Starting phenix.real_space_refine on Sat Oct 11 05:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvt_42628/10_2025/8uvt_42628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvt_42628/10_2025/8uvt_42628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uvt_42628/10_2025/8uvt_42628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvt_42628/10_2025/8uvt_42628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uvt_42628/10_2025/8uvt_42628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvt_42628/10_2025/8uvt_42628.map" } resolution = 2.9 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= 0.003 sd= 0.114 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 7892 2.51 5 N 2024 2.21 5 O 2056 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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12104 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3026 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 2.55, per 1000 atoms: 0.21 Number of scatterers: 12104 At special positions: 0 Unit cell: (110.004, 110.004, 91.848, 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 132 16.00 O 2056 8.00 N 2024 7.00 C 7892 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: 1.17 Conformation dependent library (CDL) restraints added in 486.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 83.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.874A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 79 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 340 removed outlier: 3.719A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix removed outlier: 3.704A pdb=" N VAL A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 389 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.529A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 79 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix removed outlier: 3.704A pdb=" N VAL B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 389 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.753A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.528A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 79 Processing helix chain 'C' and resid 89 through 113 Processing helix chain 'C' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix removed outlier: 3.704A pdb=" N VAL C 340 " --> pdb=" O MET C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 389 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.529A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 79 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'D' and resid 113 through 136 removed outlier: 4.380A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 175 removed outlier: 3.803A pdb=" N LYS D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 227 removed outlier: 5.029A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix removed outlier: 3.704A pdb=" N VAL D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 389 Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.528A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AA4, first strand: chain 'D' and resid 37 through 41 1040 hydrogen bonds defined for protein. 3096 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: 2.04 Time building geometry restraints manager: 1.53 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: 3754 1.34 - 1.46: 2268 1.46 - 1.58: 6118 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 12340 Sorted by residual: bond pdb=" C GLU C 367 " pdb=" N PRO C 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.96e+00 bond pdb=" C GLU A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.92e+00 bond pdb=" C GLU D 367 " pdb=" N PRO D 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.88e+00 bond pdb=" C GLU B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C LEU A 122 " pdb=" O LEU A 122 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.17e-02 7.31e+03 8.31e-01 ... (remaining 12335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 16163 1.00 - 1.99: 422 1.99 - 2.99: 81 2.99 - 3.99: 38 3.99 - 4.99: 32 Bond angle restraints: 16736 Sorted by residual: angle pdb=" N GLY B 313 " pdb=" CA GLY B 313 " pdb=" C GLY B 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY C 313 " pdb=" CA GLY C 313 " pdb=" C GLY C 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY D 313 " pdb=" CA GLY D 313 " pdb=" C GLY D 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY A 313 " pdb=" CA GLY A 313 " pdb=" C GLY A 313 " ideal model delta sigma weight residual 112.50 116.38 -3.88 1.16e+00 7.43e-01 1.12e+01 angle pdb=" C VAL D 366 " pdb=" N GLU D 367 " pdb=" CA GLU D 367 " ideal model delta sigma weight residual 120.26 124.59 -4.33 1.34e+00 5.57e-01 