Starting phenix.real_space_refine on Fri Oct 23 11:37:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wuw_66273/10_2026/9wuw_66273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wuw_66273/10_2026/9wuw_66273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wuw_66273/10_2026/9wuw_66273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wuw_66273/10_2026/9wuw_66273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wuw_66273/10_2026/9wuw_66273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wuw_66273/10_2026/9wuw_66273.map" } resolution = 2.51 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= 0.000 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5074 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 3608 2.51 5 N 948 2.21 5 O 1022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5614 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2807 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 23, 'TRANS': 327} Chain breaks: 3 Restraints were copied for chains: A Time building chain proxies: 2.21, per 1000 atoms: 0.39 Number of scatterers: 5614 At special positions: 0 Unit cell: (107.548, 87.508, 66.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1022 8.00 N 948 7.00 C 3608 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: 0.37 Conformation dependent library (CDL) restraints added in 250.5 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 46.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.856A pdb=" N ASP B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 206' Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.609A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 removed outlier: 3.532A pdb=" N LEU B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 472 through 486 removed outlier: 3.644A pdb=" N LEU B 484 " --> pdb=" O CYS B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 536 through 550 removed outlier: 3.824A pdb=" N ARG B 549 " --> pdb=" O SER B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.857A pdb=" N ASP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 207 through 218 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.609A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.532A pdb=" N LEU A 444 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 472 through 486 removed outlier: 3.644A pdb=" N LEU A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.825A pdb=" N ARG A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 565 Processing sheet with id=AA1, first strand: chain 'B' and resid 177 through 178 removed outlier: 4.192A pdb=" N TYR B 177 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 193 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.736A pdb=" N CYS B 299 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AA4, first strand: chain 'B' and resid 372 through 374 Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 178 removed outlier: 4.192A pdb=" N TYR A 177 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 193 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 300 removed outlier: 3.736A pdb=" N CYS A 299 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374 248 hydrogen bonds defined for protein. 696 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: 0.76 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1806 1.34 - 1.46: 1151 1.46 - 1.58: 2737 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 5750 Sorted by residual: bond pdb=" C GLU B 349 " pdb=" O GLU B 349 " ideal model delta sigma weight residual 1.240 1.248 -0.009 1.16e-02 7.43e+03 5.81e-01 bond pdb=" C GLU A 349 " pdb=" O GLU A 349 " ideal model delta sigma weight residual 1.240 1.248 -0.009 1.16e-02 7.43e+03 5.81e-01 bond pdb=" CA VAL A 497 " pdb=" CB VAL A 497 " ideal model delta sigma weight residual 1.539 1.528 0.012 1.58e-02 4.01e+03 5.33e-01 bond pdb=" CA VAL B 497 " pdb=" CB VAL B 497 " ideal model delta sigma weight residual 1.539 1.528 0.011 1.58e-02 4.01e+03 4.52e-01 bond pdb=" CB ASN B 287 " pdb=" CG ASN B 287 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.30e-01 ... (remaining 5745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 7462 0.95 - 1.90: 256 1.90 - 2.86: 66 2.86 - 3.81: 23 3.81 - 4.76: 7 Bond angle restraints: 7814 Sorted by residual: angle pdb=" C VAL A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 121.65 119.21 2.44 1.01e+00 9.80e-01 5.84e+00 angle pdb=" C VAL B 219 " pdb=" N PRO B 220 " pdb=" CA PRO B 220 " ideal model delta sigma weight residual 121.65 119.21 2.44 1.01e+00 9.80e-01 5.82e+00 angle pdb=" CA PRO A 220 " pdb=" C PRO A 220 " pdb=" O PRO A 220 " ideal model delta sigma weight residual 121.38 119.67 1.71 