Starting phenix.real_space_refine on Sat Jan 18 09:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvt_42628/01_2025/8uvt_42628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvt_42628/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvt_42628/01_2025/8uvt_42628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvt_42628/01_2025/8uvt_42628.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvt_42628/01_2025/8uvt_42628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvt_42628/01_2025/8uvt_42628.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: C, B, D Time building chain proxies: 7.05, per 1000 atoms: 0.58 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: 2.90 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.84 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: 4.00 Time building geometry restraints manager: 3.39 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.350 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.880 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.890 ------------------------------------------------------------------------------- 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= 0.185 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (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 TRP 0.005 0.001 TRP A 193 HIS 0.004 0.001 HIS C 392 PHE 0.014 0.001 PHE D 205 TYR 0.008 0.001 TYR C 124 ARG 0.003 0.000 ARG D 405 *********************** 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 : 1.367 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: B 387 MET cc_start: 0.8775 (mtm) cc_final: 0.8573 (mtm) 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: 1.1652 time to fit residues: 307.7480 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 : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.152045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124171 restraints weight = 12678.241| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.31 r_work: 0.3212 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.247 Angle : 0.546 6.125 16736 Z= 0.283 Chirality : 0.038 0.155 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.859 15.578 1688 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.29 % Allowed : 10.50 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.21), residues: 1520 helix: 2.85 (0.13), residues: 1228 sheet: 0.06 (0.54), residues: 40 loop : -2.09 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.005 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.030 0.002 TYR B 124 ARG 0.004 0.001 ARG A 405 *********************** 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 226 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.397 Fit side-chains REVERT: A 171 MET cc_start: 0.7739 (mmp) cc_final: 0.7469 (mmm) REVERT: A 296 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7835 (mtt90) REVERT: A 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.8076 (m-30) REVERT: A 385 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7712 (ttp-110) REVERT: A 387 MET cc_start: 0.9002 (mtm) cc_final: 0.8751 (mtm) REVERT: B 87 MET cc_start: 0.4680 (OUTLIER) cc_final: 0.4461 (mtm) REVERT: B 306 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7512 (mtp180) REVERT: B 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8012 (m-30) REVERT: B 387 MET cc_start: 0.8887 (mtm) cc_final: 0.8620 (mtm) REVERT: C 143 THR cc_start: 0.8456 (m) cc_final: 0.8155 (m) REVERT: C 310 ASP cc_start: 0.8398 (m-30) cc_final: 0.8152 (m-30) REVERT: C 427 MET cc_start: 0.8338 (ptt) cc_final: 0.8107 (ptt) REVERT: D 143 THR cc_start: 0.8479 (m) cc_final: 0.8175 (m) REVERT: D 310 ASP cc_start: 0.8352 (m-30) cc_final: 0.8110 (m-30) REVERT: D 385 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7686 (ttp-110) REVERT: D 427 MET cc_start: 0.8373 (ptt) cc_final: 0.8137 (ptt) outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 1.3169 time to fit residues: 299.6566 Evaluate side-chains 198 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 132 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.151673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124022 restraints weight = 12755.055| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.29 r_work: 0.3246 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1940 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= 0.233 Angle : 0.523 6.132 16736 Z= 0.272 Chirality : 0.037 0.130 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.817 13.616 1688 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.96 % Allowed : 13.09 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.21), residues: 1520 helix: 2.92 (0.13), residues: 1236 sheet: 0.34 (0.49), residues: 40 loop : -2.55 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS D 392 PHE 0.018 0.002 PHE A 205 TYR 0.027 0.001 TYR B 124 ARG 0.004 0.000 ARG A 405 *********************** 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 242 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.402 Fit side-chains REVERT: A 171 MET cc_start: 0.7760 (mmp) cc_final: 0.7539 (mmm) REVERT: A 296 ARG cc_start: 0.8238 (mtt90) cc_final: 0.8000 (mtt-85) REVERT: A 310 ASP cc_start: 0.8327 (m-30) cc_final: 0.8097 (m-30) REVERT: A 385 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7858 (ttp-110) REVERT: A 387 MET cc_start: 0.9011 (mtm) cc_final: 0.8778 (mtm) REVERT: B 306 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7667 (mtp180) REVERT: B 310 ASP cc_start: 0.8344 (m-30) cc_final: 0.8099 (m-30) REVERT: B 387 MET cc_start: 0.8917 (mtm) cc_final: 0.8637 (mtm) REVERT: B 401 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7756 (tm-30) REVERT: C 87 MET cc_start: 0.4126 (mtt) cc_final: 0.3143 (mtt) REVERT: C 143 THR cc_start: 0.8521 (m) cc_final: 0.8197 (m) REVERT: C 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8124 (m-30) REVERT: C 427 MET cc_start: 0.8327 (ptt) cc_final: 0.8119 (ptt) REVERT: D 143 THR cc_start: 0.8540 (m) cc_final: 0.8220 (m) REVERT: D 310 ASP cc_start: 0.8327 (m-30) cc_final: 0.8087 (m-30) REVERT: D 385 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7868 (ttp-110) REVERT: D 427 MET cc_start: 0.8389 (ptt) cc_final: 0.8171 (ptt) outliers start: 40 outliers final: 17 residues processed: 225 average time/residue: 1.3898 time to fit residues: 337.8087 Evaluate side-chains 205 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 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 132 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 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 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122869 restraints weight = 12714.601| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.29 r_work: 0.3219 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.247 Angle : 0.538 5.921 16736 Z= 0.278 Chirality : 0.037 0.175 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.866 14.160 1688 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.33 % Allowed : 15.01 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.21), residues: 1520 helix: 2.92 (0.13), residues: 1236 sheet: 0.47 (0.48), residues: 40 loop : -2.63 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS D 392 PHE 0.019 0.002 PHE A 205 TYR 0.025 0.002 TYR B 124 ARG 0.004 0.000 ARG A 405 *********************** 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: 45 poor density : 201 time to evaluate : 1.477 Fit side-chains REVERT: A 171 MET cc_start: 0.7636 (mmp) cc_final: 0.7428 (mmm) REVERT: A 296 ARG cc_start: 0.8228 (mtt90) cc_final: 0.8013 (mtt-85) REVERT: A 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8123 (m-30) REVERT: A 387 MET cc_start: 0.8999 (mtm) cc_final: 0.8693 (mtm) REVERT: B 87 MET cc_start: 0.4492 (OUTLIER) cc_final: 0.4235 (mtm) REVERT: B 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8096 (m-30) REVERT: B 387 MET cc_start: 0.8925 (mtm) cc_final: 0.8611 (mtm) REVERT: B 401 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 87 MET cc_start: 0.4122 (mtt) cc_final: 0.3162 (mtt) REVERT: C 143 THR cc_start: 0.8497 (m) cc_final: 0.8177 (m) REVERT: C 296 ARG cc_start: 0.8237 (mtt90) cc_final: 0.8028 (mtt-85) REVERT: C 310 ASP cc_start: 0.8356 (m-30) cc_final: 0.8120 (m-30) REVERT: C 427 MET cc_start: 0.8326 (ptt) cc_final: 0.8098 (ptt) REVERT: D 143 THR cc_start: 0.8492 (m) cc_final: 0.8175 (m) REVERT: D 296 ARG cc_start: 0.8238 (mtt90) cc_final: 0.8022 (mtt-85) REVERT: D 310 ASP cc_start: 0.8347 (m-30) cc_final: 0.8107 (m-30) REVERT: D 385 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7888 (ttp-110) REVERT: D 427 MET cc_start: 0.8391 (ptt) cc_final: 0.8167 (ptt) outliers start: 45 outliers final: 24 residues processed: 231 average time/residue: 1.4079 time to fit residues: 349.9203 Evaluate side-chains 216 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 289 GLU 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 431 LEU 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 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 0.0070 chunk 124 optimal weight: 0.4980 chunk 119 