1.04e+01 ... (remaining 16731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6562 17.80 - 35.60: 662 35.60 - 53.40: 108 53.40 - 71.20: 28 71.20 - 89.01: 20 Dihedral angle restraints: 7380 sinusoidal: 2876 harmonic: 4504 Sorted by residual: dihedral pdb=" CB GLU B 40 " pdb=" CG GLU B 40 " pdb=" CD GLU B 40 " pdb=" OE1 GLU B 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.33 -86.33 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " pdb=" CD GLU D 40 " pdb=" OE1 GLU D 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU A 40 " pdb=" CG GLU A 40 " pdb=" CD GLU A 40 " pdb=" OE1 GLU A 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 ... (remaining 7377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1330 0.027 - 0.054: 448 0.054 - 0.081: 186 0.081 - 0.108: 77 0.108 - 0.134: 15 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CG LEU B 386 " pdb=" CB LEU B 386 " pdb=" CD1 LEU B 386 " pdb=" CD2 LEU B 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU D 386 " pdb=" CB LEU D 386 " pdb=" CD1 LEU D 386 " pdb=" CD2 LEU D 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CG LEU C 386 " pdb=" CB LEU C 386 " pdb=" CD1 LEU C 386 " pdb=" CD2 LEU C 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2053 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 424 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO B 425 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 425 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 425 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 424 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 425 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 425 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 425 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 424 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 425 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.016 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2125 2.77 - 3.30: 12287 3.30 - 3.83: 21314 3.83 - 4.37: 23750 4.37 - 4.90: 42212 Nonbonded interactions: 101688 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" O MET A 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 84 " pdb=" O MET C 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER D 84 " pdb=" O MET D 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 84 " pdb=" O MET B 87 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP D 165 " pdb=" OH TYR D 190 " model vdw 2.253 3.040 ... (remaining 101683 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 0.026 12340 Z= 0.128 Angle : 0.474 4.985 16736 Z= 0.260 Chirality : 0.036 0.134 2056 Planarity : 0.003 0.029 2020 Dihedral : 15.275 89.006 4468 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 aren not related in a simple way. whole: 2.31 (0.21), residues: 1520 helix: 2.32 (0.14), residues: 1228 sheet: -0.45 (0.55), residues: 40 loop : -2.38 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 405 TYR 0.008 0.001 TYR C 124 PHE 0.014 0.001 PHE D 205 TRP 0.005 0.001 TRP A 193 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00282 (12340) covalent geometry : angle 0.47414 (16736) hydrogen bonds : bond 0.12930 ( 1040) hydrogen bonds : angle 5.11744 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.609 Fit side-chains REVERT: A 296 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7900 (mtt90) REVERT: A 310 ASP cc_start: 0.8256 (m-30) cc_final: 0.7970 (m-30) REVERT: B 310 ASP cc_start: 0.8288 (m-30) cc_final: 0.7960 (m-30) REVERT: C 427 MET cc_start: 0.8635 (ptt) cc_final: 0.8348 (ptt) REVERT: D 427 MET cc_start: 0.8631 (ptt) cc_final: 0.8352 (ptt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.5714 time to fit residues: 150.6692 Evaluate side-chains 183 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 392 HIS A 443 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 392 HIS C 358 HIS C 392 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 392 HIS D 443 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125283 restraints weight = 12711.627| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.30 r_work: 0.3226 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12340 Z= 0.151 Angle : 0.533 6.135 16736 Z= 0.277 Chirality : 0.037 0.158 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.819 15.060 1688 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.37 % Allowed : 10.13 % Favored : 87.50 % 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 aren not related in a simple way. whole: 3.16 (0.21), residues: 1520 helix: 2.93 (0.13), residues: 1224 sheet: 0.06 (0.53), residues: 40 loop : -2.16 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.031 0.002 TYR B 124 PHE 0.018 