7.70e-01 1.69e+00 4.92e+00 angle pdb=" CA PRO A 220 " pdb=" C PRO A 220 " pdb=" N ALA A 221 " ideal model delta sigma weight residual 116.45 118.31 -1.86 8.50e-01 1.38e+00 4.76e+00 angle pdb=" CA PRO B 220 " pdb=" C PRO B 220 " pdb=" O PRO B 220 " ideal model delta sigma weight residual 121.38 119.71 1.67 7.70e-01 1.69e+00 4.72e+00 ... (remaining 7809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3274 17.59 - 35.19: 176 35.19 - 52.78: 22 52.78 - 70.37: 6 70.37 - 87.96: 4 Dihedral angle restraints: 3482 sinusoidal: 1412 harmonic: 2070 Sorted by residual: dihedral pdb=" CA LEU A 495 " pdb=" C LEU A 495 " pdb=" N LYS A 496 " pdb=" CA LYS A 496 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA LEU B 495 " pdb=" C LEU B 495 " pdb=" N LYS B 496 " pdb=" CA LYS B 496 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLY A 494 " pdb=" C GLY A 494 " pdb=" N LEU A 495 " pdb=" CA LEU A 495 " ideal model delta harmonic sigma weight residual 180.00 166.18 13.82 0 5.00e+00 4.00e-02 7.64e+00 ... (remaining 3479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 455 0.024 - 0.047: 240 0.047 - 0.071: 116 0.071 - 0.095: 39 0.095 - 0.118: 26 Chirality restraints: 876 Sorted by residual: chirality pdb=" CA VAL B 451 " pdb=" N VAL B 451 " pdb=" C VAL B 451 " pdb=" CB VAL B 451 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 873 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 247 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO B 248 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 248 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 248 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 247 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 248 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 495 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C LEU B 495 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU B 495 " 0.008 2.00e-02 2.50e+03 pdb=" N LYS B 496 " 0.007 2.00e-02 2.50e+03 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5424 3.27 - 3.81: 8239 3.81 - 4.36: 10994 4.36 - 4.90: 18194 Nonbonded interactions: 43035 Sorted by model distance: nonbonded pdb=" OH TYR B 225 " pdb=" OG1 THR A 511 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR B 511 " pdb=" OH TYR A 225 " model vdw 2.188 3.040 nonbonded pdb=" ND2 ASN A 200 " pdb=" OD1 ASP A 205 " model vdw 2.293 3.120 nonbonded pdb=" ND2 ASN B 200 " pdb=" OD1 ASP B 205 " model vdw 2.293 3.120 nonbonded pdb=" O SER B 226 " pdb=" NZ LYS A 551 " model vdw 2.331 3.120 ... (remaining 43030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.002 0.018 5750 Z= 0.102 Angle : 0.490 4.759 7814 Z= 0.258 Chirality : 0.039 0.118 876 Planarity : 0.004 0.031 996 Dihedral : 11.232 87.962 2134 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.06 (0.31), residues: 686 helix: 0.56 (0.30), residues: 280 sheet: 1.29 (0.71), residues: 64 loop : -0.59 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.014 0.001 TYR A 215 PHE 0.008 0.001 PHE B 437 TRP 0.003 0.001 TRP B 533 HIS 0.002 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 5750) covalent geometry : angle 0.49029 / 0.26 ( 7814) hydrogen bonds : bond 0.25327 / 15.45 ( 248) hydrogen bonds : angle 6.35406 / 4.48 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.7195 time to fit residues: 69.2375 Evaluate side-chains 74 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 ASN B 243 HIS ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 243 HIS A 423 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131059 restraints weight = 5075.454| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.83 r_work: 0.3294 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.123 Angle : 0.536 4.718 7814 Z= 0.278 Chirality : 0.041 0.129 876 Planarity : 0.005 0.036 996 Dihedral : 3.895 17.339 754 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.96 % Allowed : 6.91 % Favored : 92.12 % 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: 0.66 (0.32), residues: 686 helix: 1.36 (0.32), residues: 294 sheet: 1.60 (0.72), residues: 64 loop : -0.65 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 433 TYR 0.009 0.001 TYR A 215 PHE 0.016 0.002 PHE B 437 TRP 0.006 0.001 TRP A 233 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 5750) covalent geometry : angle 0.53582 / 0.28 ( 7814) hydrogen bonds : bond 0.04843 / 3.01 ( 248) hydrogen bonds : angle 4.36935 / 3.09 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.279 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 0.7214 time to fit residues: 56.0965 Evaluate side-chains 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [57, 13, 39, 41, 9, 55, 43, 0, 42, 