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 135 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120603 restraints weight = 12836.259| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.42 r_work: 0.3230 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2289 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= 0.189 Angle : 0.511 7.080 16736 Z= 0.262 Chirality : 0.036 0.145 2056 Planarity : 0.003 0.030 2020 Dihedral : 3.757 13.617 1688 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.33 % Allowed : 16.20 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.21), residues: 1520 helix: 3.09 (0.14), residues: 1236 sheet: 1.03 (0.54), residues: 40 loop : -2.68 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.003 0.001 HIS C 139 PHE 0.015 0.001 PHE A 205 TYR 0.022 0.001 TYR B 124 ARG 0.003 0.000 ARG B 405 *********************** 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: 45 poor density : 197 time to evaluate : 1.446 Fit side-chains REVERT: A 296 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7885 (mtt-85) REVERT: A 310 ASP cc_start: 0.8281 (m-30) cc_final: 0.8002 (m-30) REVERT: A 387 MET cc_start: 0.8896 (mtm) cc_final: 0.8610 (mtm) REVERT: B 310 ASP cc_start: 0.8293 (m-30) cc_final: 0.8011 (m-30) REVERT: B 387 MET cc_start: 0.8873 (mtm) cc_final: 0.8591 (mtm) REVERT: B 401 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 52 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7123 (pttp) REVERT: C 87 MET cc_start: 0.3978 (mtt) cc_final: 0.2861 (mtt) REVERT: C 143 THR cc_start: 0.8252 (m) cc_final: 0.7944 (m) REVERT: C 310 ASP cc_start: 0.8317 (m-30) cc_final: 0.8022 (m-30) REVERT: C 427 MET cc_start: 0.8324 (ptt) cc_final: 0.8074 (ptt) REVERT: D 52 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7148 (pttp) REVERT: D 143 THR cc_start: 0.8269 (m) cc_final: 0.7958 (m) REVERT: D 310 ASP cc_start: 0.8278 (m-30) cc_final: 0.7980 (m-30) REVERT: D 385 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7314 (ttm110) REVERT: D 427 MET cc_start: 0.8378 (ptt) cc_final: 0.8146 (ptt) outliers start: 45 outliers final: 24 residues processed: 224 average time/residue: 1.3694 time to fit residues: 331.3275 Evaluate side-chains 212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 289 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.149841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122288 restraints weight = 12893.740| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.32 r_work: 0.3213 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2394 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= 0.264 Angle : 0.553 8.490 16736 Z= 0.283 Chirality : 0.038 0.131 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.877 13.980 1688 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.11 % Allowed : 17.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.21), residues: 1520 helix: 2.92 (0.13), residues: 1236 sheet: 0.97 (0.53), residues: 40 loop : -2.71 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 193 HIS 0.003 0.001 HIS D 370 PHE 0.019 0.002 PHE A 205 TYR 0.024 0.002 TYR D 124 ARG 0.005 0.000 ARG D 405 *********************** 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 236 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.368 Fit side-chains REVERT: A 296 ARG cc_start: 0.8218 (mtt90) cc_final: 0.8000 (mtt-85) REVERT: A 310 ASP cc_start: 0.8344 (m-30) cc_final: 0.8121 (m-30) REVERT: A 387 MET cc_start: 0.9010 (mtm) cc_final: 0.8658 (mtm) REVERT: B 310 ASP cc_start: 0.8344 (m-30) cc_final: 0.8100 (m-30) REVERT: B 387 MET cc_start: 0.8954 (mtm) cc_final: 0.8646 (mtm) REVERT: B 401 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7790 (tm-30) REVERT: C 87 MET cc_start: 0.4265 (OUTLIER) cc_final: 0.3156 (mtt) REVERT: C 143 THR cc_start: 0.8426 (m) cc_final: 0.8114 (m) REVERT: C 151 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7901 (tt) REVERT: C 296 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7971 (mtt-85) REVERT: C 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8123 (m-30) REVERT: C 427 MET cc_start: 0.8347 (ptt) cc_final: 0.8114 (ptt) REVERT: D 143 THR cc_start: 0.8430 (m) cc_final: 0.8124 (m) REVERT: D 151 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7912 (tt) REVERT: D 296 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7957 (mtt-85) REVERT: D 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8120 (m-30) REVERT: D 385 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7828 (ttp-110) REVERT: D 427 MET cc_start: 0.8360 (ptt) cc_final: 0.8139 (ptt) outliers start: 42 outliers final: 27 residues processed: 219 average time/residue: 1.4739 time to fit residues: 348.2584 Evaluate side-chains 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 87 MET Chi-restraints excluded: chain C residue 151 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 C residue 431 LEU Chi-restraints excluded: chain D residue 151 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 75 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.0000 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.151226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123942 restraints weight = 12875.852| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.30 r_work: 0.3272 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 0.031 12340 Z= 0.219 Angle : 0.532 8.074 16736 Z= 0.273 Chirality : 0.037 0.131 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.823 13.602 1688 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.33 % Allowed : 17.16 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.21), residues: 1520 helix: 2.97 (0.14), residues: 1236 sheet: 1.23 (0.56), residues: 40 loop : -2.72 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS B 392 PHE 0.016 0.002 PHE A 205 TYR 0.022 0.001 TYR D 124 ARG 0.004 0.000 ARG B 405 *********************** 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 232 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.457 Fit side-chains REVERT: A 296 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7992 (mtt-85) REVERT: A 310 ASP cc_start: 0.8309 (m-30) cc_final: 0.8044 (m-30) REVERT: A 387 MET cc_start: 0.8936 (mtm) cc_final: 0.8644 (mtm) REVERT: B 87 MET cc_start: 0.4111 (mtt) cc_final: 0.2935 (mtt) REVERT: B 310 ASP cc_start: 0.8330 (m-30) cc_final: 0.8048 (m-30) REVERT: B 387 MET cc_start: 0.8904 (mtm) cc_final: 0.8545 (mtm) REVERT: B 401 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7841 (tm-30) REVERT: C 52 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7259 (pttp) REVERT: C 87 MET cc_start: 0.4095 (OUTLIER) cc_final: 0.2975 (mtt) REVERT: C 143 THR cc_start: 0.8471 (m) cc_final: 0.8150 (m) REVERT: C 151 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7895 (tt) REVERT: C 296 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7992 (mtt-85) REVERT: C 310 ASP cc_start: 0.8339 (m-30) cc_final: 0.8080 (m-30) REVERT: C 427 MET cc_start: 0.8309 (ptt) cc_final: 0.8079 (ptt) REVERT: D 52 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7280 (pttp) REVERT: D 87 MET cc_start: 0.4193 (mtt) cc_final: 0.3000 (mtt) REVERT: D 143 THR cc_start: 0.8454 (m) cc_final: 0.8131 (m) REVERT: D 151 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7889 (tt) REVERT: D 296 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7986 (mtt-85) REVERT: D 310 ASP cc_start: 0.8313 (m-30) cc_final: 0.8048 (m-30) REVERT: D 385 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7651 (ttm110) REVERT: D 427 MET cc_start: 0.8368 (ptt) cc_final: 0.8140 (ptt) outliers start: 45 outliers final: 26 residues processed: 216 average time/residue: 1.4459 time to fit residues: 335.8263 Evaluate side-chains 214 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 87 MET Chi-restraints excluded: chain C residue 151 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 C residue 431 LEU Chi-restraints excluded: chain D residue 151 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124481 restraints weight = 12886.272| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.31 r_work: 0.3244 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2436 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= 0.208 Angle : 0.532 10.277 16736 Z= 0.272 Chirality : 0.037 0.133 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.803 13.391 1688 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.88 % Allowed : 17.68 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.21), residues: 1520 helix: 2.99 (0.14), residues: 1236 sheet: 1.45 (0.60), residues: 40 loop : -2.76 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.002 0.001 HIS D 370 PHE 0.020 0.001 PHE A 444 TYR 0.021 0.001 TYR C 124 ARG 0.004 0.000 ARG B 405 *********************** 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 232 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.538 Fit side-chains REVERT: A 296 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7999 (mtt-85) REVERT: A 310 ASP cc_start: 0.8318 (m-30) cc_final: 0.8068 (m-30) REVERT: A 387 MET cc_start: 0.8929 (mtm) cc_final: 0.8633 (mtm) REVERT: B 87 MET cc_start: 0.4019 (mtt) cc_final: 0.2871 (mtt) REVERT: B 129 VAL cc_start: 0.8354 (t) cc_final: 0.7855 (m) REVERT: B 310 ASP cc_start: 0.8325 (m-30) cc_final: 0.8045 (m-30) REVERT: B 387 MET cc_start: 0.8918 (mtm) cc_final: 0.8555 (mtm) REVERT: B 401 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7870 (tm-30) REVERT: C 52 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7220 (pttp) REVERT: C 87 MET cc_start: 0.4091 (OUTLIER) cc_final: 0.2984 (mtt) REVERT: C 143 THR cc_start: 0.8417 (m) cc_final: 0.8109 (m) REVERT: C 165 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7775 (t70) REVERT: C 284 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: C 296 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7994 (mtt-85) REVERT: C 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8078 (m-30) REVERT: C 427 MET cc_start: 0.8309 (ptt) cc_final: 0.8078 (ptt) REVERT: C 445 GLN cc_start: 0.6598 (mp-120) cc_final: 0.6288 (mp10) REVERT: D 52 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7246 (pttp) REVERT: D 87 MET cc_start: 0.3950 (mtt) cc_final: 0.2743 (mtt) REVERT: D 143 THR cc_start: 0.8429 (m) cc_final: 0.8116 (m) REVERT: D 151 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7886 (tt) REVERT: D 296 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7974 (mtt-85) REVERT: D 310 ASP cc_start: 0.8323 (m-30) cc_final: 0.8055 (m-30) REVERT: D 385 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7601 (ttm110) REVERT: D 427 MET cc_start: 0.8357 (ptt) cc_final: 0.8127 (ptt) REVERT: D 445 GLN cc_start: 0.6402 (mp-120) cc_final: 0.6143 (mp10) outliers start: 39 outliers final: 28 residues processed: 217 average time/residue: 1.4170 time to fit residues: 330.8046 Evaluate side-chains 216 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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 87 MET Chi-restraints excluded: chain C residue 165 ASP 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 284 GLN Chi-restraints excluded: chain C residue 289 GLU 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 151 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122926 restraints weight = 12850.649| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.30 r_work: 0.3203 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.250 Angle : 0.557 10.293 16736 Z= 0.286 Chirality : 0.038 0.142 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.891 13.766 1688 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.81 % Allowed : 17.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.21), residues: 1520 helix: 2.88 (0.13), residues: 1236 sheet: 1.36 (0.60), residues: 40 loop : -2.80 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS B 392 PHE 0.025 0.002 PHE A 444 TYR 0.023 0.002 TYR B 124 ARG 0.004 0.000 ARG D 405 *********************** 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 230 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.364 Fit side-chains REVERT: A 87 MET cc_start: 0.3788 (mtt) cc_final: 0.2905 (mtt) REVERT: A 296 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7910 (mtt-85) REVERT: A 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8110 (m-30) REVERT: A 387 MET cc_start: 0.8974 (mtm) cc_final: 0.8632 (mtm) REVERT: B 87 MET cc_start: 0.3925 (mtt) cc_final: 0.2777 (mtt) REVERT: B 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8090 (m-30) REVERT: B 387 MET cc_start: 0.8910 (mtm) cc_final: 0.8588 (mtm) REVERT: B 401 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 87 MET cc_start: 0.3991 (OUTLIER) cc_final: 0.2912 (mtt) REVERT: C 143 THR cc_start: 0.8347 (m) cc_final: 0.8044 (m) REVERT: C 284 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: C 296 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7926 (mtt-85) REVERT: C 310 ASP cc_start: 0.8355 (m-30) cc_final: 0.8114 (m-30) REVERT: C 427 MET cc_start: 0.8319 (ptt) cc_final: 0.8093 (ptt) REVERT: D 87 MET cc_start: 0.3908 (mtt) cc_final: 0.2735 (mtt) REVERT: D 143 THR cc_start: 0.8350 (m) cc_final: 0.8045 (m) REVERT: D 151 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7871 (tt) REVERT: D 165 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7883 (t70) REVERT: D 296 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7910 (mtt-85) REVERT: D 310 ASP cc_start: 0.8347 (m-30) cc_final: 0.8104 (m-30) REVERT: D 385 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7543 (ttm110) REVERT: D 427 MET cc_start: 0.8337 (ptt) cc_final: 0.8118 (ptt) REVERT: D 445 GLN cc_start: 0.6375 (mp-120) cc_final: 0.6134 (mp10) outliers start: 38 outliers final: 28 residues processed: 218 average time/residue: 1.4723 time to fit residues: 344.1715 Evaluate side-chains 215 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 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 284 GLN Chi-restraints excluded: chain C residue 289 GLU 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 151 LEU Chi-restraints excluded: chain D residue 165 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 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 = 0.3705 r_free = 0.3705 target = 0.150951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123868 restraints weight = 12799.530| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.30 r_work: 0.3206 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2505 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= 0.229 Angle : 0.550 10.113 16736 Z= 0.282 Chirality : 0.037 0.145 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.857 13.423 1688 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 18.49 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.21), residues: 1520 helix: 2.90 (0.14), residues: 1236 sheet: 1.39 (0.60), residues: 40 loop : -2.81 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS B 392 PHE 0.022 0.002 PHE A 444 TYR 0.021 0.002 TYR B 124 ARG 0.004 0.000 ARG D 405 ********************** 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 220 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 1.376 Fit side-chains REVERT: A 52 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7095 (pttp) REVERT: A 296 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7878 (mtt-85) REVERT: A 310 ASP cc_start: 0.8322 (m-30) cc_final: 0.8090 (m-30) REVERT: A 387 MET cc_start: 0.8916 (mtm) cc_final: 0.8603 (mtm) REVERT: B 52 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7086 (pttp) REVERT: B 129 VAL cc_start: 0.8213 (t) cc_final: 0.7660 (m) REVERT: B 310 ASP cc_start: 0.8303 (m-30) cc_final: 0.8012 (m-30) REVERT: B 387 MET cc_start: 0.8868 (mtm) cc_final: 0.8536 (mtm) REVERT: B 401 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 52 LYS cc_start: 0.7656 (mmtm) cc_final: 0.7079 (pttp) REVERT: C 87 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.2607 (mtt) REVERT: C 143 THR cc_start: 0.8280 (m) cc_final: 0.7993 (m) REVERT: C 296 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7876 (mtt-85) REVERT: C 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.8062 (m-30) REVERT: C 427 MET cc_start: 0.8296 (ptt) cc_final: 0.8070 (ptt) REVERT: D 52 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7109 (pttp) REVERT: D 87 MET cc_start: 0.3789 (mtt) cc_final: 0.2607 (mtt) REVERT: D 143 THR cc_start: 0.8273 (m) cc_final: 0.7985 (m) REVERT: D 151 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7835 (tt) REVERT: D 165 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7805 (t70) REVERT: D 296 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7853 (mtt-85) REVERT: D 310 ASP cc_start: 0.8336 (m-30) cc_final: 0.8097 (m-30) REVERT: D 385 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7673 (ttp-110) REVERT: D 427 MET cc_start: 0.8304 (ptt) cc_final: 0.8077 (ptt) outliers start: 33 outliers final: 28 residues processed: 209 average time/residue: 1.5041 time to fit residues: 338.2740 Evaluate side-chains 215 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 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 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 289 GLU 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 151 LEU Chi-restraints excluded: chain D residue 165 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.150417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123205 restraints weight = 12868.337| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.31 r_work: 0.3218 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12340 Z= 0.242 Angle : 0.559 9.806 16736 Z= 0.286 Chirality : 0.038 0.178 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.887 13.553 1688 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.51 % Allowed : 18.49 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.21), residues: 1520 helix: 2.84 (0.13), residues: 1236 sheet: 1.37 (0.60), residues: 40 loop : -2.81 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS B 392 PHE 0.024 0.002 PHE B 444 TYR 0.021 0.002 TYR A 124 ARG 0.004 0.000 ARG D 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8979.90 seconds wall clock time: 159 minutes 35.54 seconds (9575.54 seconds total)