0.002 PHE A 205 TRP 0.006 0.001 TRP D 193 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00345 (12340) covalent geometry : angle 0.53276 (16736) hydrogen bonds : bond 0.04852 ( 1040) hydrogen bonds : angle 3.56177 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.470 Fit side-chains REVERT: A 171 MET cc_start: 0.7733 (mmp) cc_final: 0.7453 (mmm) REVERT: A 296 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7836 (mtt90) REVERT: A 310 ASP cc_start: 0.8314 (m-30) cc_final: 0.8027 (m-30) REVERT: A 385 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7654 (ttp-110) REVERT: A 387 MET cc_start: 0.8984 (mtm) cc_final: 0.8718 (mtm) REVERT: B 87 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.4420 (mtm) REVERT: B 306 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7551 (mtp180) REVERT: B 310 ASP cc_start: 0.8337 (m-30) cc_final: 0.7999 (m-30) REVERT: C 143 THR cc_start: 0.8434 (m) cc_final: 0.8131 (m) REVERT: C 310 ASP cc_start: 0.8376 (m-30) cc_final: 0.8129 (m-30) REVERT: C 385 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7482 (ttp80) REVERT: C 427 MET cc_start: 0.8352 (ptt) cc_final: 0.8123 (ptt) REVERT: D 143 THR cc_start: 0.8463 (m) cc_final: 0.8156 (m) REVERT: D 310 ASP cc_start: 0.8359 (m-30) cc_final: 0.8116 (m-30) REVERT: D 385 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7504 (ttm110) REVERT: D 427 MET cc_start: 0.8372 (ptt) cc_final: 0.8131 (ptt) outliers start: 32 outliers final: 16 residues processed: 213 average time/residue: 0.6452 time to fit residues: 148.5998 Evaluate side-chains 201 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124564 restraints weight = 12791.532| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.33 r_work: 0.3218 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12340 Z= 0.142 Angle : 0.512 6.140 16736 Z= 0.267 Chirality : 0.036 0.126 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.765 13.737 1688 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.96 % Allowed : 13.46 % Favored : 83.58 % 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 aren not related in a simple way. whole: 3.26 (0.21), residues: 1520 helix: 3.01 (0.13), residues: 1236 sheet: 0.44 (0.49), residues: 40 loop : -2.53 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.027 0.001 TYR B 124 PHE 0.017 0.001 PHE A 205 TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00322 (12340) covalent geometry : angle 0.51157 (16736) hydrogen bonds : bond 0.04720 ( 1040) hydrogen bonds : angle 3.44724 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.566 Fit side-chains REVERT: A 171 MET cc_start: 0.7668 (mmp) cc_final: 0.7464 (mmm) REVERT: A 296 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7803 (mtt90) REVERT: A 310 ASP cc_start: 0.8313 (m-30) cc_final: 0.8032 (m-30) REVERT: A 385 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7746 (ttp-110) REVERT: A 387 MET cc_start: 0.8949 (mtm) cc_final: 0.8711 (mtm) REVERT: B 284 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: B 310 ASP cc_start: 0.8322 (m-30) cc_final: 0.8021 (m-30) REVERT: B 401 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 52 LYS cc_start: 0.7803 (mppt) cc_final: 0.7561 (mmtm) REVERT: C 87 MET cc_start: 0.4030 (mtt) cc_final: 0.3038 (mtt) REVERT: C 143 THR cc_start: 0.8389 (m) cc_final: 0.8076 (m) REVERT: C 310 ASP cc_start: 0.8346 (m-30) cc_final: 0.8116 (m-30) REVERT: C 385 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7616 (ttp80) REVERT: C 427 MET cc_start: 0.8333 (ptt) cc_final: 0.8109 (ptt) REVERT: C 431 LEU cc_start: 0.8646 (mm) cc_final: 0.8443 (mp) REVERT: D 52 LYS cc_start: 0.7800 (mppt) cc_final: 0.7564 (mmtm) REVERT: D 87 MET cc_start: 0.4072 (mtt) cc_final: 0.3046 (mtt) REVERT: D 143 THR cc_start: 0.8408 (m) cc_final: 0.8096 (m) REVERT: D 310 ASP cc_start: 0.8328 (m-30) cc_final: 0.8083 (m-30) REVERT: D 385 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7569 (ttm110) REVERT: D 427 MET cc_start: 0.8336 (ptt) cc_final: 0.8108 (ptt) REVERT: D 431 LEU cc_start: 0.8650 (mm) cc_final: 0.8446 (mp) outliers start: 40 outliers final: 17 residues processed: 222 average time/residue: 0.6484 time to fit residues: 155.6627 Evaluate side-chains 208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.152144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124282 restraints weight = 12912.443| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.32 r_work: 0.3226 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12340 Z= 0.144 Angle : 0.518 6.630 16736 Z= 0.268 Chirality : 0.037 0.175 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.790 14.021 1688 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.03 % Allowed : 15.61 % Favored : 81.36 % 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 aren not related in a simple way. whole: 3.27 (0.21), residues: 1520 helix: 3.03 (0.13), residues: 1236 sheet: 0.71 (0.50), residues: 40 loop : -2.64 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.024 0.001 TYR C 124 PHE 0.018 0.002 PHE A 205 TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00331 (12340) covalent geometry : angle 0.51754 (16736) hydrogen bonds : bond 0.04744 ( 1040) hydrogen bonds : angle 3.40324 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.480 Fit side-chains REVERT: A 87 MET cc_start: 0.4305 (OUTLIER) cc_final: 0.4085 (mtm) REVERT: A 296 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7942 (mtt-85) REVERT: A 310 ASP cc_start: 0.8308 (m-30) cc_final: 0.8035 (m-30) REVERT: A 385 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7795 (ttp-110) REVERT: A 387 MET cc_start: 0.8946 (mtm) cc_final: 0.8632 (mtm) REVERT: B 310 ASP cc_start: 0.8313 (m-30) cc_final: 0.8019 (m-30) REVERT: B 401 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 87 MET cc_start: 0.4152 (mtt) cc_final: 0.3048 (mtt) REVERT: C 143 THR cc_start: 0.8425 (m) cc_final: 0.8103 (m) REVERT: C 310 ASP cc_start: 0.8351 (m-30) cc_final: 0.8113 (m-30) REVERT: C 385 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7718 (ttp80) REVERT: C 427 MET cc_start: 0.8324 (ptt) cc_final: 0.8105 (ptt) REVERT: D 87 MET cc_start: 0.4212 (mtt) cc_final: 0.3074 (mtt) REVERT: D 143 THR cc_start: 0.8440 (m) cc_final: 0.8121 (m) REVERT: D 310 ASP cc_start: 0.8321 (m-30) cc_final: 0.8094 (m-30) REVERT: D 385 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7644 (ttm110) REVERT: D 427 MET cc_start: 0.8321 (ptt) cc_final: 0.8106 (ptt) outliers start: 41 outliers final: 19 residues processed: 228 average time/residue: 0.6653 time to fit residues: 163.9540 Evaluate side-chains 215 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 40 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN C 443 GLN D 185 ASN D 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122913 restraints weight = 12856.263| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.31 r_work: 0.3202 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12340 Z= 0.160 Angle : 0.542 7.110 16736 Z= 0.279 Chirality : 0.037 0.143 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.850 14.020 1688 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.48 % Allowed : 16.12 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.21), residues: 1520 helix: 2.96 (0.13), residues: 1236 sheet: 0.82 (0.51), residues: 40 loop : -2.67 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 405 TYR 0.024 0.001 TYR D 124 PHE 0.019 0.002 PHE A 444 TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00379 (12340) covalent geometry : angle 0.54246 (16736) hydrogen bonds : bond 0.04981 ( 1040) hydrogen bonds : angle 3.46087 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.499 Fit side-chains REVERT: A 87 MET cc_start: 0.4261 (OUTLIER) cc_final: 0.3703 (mtt) REVERT: A 296 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7947 (mtt-85) REVERT: A 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8102 (m-30) REVERT: A 385 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7739 (ttp-110) REVERT: A 387 MET cc_start: 0.8974 (mtm) cc_final: 0.8671 (mtm) REVERT: B 87 MET cc_start: 0.4204 (OUTLIER) cc_final: 0.3952 (mtm) REVERT: B 310 ASP cc_start: 0.8317 (m-30) cc_final: 0.8024 (m-30) REVERT: B 401 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 87 MET cc_start: 0.4167 (mtt) cc_final: 0.3072 (mtt) REVERT: C 143 THR cc_start: 0.8384 (m) cc_final: 0.8062 (m) REVERT: C 296 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7945 (mtt-85) REVERT: C 310 ASP cc_start: 0.8349 (m-30) cc_final: 0.8105 (m-30) REVERT: C 385 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7651 (ttp80) REVERT: C 427 MET cc_start: 0.8293 (ptt) cc_final: 0.8060 (ptt) REVERT: D 87 MET cc_start: 0.4213 (mtt) cc_final: 0.3107 (mtt) REVERT: D 143 THR cc_start: 0.8387 (m) cc_final: 0.8074 (m) REVERT: D 310 ASP cc_start: 0.8345 (m-30) cc_final: 0.8094 (m-30) REVERT: D 385 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7749 (ttp-110) REVERT: D 427 MET cc_start: 0.8326 (ptt) cc_final: 0.8097 (ptt) outliers start: 47 outliers final: 27 residues processed: 221 average time/residue: 0.7166 time to fit residues: 169.9568 Evaluate side-chains 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 63 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 136 optimal weight: 0.0020 chunk 114 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123588 restraints weight = 