Starting phenix.real_space_refine on Tue Jun 10 20:50:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvt_42628/06_2025/8uvt_42628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvt_42628/06_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_42628/06_2025/8uvt_42628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvt_42628/06_2025/8uvt_42628.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvt_42628/06_2025/8uvt_42628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvt_42628/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.43, per 1000 atoms: 0.53 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: 3.03 Conformation dependent library (CDL) restraints added in 1.6 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: 0.93 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: 3.86 Time building geometry restraints manager: 3.56 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: 3.000 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.000 Find NCS groups from input model: 0.500 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:15.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.950 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12930 ( 1040) hydrogen bonds : angle 5.11744 ( 3096) covalent geometry : bond 0.00282 (12340) covalent geometry : angle 0.47414 (16736) *********************** 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 : 1.296 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: 1.1739 time to fit residues: 310.0386 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 : 1.683 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124172 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= 0.162 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 Details of bonding type rmsd hydrogen bonds : bond 0.05006 ( 1040) hydrogen bonds : angle 3.59974 ( 3096) covalent geometry : bond 0.00375 (12340) covalent geometry : angle 0.54617 (16736) *********************** 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 : 1.403 Fit side-chains REVERT: A 171 MET cc_start: 0.7737 (mmp) cc_final: 0.7467 (mmm) REVERT: A 296 ARG cc_start: 0.8188 (mtt90) cc_final: 0.7834 (mtt90) REVERT: A 310 ASP cc_start: 0.8328 (m-30) cc_final: 0.8074 (m-30) REVERT: A 385 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7711 (ttp-110) REVERT: A 387 MET cc_start: 0.9004 (mtm) cc_final: 0.8753 (mtm) REVERT: B 87 MET cc_start: 0.4679 (OUTLIER) cc_final: 0.4459 (mtm) REVERT: B 306 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7512 (mtp180) REVERT: B 310 ASP cc_start: 0.8339 (m-30) cc_final: 0.8011 (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: 0.8397 (m-30) cc_final: 0.8152 (m-30) REVERT: C 427 MET cc_start: 0.8337 (ptt) cc_final: 0.8106 (ptt) REVERT: D 143 THR cc_start: 0.8481 (m) cc_final: 0.8176 (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: 0.8371 (ptt) cc_final: 0.8135 (ptt) outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 1.2777 time to fit residues: 290.8325 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 : 1.271 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.6980 chunk 124 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.150833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123189 restraints weight = 12769.238| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.29 r_work: 0.3236 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12340 Z= 0.162 Angle : 0.534 5.726 16736 Z= 0.278 Chirality : 0.037 0.131 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.860 13.678 1688 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.11 % Allowed : 12.94 % 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: 3.05 (0.21), residues: 1520 helix: 2.89 (0.13), residues: 1232 sheet: 0.25 (0.49), residues: 40 loop : -2.61 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.004 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.027 0.002 TYR B 124 ARG 0.005 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 1040) hydrogen bonds : angle 3.52030 ( 3096) covalent geometry : bond 0.00381 (12340) covalent geometry : angle 0.53356 (16736) *********************** 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 246 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.302 Fit side-chains REVERT: A 171 MET cc_start: 0.7748 (mmp) cc_final: 0.7538 (mmm) REVERT: A 296 ARG cc_start: 0.8239 (mtt90) cc_final: 0.8028 (mtt-85) REVERT: A 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8110 (m-30) REVERT: A 385 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7881 (ttp-110) REVERT: A 387 MET cc_start: 0.9003 (mtm) cc_final: 0.8765 (mtm) REVERT: B 306 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7654 (mtp180) REVERT: B 310 ASP cc_start: 0.8348 (m-30) cc_final: 0.8112 (m-30) REVERT: B 387 MET