25, 2] chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 396 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 436 ASN ** 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 = 0.4008 r_free = 0.4008 target = 0.173495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127284 restraints weight = 5029.331| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.08 r_work: 0.3245 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.138 Angle : 0.556 5.818 7814 Z= 0.286 Chirality : 0.042 0.136 876 Planarity : 0.005 0.039 996 Dihedral : 4.133 19.156 754 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.13 % Allowed : 7.40 % Favored : 91.48 % 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: 0.62 (0.32), residues: 686 helix: 1.39 (0.32), residues: 294 sheet: 1.51 (0.72), residues: 64 loop : -0.71 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 433 TYR 0.009 0.001 TYR B 215 PHE 0.012 0.002 PHE A 437 TRP 0.004 0.001 TRP B 485 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 5750) covalent geometry : angle 0.55554 / 0.29 ( 7814) hydrogen bonds : bond 0.05349 / 3.30 ( 248) hydrogen bonds : angle 4.14398 / 2.94 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.192 Fit side-chains REVERT: B 216 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7604 (mtm-85) REVERT: A 216 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7588 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 0.6893 time to fit residues: 58.4699 Evaluate side-chains 82 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [40, 23, 24, 31, 48, 13, 49, 38, 1, 46, 41] chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 396 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 436 ASN ** 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 = 0.4000 r_free = 0.4000 target = 0.172832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129324 restraints weight = 5090.971| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.81 r_work: 0.3259 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5750 Z= 0.157 Angle : 0.588 6.109 7814 Z= 0.302 Chirality : 0.043 0.133 876 Planarity : 0.005 0.041 996 Dihedral : 4.322 20.421 754 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.96 % Allowed : 8.20 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.32), residues: 686 helix: 1.30 (0.32), residues: 294 sheet: 1.15 (0.69), residues: 64 loop : -0.75 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 433 TYR 0.009 0.001 TYR A 177 PHE 0.018 0.002 PHE A 199 TRP 0.005 0.001 TRP B 485 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 5750) covalent geometry : angle 0.58776 / 0.30 ( 7814) hydrogen bonds : bond 0.05246 / 3.24 ( 248) hydrogen bonds : angle 4.13146 / 2.93 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.183 Fit side-chains REVERT: B 198 MET cc_start: 0.7633 (mmm) cc_final: 0.7177 (mmm) REVERT: B 216 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7708 (mtm110) REVERT: A 216 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7689 (mtm110) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 0.6503 time to fit residues: 55.9414 Evaluate side-chains 79 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [67, 47, 64, 40, 49, 15, 16, 45, 60, 31, 52] chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 436 ASN ** 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 = 0.3998 r_free = 0.3998 target = 0.172994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128907 restraints weight = 5189.009| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.82 r_work: 0.3257 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5750 Z= 0.137 Angle : 0.547 6.200 7814 Z= 0.282 Chirality : 0.042 0.132 876 Planarity : 0.005 0.041 996 Dihedral : 4.280 20.262 754 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.29 % Allowed : 9.32 % Favored : 89.39 % 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: 0.53 (0.32), residues: 686 helix: 1.35 (0.32), residues: 294 sheet: 1.33 (0.70), residues: 64 loop : -0.77 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.015 0.001 TYR B 215 PHE 0.013 0.002 PHE B 437 TRP 0.004 0.001 TRP A 485 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 5750) covalent geometry : angle 0.54678 / 0.28 ( 7814) hydrogen bonds : bond 0.04778 / 2.95 ( 248) hydrogen bonds : angle 4.04569 / 2.88 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.165 Fit side-chains REVERT: B 198 MET cc_start: 0.7455 (mmm) cc_final: 0.7110 (mmm) REVERT: B 216 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7700 (mtm110) REVERT: A 198 MET cc_start: 0.7473 (mmm) cc_final: 0.7103 (mmm) REVERT: A 216 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7688 (mtm110) outliers start: 8 outliers final: 3 residues processed: 75 average time/residue: 0.6571 time to fit residues: 51.1534 Evaluate side-chains 74 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [34, 62, 13, 15, 45, 44, 20, 54, 21, 27, 42] chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 436 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.173409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128103 restraints weight = 5137.871| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.91 r_work: 0.3251 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5750 Z= 0.124 Angle : 0.530 6.037 7814 Z= 0.274 Chirality : 0.042 0.132 876 Planarity : 0.005 0.041 996 Dihedral : 4.218 20.103 754 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.13 % Allowed : 9.81 % Favored : 89.07 % 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: 0.61 (0.32), residues: 686 helix: 1.41 (0.32), residues: 294 sheet: 1.48 (0.70), residues: 64 loop : -0.76 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 241 TYR 0.017 0.001 TYR B 215 PHE 0.009 0.001 PHE A 437 TRP 0.004 0.001 TRP B 233 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5750) covalent geometry : angle 0.53039 / 0.27 ( 7814) hydrogen bonds : bond 0.04496 / 2.78 ( 248) hydrogen bonds : angle 3.97596 / 2.83 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.236 Fit side-chains REVERT: B 198 MET cc_start: 0.7467 (mmm) cc_final: 0.7118 (mmm) REVERT: B 216 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7697 (mtm110) REVERT: A 198 MET cc_start: 0.7495 (mmm) cc_final: 0.7139 (mmm) REVERT: A 216 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7686 (mtm110) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 0.6478 time to fit residues: 49.2223 Evaluate side-chains 75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [63, 4, 66, 44, 46, 13, 23, 0, 1, 43, 41] chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 423 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 423 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125528 restraints weight = 5181.406| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.83 r_work: 0.3218 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5750 Z= 0.231 Angle : 0.685 7.202 7814 Z= 0.354 Chirality : 0.048 0.142 876 Planarity : 0.006 0.047 996 Dihedral : 4.789 22.963 754 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.61 % Allowed : 10.29 % Favored : 88.10 % 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: 0.18 (0.32), residues: 686 helix: 1.03 (0.32), residues: 294 sheet: 1.08 (0.63), residues: 68 loop : -0.95 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 336 TYR 0.025 0.002 TYR B 215 PHE 0.012 0.003 PHE B 199 TRP 0.009 0.002 TRP B 485 HIS 0.007 0.002 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 5750) covalent geometry : angle 0.68487 / 0.35 ( 7814) hydrogen bonds : bond 0.06302 / 3.92 ( 248) hydrogen bonds : angle 4.27047 / 3.03 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.229 Fit side-chains REVERT: B 216 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7736 (mtm110) REVERT: A 216 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7727 (mtm110) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.6734 time to fit residues: 55.1700 Evaluate side-chains 80 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [25, 66, 18, 59, 30, 6, 36, 44, 14, 35, 23] chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** 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 = 0.3995 r_free = 0.3995 target = 0.172685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127674 restraints weight = 5097.719| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.90 r_work: 0.3242 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5750 Z= 0.131 Angle : 0.544 6.579 7814 Z= 0.282 Chirality : 0.042 0.132 876 Planarity : 0.005 0.042 996 Dihedral : 4.437 20.936 754 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.13 % Allowed : 9.97 % Favored : 88.91 % 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: 0.44 (0.32), residues: 686 helix: 1.26 (0.32), residues: 294 sheet: 1.47 (0.66), residues: 64 loop : -0.85 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.018 0.001 TYR B 215 PHE 0.008 0.001 PHE B 199 TRP 0.006 0.001 TRP A 233 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 5750) covalent geometry : angle 0.54406 / 0.28 ( 7814) hydrogen bonds : bond 0.04594 / 2.84 ( 248) hydrogen bonds : angle 4.01931 / 2.86 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.178 Fit side-chains REVERT: B 216 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7694 (mtm110) REVERT: A 198 