12778.022| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.30 r_work: 0.3251 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12340 Z= 0.150 Angle : 0.533 7.754 16736 Z= 0.274 Chirality : 0.037 0.128 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.840 13.886 1688 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.11 % Allowed : 16.86 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.21), residues: 1520 helix: 2.97 (0.13), residues: 1236 sheet: 1.03 (0.52), residues: 40 loop : -2.68 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 405 TYR 0.024 0.001 TYR C 124 PHE 0.017 0.002 PHE A 205 TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00351 (12340) covalent geometry : angle 0.53261 (16736) hydrogen bonds : bond 0.04847 ( 1040) hydrogen bonds : angle 3.41806 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.488 Fit side-chains REVERT: A 87 MET cc_start: 0.4364 (OUTLIER) cc_final: 0.4109 (mtm) REVERT: A 296 ARG cc_start: 0.8223 (mtt90) cc_final: 0.8010 (mtt-85) REVERT: A 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8115 (m-30) REVERT: A 385 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7606 (ttm110) REVERT: A 387 MET cc_start: 0.8976 (mtm) cc_final: 0.8691 (mtm) REVERT: B 87 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.4014 (mtm) REVERT: B 310 ASP cc_start: 0.8325 (m-30) cc_final: 0.8046 (m-30) REVERT: B 397 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8179 (p) REVERT: B 401 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 87 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3055 (mtt) REVERT: C 143 THR cc_start: 0.8441 (m) cc_final: 0.8138 (m) REVERT: C 296 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7997 (mtt-85) REVERT: C 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8124 (m-30) REVERT: C 385 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7744 (ttp80) REVERT: C 427 MET cc_start: 0.8339 (ptt) cc_final: 0.8095 (ptt) REVERT: D 87 MET cc_start: 0.4158 (mtt) cc_final: 0.3006 (mtt) REVERT: D 143 THR cc_start: 0.8427 (m) cc_final: 0.8128 (m) REVERT: D 296 ARG cc_start: 0.8216 (mtt90) cc_final: 0.8007 (mtt-85) REVERT: D 310 ASP cc_start: 0.8333 (m-30) cc_final: 0.8101 (m-30) REVERT: D 385 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7643 (ttm110) REVERT: D 427 MET cc_start: 0.8362 (ptt) cc_final: 0.8119 (ptt) outliers start: 42 outliers final: 27 residues processed: 215 average time/residue: 0.7483 time to fit residues: 172.4773 Evaluate side-chains 211 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 142 optimal weight: 0.2980 chunk 60 optimal weight: 0.0970 chunk 122 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.153309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126023 restraints weight = 12755.394| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.30 r_work: 0.3244 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.127 Angle : 0.513 8.768 16736 Z= 0.264 Chirality : 0.036 0.127 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.750 13.571 1688 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.18 % Allowed : 17.09 % Favored : 79.73 % 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 aren not related in a simple way. whole: 3.38 (0.21), residues: 1520 helix: 3.10 (0.14), residues: 1236 sheet: 1.45 (0.58), residues: 40 loop : -2.70 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.021 0.001 TYR D 124 PHE 0.015 0.001 PHE A 205 TRP 0.007 0.001 TRP C 193 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00279 (12340) covalent geometry : angle 0.51251 (16736) hydrogen bonds : bond 0.04490 ( 1040) hydrogen bonds : angle 3.34136 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.528 Fit side-chains REVERT: A 52 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7048 (pttp) REVERT: A 296 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7899 (mtt-85) REVERT: A 310 ASP cc_start: 0.8287 (m-30) cc_final: 0.8020 (m-30) REVERT: A 385 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7328 (ttm110) REVERT: A 387 MET cc_start: 0.8915 (mtm) cc_final: 0.8639 (mtm) REVERT: B 52 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7035 (pttp) REVERT: B 87 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3917 (mtm) REVERT: B 310 ASP cc_start: 0.8299 (m-30) cc_final: 0.8013 (m-30) REVERT: B 397 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8084 (p) REVERT: B 401 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 52 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7204 (pttp) REVERT: C 87 MET cc_start: 0.3953 (mtt) cc_final: 0.2851 (mtt) REVERT: C 143 THR cc_start: 0.8335 (m) cc_final: 0.8035 (m) REVERT: C 165 