cc_start: 0.8932 (mtm) cc_final: 0.8646 (mtm) REVERT: B 401 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 87 MET cc_start: 0.4133 (mtt) cc_final: 0.3137 (mtt) REVERT: C 143 THR cc_start: 0.8528 (m) cc_final: 0.8208 (m) REVERT: C 296 ARG cc_start: 0.8257 (mtt90) cc_final: 0.8018 (mtt-85) REVERT: C 310 ASP cc_start: 0.8376 (m-30) cc_final: 0.8149 (m-30) REVERT: D 143 THR cc_start: 0.8538 (m) cc_final: 0.8219 (m) REVERT: D 296 ARG cc_start: 0.8259 (mtt90) cc_final: 0.8015 (mtt-85) REVERT: D 310 ASP cc_start: 0.8351 (m-30) cc_final: 0.8118 (m-30) REVERT: D 385 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7896 (ttp-110) REVERT: D 427 MET cc_start: 0.8373 (ptt) cc_final: 0.8166 (ptt) outliers start: 42 outliers final: 19 residues processed: 228 average time/residue: 1.2859 time to fit residues: 316.5818 Evaluate side-chains 212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 348 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: 0.9990 chunk 128 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.150614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.123147 restraints weight = 12704.591| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.30 r_work: 0.3234 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2208 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= 0.155 Angle : 0.534 6.453 16736 Z= 0.276 Chirality : 0.037 0.175 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.864 14.155 1688 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.25 % Allowed : 15.09 % 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: 3.12 (0.21), residues: 1520 helix: 2.93 (0.13), residues: 1236 sheet: 0.50 (0.48), residues: 40 loop : -2.64 (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 0.018 0.002 PHE A 205 TYR 0.025 0.001 TYR B 124 ARG 0.004 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 1040) hydrogen bonds : angle 3.45665 ( 3096) covalent geometry : bond 0.00363 (12340) covalent geometry : angle 0.53413 (16736) *********************** 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 245 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.650 Fit side-chains REVERT: A 296 ARG cc_start: 0.8239 (mtt90) cc_final: 0.8035 (mtt-85) REVERT: A 310 ASP cc_start: 0.8350 (m-30) cc_final: 0.8124 (m-30) REVERT: A 385 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7850 (ttp-110) REVERT: A 387 MET cc_start: 0.8983 (mtm) cc_final: 0.8680 (mtm) REVERT: B 87 MET cc_start: 0.4507 (OUTLIER) cc_final: 0.4247 (mtm) REVERT: B 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8121 (m-30) REVERT: B 387 MET cc_start: 0.8923 (mtm) cc_final: 0.8608 (mtm) REVERT: B 401 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 87 MET cc_start: 0.4160 (mtt) cc_final: 0.3046 (mtt) REVERT: C 143 THR cc_start: 0.8525 (m) cc_final: 0.8204 (m) REVERT: C 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8122 (m-30) REVERT: D 143 THR cc_start: 0.8519 (m) cc_final: 0.8205 (m) REVERT: D 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8100 (m-30) REVERT: D 385 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7901 (ttp-110) REVERT: D 427 MET cc_start: 0.8380 (ptt) cc_final: 0.8139 (ptt) outliers start: 44 outliers final: 26 residues processed: 229 average time/residue: 1.4411 time to fit residues: 355.8689 Evaluate side-chains 220 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 362 MET 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 362 MET 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: 0.6980 chunk 124 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 0.0170 chunk 120 optimal weight: 3.9990 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: 1.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.152447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125018 restraints weight = 12730.562| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.30 r_work: 0.3232 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2316 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= 0.135 Angle : 0.513 7.086 16736 Z= 0.264 Chirality : 0.036 0.146 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.780 13.690 1688 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.48 % Allowed : 16.27 % Favored : 80.25 % 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: 3.30 (0.21), residues: 1520 helix: 3.06 (0.14), residues: 1236 sheet: 0.84 (0.52), residues: 40 loop : -2.66 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 193 HIS 0.002 0.001 HIS D 139 PHE 0.016 0.001 PHE A 205 TYR 0.022 0.001 TYR D 124 ARG 0.004 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 1040) hydrogen bonds : angle 3.38563 ( 3096) covalent geometry : bond 0.00304 (12340) covalent geometry : angle 0.51344 (16736) *********************** 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 