target = 0.195340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149818 restraints weight = 1231.062| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.10 r_work: 0.3460 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3072 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= 0.120 Angle : 0.514 6.208 4321 Z= 0.268 Chirality : 0.039 0.140 549 Planarity : 0.003 0.025 527 Dihedral : 3.750 27.602 433 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.91 % Allowed : 23.84 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.41), residues: 406 helix: 1.85 (0.29), residues: 323 sheet: -0.91 (1.14), residues: 18 loop : -0.45 (0.67), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.010 0.001 PHE A 264 TRP 0.002 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3184) covalent geometry : angle 0.51414 / 0.27 ( 4321) hydrogen bonds : bond 0.03613 / 2.57 ( 249) hydrogen bonds : angle 4.57602 / 3.36 ( 744) ********************** 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 68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.102 Fit side-chains REVERT: A 138 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6911 (p) REVERT: A 248 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7403 (mmm) REVERT: A 252 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7399 (mm-40) REVERT: A 290 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7564 (mm) REVERT: A 297 SER cc_start: 0.8984 (m) cc_final: 0.8768 (p) REVERT: A 310 ARG cc_start: 0.7759 (mmt90) cc_final: 0.7256 (tpp80) REVERT: A 342 ARG cc_start: 0.6449 (ttp-110) cc_final: 0.6215 (mtm110) REVERT: A 439 VAL cc_start: 0.7715 (m) cc_final: 0.7468 (p) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.3271 time to fit residues: 22.0403 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 : 0.125 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain A residue 248 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.191561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144941 restraints weight = 1279.244| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.13 r_work: 0.3466 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3184 Z= 0.128 Angle : 0.526 6.285 4321 Z= 0.274 Chirality : 0.039 0.139 549 Planarity : 0.003 0.025 527 Dihedral : 3.780 27.862 433 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.33 % Allowed : 25.00 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.41), residues: 406 helix: 1.83 (0.29), residues: 322 sheet: -0.92 (1.12), residues: 18 loop : -0.51 (0.66), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.011 0.001 PHE A 240 TRP 0.003 0.000 TRP A 256 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 3184) covalent geometry : angle 0.52599 / 0.27 ( 4321) hydrogen bonds : bond 0.03671 / 2.61 ( 249) hydrogen bonds : angle 4.61084 / 3.40 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.44 seconds wall clock time: 20 minutes 29.91 seconds (1229.91 seconds total)