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7720 (t70) REVERT: C 310 ASP cc_start: 0.8309 (m-30) cc_final: 0.8028 (m-30) REVERT: C 385 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7530 (ttp80) REVERT: C 427 MET cc_start: 0.8307 (ptt) cc_final: 0.8056 (ptt) REVERT: D 52 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7221 (pttp) REVERT: D 87 MET cc_start: 0.3809 (mtt) cc_final: 0.2677 (mtt) REVERT: D 143 THR cc_start: 0.8342 (m) cc_final: 0.8048 (m) REVERT: D 310 ASP cc_start: 0.8283 (m-30) cc_final: 0.7996 (m-30) REVERT: D 427 MET cc_start: 0.8342 (ptt) cc_final: 0.8106 (ptt) outliers start: 43 outliers final: 25 residues processed: 227 average time/residue: 0.6704 time to fit residues: 164.1963 Evaluate side-chains 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.0570 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 142 optimal weight: 0.0970 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN C 445 GLN D 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125588 restraints weight = 12470.680| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.67 r_work: 0.3292 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12340 Z= 0.123 Angle : 0.510 10.633 16736 Z= 0.262 Chirality : 0.036 0.129 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.716 13.511 1688 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.74 % Allowed : 18.05 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.44 (0.21), residues: 1520 helix: 3.14 (0.14), residues: 1236 sheet: 1.72 (0.62), residues: 40 loop : -2.71 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.021 0.001 TYR D 124 PHE 0.014 0.001 PHE A 205 TRP 0.007 0.001 TRP B 193 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00268 (12340) covalent geometry : angle 0.50969 (16736) hydrogen bonds : bond 0.04396 ( 1040) hydrogen bonds : angle 3.30402 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.525 Fit side-chains REVERT: A 52 LYS cc_start: 0.7312 (mmtm) cc_final: 0.6643 (pttp) REVERT: A 87 MET cc_start: 0.3571 (mtt) cc_final: 0.2590 (mtt) REVERT: A 296 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7593 (mtt-85) REVERT: A 387 MET cc_start: 0.8763 (mtm) cc_final: 0.8503 (mtm) REVERT: B 129 VAL cc_start: 0.8020 (t) cc_final: 0.7473 (m) REVERT: B 310 ASP cc_start: 0.8156 (m-30) cc_final: 0.7858 (m-30) REVERT: B 397 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7793 (p) REVERT: B 401 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 52 LYS cc_start: 0.7480 (mmtm) cc_final: 0.6772 (pttp) REVERT: C 87 MET cc_start: 0.3519 (mtt) cc_final: 0.2408 (mtt) REVERT: C 143 THR cc_start: 0.8015 (m) cc_final: 0.7734 (m) REVERT: C 310 ASP cc_start: 0.8194 (m-30) cc_final: 0.7896 (m-30) REVERT: C 385 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7048 (ttp-110) REVERT: C 427 MET cc_start: 0.8272 (ptt) cc_final: 0.8038 (ptt) REVERT: D 52 LYS cc_start: 0.7475 (mmtm) cc_final: 0.6767 (pttp) REVERT: D 87 MET cc_start: 0.3471 (OUTLIER) cc_final: 0.2359 (mtt) REVERT: D 143 THR cc_start: 0.8025 (m) cc_final: 0.7748 (m) REVERT: D 310 ASP cc_start: 0.8193 (m-30) cc_final: 0.7900 (m-30) REVERT: D 427 MET cc_start: 0.8257 (ptt) cc_final: 0.8014 (ptt) outliers start: 37 outliers final: 24 residues processed: 219 average time/residue: 0.6657 time to fit residues: 157.6734 Evaluate side-chains 214 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.0670 chunk 137 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 142 optimal weight: 0.0030 chunk 16 optimal weight: 0.9980 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125010 restraints weight = 12438.508| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.67 r_work: 0.3299 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.129 Angle : 0.519 10.748 16736 Z= 0.266 Chirality : 0.036 0.138 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.732 13.546 1688 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.22 % Allowed : 18.71 % 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 aren not related in a simple way. whole: 3.39 (0.21), residues: 1520 helix: 3.10 (0.14), residues: 1236 sheet: 1.78 (0.62), residues: 40 loop : -2.72 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.020 0.001 TYR B 124 PHE 0.016 0.001 PHE A 205 TRP 0.007 0.001 TRP B 193 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00286 (12340) covalent geometry : angle 0.51850 (16736) hydrogen bonds : bond 0.04483 ( 1040) hydrogen bonds : angle 3.32032 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.525 Fit side-chains REVERT: A 129 VAL cc_start: 0.8002 (t) cc_final: 0.7425 (m) REVERT: A 296 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7618 (mtt-85) REVERT: A 310 ASP cc_start: 