250 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 1.339 Fit side-chains REVERT: A 296 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: A 310 ASP cc_start: 0.8310 (m-30) cc_final: 0.8050 (m-30) REVERT: A 385 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7357 (ttm110) REVERT: A 387 MET cc_start: 0.8904 (mtm) cc_final: 0.8643 (mtm) REVERT: B 310 ASP cc_start: 0.8326 (m-30) cc_final: 0.8038 (m-30) REVERT: B 387 MET cc_start: 0.8890 (mtm) cc_final: 0.8547 (mtm) REVERT: B 397 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8126 (p) REVERT: B 401 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7819 (tm-30) REVERT: C 52 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7155 (pttp) REVERT: C 87 MET cc_start: 0.4128 (OUTLIER) cc_final: 0.3027 (mtt) REVERT: C 143 THR cc_start: 0.8327 (m) cc_final: 0.8027 (m) REVERT: C 310 ASP cc_start: 0.8330 (m-30) cc_final: 0.8040 (m-30) REVERT: D 52 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7188 (pttp) REVERT: D 143 THR cc_start: 0.8331 (m) cc_final: 0.8029 (m) REVERT: D 310 ASP cc_start: 0.8303 (m-30) cc_final: 0.8007 (m-30) REVERT: D 385 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7382 (ttm110) REVERT: D 427 MET cc_start: 0.8320 (ptt) cc_final: 0.8090 (ptt) outliers start: 47 outliers final: 25 residues processed: 231 average time/residue: 1.2924 time to fit residues: 322.6648 Evaluate side-chains 213 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 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 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 18 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 chunk 131 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 19 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: C 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124789 restraints weight = 12864.926| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.31 r_work: 0.3244 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2361 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= 0.137 Angle : 0.519 8.594 16736 Z= 0.266 Chirality : 0.036 0.129 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.773 13.548 1688 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: 3.30 (0.21), residues: 1520 helix: 3.05 (0.14), residues: 1236 sheet: 1.04 (0.53), residues: 40 loop : -2.67 (0.36), 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 139 PHE 0.016 0.001 PHE A 205 TYR 0.022 0.001 TYR C 124 ARG 0.004 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 1040) hydrogen bonds : angle 3.36662 ( 3096) covalent geometry : bond 0.00309 (12340) covalent geometry : angle 0.51890 (16736) *********************** 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 237 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.319 Fit side-chains REVERT: A 296 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7986 (mtt-85) REVERT: A 310 ASP cc_start: 0.8323 (m-30) cc_final: 0.8061 (m-30) REVERT: A 385 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7527 (ttm110) REVERT: A 387 MET cc_start: 0.8970 (mtm) cc_final: 0.8678 (mtm) REVERT: B 87 MET cc_start: 0.4127 (OUTLIER) cc_final: 0.3855 (mtm) REVERT: B 310 ASP cc_start: 0.8319 (m-30) cc_final: 0.8049 (m-30) REVERT: B 387 MET cc_start: 0.8919 (mtm) cc_final: 0.8556 (mtm) REVERT: B 397 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 401 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 87 MET cc_start: 0.4037 (OUTLIER) cc_final: 0.2897 (mtt) REVERT: C 143 THR cc_start: 0.8469 (m) cc_final: 0.8156 (m) REVERT: C 310 ASP cc_start: 0.8347 (m-30) cc_final: 0.8067 (m-30) REVERT: D 143 THR cc_start: 0.8470 (m) cc_final: 0.8160 (m) REVERT: D 310 ASP cc_start: 0.8314 (m-30) cc_final: 0.8041 (m-30) REVERT: D 385 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7716 (ttp-110) REVERT: D 427 MET cc_start: 0.8371 (ptt) cc_final: 0.8150 (ptt) outliers start: 42 outliers final: 27 residues processed: 220 average time/residue: 1.3815 time to fit residues: 327.5612 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 : 1.371 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 97 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN B 445 GLN C 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122603 restraints weight = 12877.568| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.31 r_work: 0.3217 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12340 Z= 0.165 Angle : 0.555 8.675 16736 Z= 0.284 Chirality : 0.037 0.133 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.890 13.870 1688 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.25 % Allowed : 17.16 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.10 (0.21), residues: 1520 helix: 2.90 (0.13), residues: 1236 sheet: 1.07 (0.55), residues: 40 loop : -2.71 (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 0.018 0.002 PHE A 205 TYR 0.024 0.002 TYR C 124 ARG 0.004 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 1040) hydrogen bonds : angle 3.45706 ( 3096) covalent geometry : bond 0.00393 (12340) covalent geometry : angle 0.55454 (16736) *********************** 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 235 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.339 Fit side-chains REVERT: A 87 MET cc_start: 0.3960 (mtt) cc_final: 0.3054 (mtt) REVERT: A 296 ARG cc_start: 0.8214 (mtt90) cc_final: 0.8013 (mtt-85) REVERT: A 310 ASP cc_start: 0.8357 (m-30) cc_final: 0.8133 (m-30) REVERT: A 385 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7656 (ttm110) REVERT: A 387 MET cc_start: 0.9016 (mtm) cc_final: 0.8734 (mtm) REVERT: B 310 ASP cc_start: 0.8377 (m-30) cc_final: 0.8140 (m-30) REVERT: B 387 MET cc_start: 0.8948 (mtm) cc_final: 0.8634 (mtm) REVERT: B 401 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 52 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7253 (pttp) REVERT: C 87 MET cc_start: 0.4070 (OUTLIER) cc_final: 0.2947 (mtt) REVERT: C 143 THR cc_start: 0.8454 (m) cc_final: 0.8143 (m) REVERT: C 151 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7904 (tt) REVERT: C 310 ASP cc_start: 0.8370 (m-30) cc_final: 0.8131 (m-30) REVERT: D 52 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7258 (pttp) REVERT: D 87 MET cc_start: 0.4167 (mtt) cc_final: 0.3013 (mtt) REVERT: D 143 THR cc_start: 0.8461 (m) cc_final: 0.8152 (m) REVERT: D 151 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7915 (tt) REVERT: D 296 ARG cc_start: 0.8249 (mtt90) cc_final: 0.8023 (mtt-85) REVERT: D 310 ASP cc_start: 0.8376 (m-30) cc_final: 0.8147 (m-30) REVERT: D 385 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7673 (ttm110) REVERT: D 427 MET cc_start: 0.8386 (ptt) cc_final: 0.8163 (ptt) outliers start: 44 outliers final: 27 residues processed: 218 average time/residue: 1.4578 time to fit residues: 340.8344 Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.150623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123416 restraints weight = 12901.220| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.31 r_work: 0.3219 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: 0.8048 moved from start: 0.2456 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= 0.151 Angle : 0.541 8.620 16736 Z= 0.279 Chirality : 0.037 0.135 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.874 13.631 1688 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.11 % Allowed : 17.23 % Favored : 79.66 % 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: 3.12 (0.21), residues: 1520 helix: 2.92 (0.14), residues: 1236 sheet: 1.18 (0.57), residues: 40 loop : -2.74 (0.34), 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 370 PHE 0.017 0.002 PHE A 205 TYR 0.022 0.001 TYR B 124 ARG 0.004 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 1040) hydrogen bonds : angle 3.41762 ( 3096) covalent geometry : bond 0.00353 (12340) covalent geometry : angle 0.54141 (16736) *********************** 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 230 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.499 Fit side-chains REVERT: A 296 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7982 (mtt-85) REVERT: A 310 ASP cc_start: 0.8346 (m-30) cc_final: 0.8111 (m-30) REVERT: A 385 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7576 (ttm110) REVERT: A 387 MET cc_start: 0.8952 (mtm) cc_final: 0.8647 (mtm) REVERT: B 87 MET cc_start: 0.4018 (mtt) cc_final: 0.2853 (mtt) REVERT: B 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8119 (m-30) REVERT: B 387 MET cc_start: 0.8904 (mtm) cc_final: 0.8581 (mtm) REVERT: B 397 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 401 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 52 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7228 (pttp) REVERT: C 87 MET cc_start: 0.4022 (OUTLIER) cc_final: 0.2897 (mtt) REVERT: C 143 THR cc_start: 0.8384 (m) cc_final: 0.8078 (m) REVERT: C 151 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7883 (tt) REVERT: C 284 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: C 310 ASP cc_start: 0.8349 (m-30) cc_final: 0.8067 (m-30) REVERT: D 52 LYS cc_start: 0.7747 (mmtm) cc_final: 0.7251 (pttp) REVERT: D 87 MET cc_start: 0.4074 (mtt) cc_final: 0.2905 (mtt) REVERT: D 143 THR cc_start: 0.8394 (m) cc_final: 0.8092 (m) REVERT: D 151 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7888 (tt) REVERT: D 296 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7980 (mtt-85) REVERT: D 310 ASP cc_start: 0.8350 (m-30) cc_final: 0.8112 (m-30) REVERT: D 385 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7613 (ttm110) REVERT: D 427 MET cc_start: 0.8356 (ptt) cc_final: 