MET cc_start: 0.7543 (mmm) cc_final: 0.7168 (mmm) REVERT: A 216 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7696 (mtm110) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.6730 time to fit residues: 50.3234 Evaluate side-chains 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [12, 42, 11, 64, 33, 62, 37, 15, 39, 8, 53] chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 ASN B 423 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** 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 = 0.3997 r_free = 0.3997 target = 0.172955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127221 restraints weight = 5084.062| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.93 r_work: 0.3243 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.130 Angle : 0.541 6.395 7814 Z= 0.279 Chirality : 0.042 0.132 876 Planarity : 0.005 0.042 996 Dihedral : 4.354 20.916 754 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.13 % Allowed : 10.29 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.32), residues: 686 helix: 1.27 (0.32), residues: 294 sheet: 1.53 (0.67), residues: 64 loop : -0.86 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.016 0.001 TYR A 215 PHE 0.014 0.002 PHE B 437 TRP 0.006 0.001 TRP B 490 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 5750) covalent geometry : angle 0.54078 / 0.28 ( 7814) hydrogen bonds : bond 0.04603 / 2.85 ( 248) hydrogen bonds : angle 4.00311 / 2.85 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.218 Fit side-chains REVERT: B 216 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (mtm110) REVERT: A 216 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7688 (mtm110) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.6557 time to fit residues: 50.4411 Evaluate side-chains 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [53, 16, 43, 31, 59, 48, 69, 5, 20, 24, 8] chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 423 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN ** A 436 ASN ** 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 = 0.3989 r_free = 0.3989 target = 0.172201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126479 restraints weight = 5152.825| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5750 Z= 0.150 Angle : 0.575 6.547 7814 Z= 0.297 Chirality : 0.043 0.134 876 Planarity : 0.005 0.042 996 Dihedral : 4.462 21.374 754 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.80 % Allowed : 11.09 % Favored : 88.10 % 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: 0.33 (0.32), residues: 686 helix: 1.18 (0.32), residues: 294 sheet: 1.42 (0.66), residues: 64 loop : -0.92 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.017 0.001 TYR A 215 PHE 0.009 0.002 PHE A 199 TRP 0.007 0.001 TRP B 490 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 5750) covalent geometry : angle 0.57488 / 0.30 ( 7814) hydrogen bonds : bond 0.04969 / 3.08 ( 248) hydrogen bonds : angle 4.06510 / 2.89 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.228 Fit side-chains REVERT: B 216 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7698 (mtm110) REVERT: A 216 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7698 (mtm110) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.6923 time to fit residues: 51.7007 Evaluate side-chains 78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: [16, 68, 15, 19, 8, 21, 17, 40, 56, 22, 6] chunk 16 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.913 > 50:) chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** 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 = 0.3998 r_free = 0.3998 target = 0.173135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127757 restraints weight = 5067.527| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.88 r_work: 0.3245 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.128 Angle : 0.541 6.346 7814 Z= 0.279 Chirality : 0.042 0.130 876 Planarity : 0.005 0.041 996 Dihedral : 4.350 20.785 754 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.80 % Allowed : 10.61 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.42 (0.32), residues: 686 helix: 1.26 (0.32), residues: 294 sheet: 1.40 (0.67), residues: 64 loop : -0.87 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.015 0.001 TYR A 215 PHE 0.015 0.002 PHE B 437 TRP 0.006 0.001 TRP A 490 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 5750) covalent geometry : angle 0.54127 / 0.28 ( 7814) hydrogen bonds : bond 0.04542 / 2.81 ( 248) hydrogen bonds : angle 4.00330 / 2.85 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.71 seconds wall clock time: 41 minutes 22.67 seconds (2482.67 seconds total)