0.8191 (m-30) cc_final: 0.7898 (m-30) REVERT: A 387 MET cc_start: 0.8780 (mtm) cc_final: 0.8518 (mtm) REVERT: B 52 LYS cc_start: 0.7409 (mmtm) cc_final: 0.6734 (pttp) REVERT: B 87 MET cc_start: 0.3609 (mtt) cc_final: 0.2527 (mtt) REVERT: B 310 ASP cc_start: 0.8218 (m-30) cc_final: 0.7913 (m-30) REVERT: B 397 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7798 (p) REVERT: B 401 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 52 LYS cc_start: 0.7511 (mmtm) cc_final: 0.6817 (pttp) REVERT: C 87 MET cc_start: 0.3504 (mtt) cc_final: 0.2398 (mtt) REVERT: C 143 THR cc_start: 0.8077 (m) cc_final: 0.7806 (m) REVERT: C 310 ASP cc_start: 0.8208 (m-30) cc_final: 0.7906 (m-30) REVERT: C 385 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7480 (ttm110) REVERT: C 427 MET cc_start: 0.8272 (ptt) cc_final: 0.8038 (ptt) REVERT: D 52 LYS cc_start: 0.7552 (mmtm) cc_final: 0.6841 (pttp) REVERT: D 87 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.2341 (mtt) REVERT: D 143 THR cc_start: 0.8088 (m) cc_final: 0.7819 (m) REVERT: D 310 ASP cc_start: 0.8214 (m-30) cc_final: 0.7911 (m-30) REVERT: D 427 MET cc_start: 0.8263 (ptt) cc_final: 0.8024 (ptt) outliers start: 30 outliers final: 23 residues processed: 213 average time/residue: 0.6827 time to fit residues: 156.7414 Evaluate side-chains 215 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.0980 chunk 105 optimal weight: 0.5980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128969 restraints weight = 12419.738| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.59 r_work: 0.3366 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12340 Z= 0.114 Angle : 0.503 10.195 16736 Z= 0.258 Chirality : 0.036 0.139 2056 Planarity : 0.003 0.032 2020 Dihedral : 3.659 13.729 1688 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.00 % Allowed : 18.71 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.21), residues: 1520 helix: 3.20 (0.14), residues: 1236 sheet: 1.93 (0.63), residues: 40 loop : -2.69 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.018 0.001 TYR D 124 PHE 0.014 0.001 PHE A 444 TRP 0.008 0.001 TRP C 193 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00235 (12340) covalent geometry : angle 0.50250 (16736) hydrogen bonds : bond 0.04128 ( 1040) hydrogen bonds : angle 3.25079 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.484 Fit side-chains REVERT: A 52 LYS cc_start: 0.7346 (mmtm) cc_final: 0.6643 (pttp) REVERT: A 129 VAL cc_start: 0.7913 (t) cc_final: 0.7346 (m) REVERT: A 296 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7474 (mtt-85) REVERT: A 387 MET cc_start: 0.8693 (mtm) cc_final: 0.8443 (mtm) REVERT: B 52 LYS cc_start: 0.7432 (mmtm) cc_final: 0.6706 (pttp) REVERT: B 129 VAL cc_start: 0.7930 (t) cc_final: 0.7397 (m) REVERT: B 397 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 401 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 52 LYS cc_start: 0.7474 (mmtm) cc_final: 0.6719 (pttp) REVERT: C 143 THR cc_start: 0.7968 (m) cc_final: 0.7697 (m) REVERT: C 385 ARG cc_start: 0.7439 (ttm110) cc_final: 0.6819 (ttp-110) REVERT: C 427 MET cc_start: 0.8218 (ptt) cc_final: 0.7960 (ptt) REVERT: D 52 LYS cc_start: 0.7470 (mmtm) cc_final: 0.6711 (pttp) REVERT: D 87 MET cc_start: 0.3312 (OUTLIER) cc_final: 0.2216 (mtt) REVERT: D 143 THR cc_start: 0.7977 (m) cc_final: 0.7709 (m) REVERT: D 427 MET cc_start: 0.8165 (ptt) cc_final: 0.7912 (ptt) outliers start: 27 outliers final: 13 residues processed: 208 average time/residue: 0.6755 time to fit residues: 151.5999 Evaluate side-chains 202 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 0.0040 chunk 60 optimal weight: 0.0170 chunk 54 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125599 restraints weight = 12474.740| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.67 r_work: 0.3290 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.131 Angle : 0.526 9.821 16736 Z= 0.270 Chirality : 0.037 0.163 2056 Planarity : 0.004 0.037 2020 Dihedral : 3.703 13.486 1688 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 19.23 % 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 aren not related in a simple way. whole: 3.39 (0.21), residues: 1520 helix: 3.09 (0.14), residues: 1236 sheet: 2.03 (0.66), residues: 40 loop : -2.72 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.020 0.001 TYR C 124 PHE 0.018 0.001 PHE A 444 TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00293 (12340) covalent geometry : angle 0.52636 (16736) hydrogen bonds : bond 0.04476 ( 1040) hydrogen bonds : angle 3.31208 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4742.36 seconds wall clock time: 81 minutes 44.71 seconds (4904.71 seconds total)