0.8123 (ptt) REVERT: D 445 GLN cc_start: 0.6391 (mp10) cc_final: 0.6173 (mp10) outliers start: 42 outliers final: 25 residues processed: 216 average time/residue: 1.5189 time to fit residues: 355.4839 Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 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 284 GLN 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: 0.8980 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.150051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122882 restraints weight = 12860.371| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.30 r_work: 0.3210 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2495 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= 0.159 Angle : 0.551 9.034 16736 Z= 0.284 Chirality : 0.037 0.137 2056 Planarity : 0.004 0.033 2020 Dihedral : 3.898 13.929 1688 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.81 % Allowed : 17.90 % 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 (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: 3.03 (0.21), residues: 1520 helix: 2.86 (0.13), residues: 1236 sheet: 1.18 (0.58), residues: 40 loop : -2.79 (0.34), 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 0.026 0.002 PHE A 444 TYR 0.023 0.002 TYR B 124 ARG 0.004 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 1040) hydrogen bonds : angle 3.45314 ( 3096) covalent geometry : bond 0.00375 (12340) covalent geometry : angle 0.55080 (16736) *********************** 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 225 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.373 Fit side-chains REVERT: A 296 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7985 (mtt-85) REVERT: A 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8123 (m-30) REVERT: A 385 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7603 (ttm110) REVERT: A 387 MET cc_start: 0.8997 (mtm) cc_final: 0.8708 (mtm) REVERT: B 87 MET cc_start: 0.4001 (mtt) cc_final: 0.2826 (mtt) REVERT: B 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8106 (m-30) REVERT: B 387 MET cc_start: 0.8932 (mtm) cc_final: 0.8617 (mtm) REVERT: B 397 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 401 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 87 MET cc_start: 0.4048 (OUTLIER) cc_final: 0.2922 (mtt) REVERT: C 143 THR cc_start: 0.8406 (m) cc_final: 0.8118 (m) REVERT: C 151 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 310 ASP cc_start: 0.8369 (m-30) cc_final: 0.8130 (m-30) REVERT: D 87 MET cc_start: 0.3760 (mtt) cc_final: 0.2573 (mtt) REVERT: D 143 THR cc_start: 0.8388 (m) cc_final: 0.8096 (m) REVERT: D 151 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7895 (tt) REVERT: D 296 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7979 (mtt-85) REVERT: D 310 ASP cc_start: 0.8347 (m-30) cc_final: 0.8104 (m-30) REVERT: D 385 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7629 (ttm110) REVERT: D 427 MET cc_start: 0.8358 (ptt) cc_final: 0.8129 (ptt) outliers start: 38 outliers final: 28 residues processed: 210 average time/residue: 1.4929 time to fit residues: 336.3067 Evaluate side-chains 212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 211 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 54 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 = 0.3705 r_free = 0.3705 target = 0.150818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123635 restraints weight = 12799.052| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.31 r_work: 0.3223 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2502 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= 0.148 Angle : 0.542 8.045 16736 Z= 0.280 Chirality : 0.037 0.143 2056 Planarity : 0.004 0.034 2020 Dihedral : 3.877 13.454 1688 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 3.07 (0.21), residues: 1520 helix: 2.89 (0.14), residues: 1236 sheet: 1.28 (0.59), 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 0.002 0.001 HIS B 392 PHE 0.024 0.002 PHE A 444 TYR 0.022 0.002 TYR B 124 ARG 0.004 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 1040) hydrogen bonds : angle 3.41856 ( 3096) covalent geometry : bond 0.00343 (12340) covalent geometry : angle 0.54245 (16736) ********************** 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 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.316 Fit side-chains REVERT: A 52 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7194 (pttp) REVERT: A 296 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7968 (mtt-85) REVERT: A 310 ASP cc_start: 0.8352 (m-30) cc_final: 0.8123 (m-30) REVERT: A 385 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7566 (ttm110) REVERT: A 387 MET cc_start: 0.8934 (mtm) cc_final: 0.8632 (mtm) REVERT: B 52 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7206 (pttp) REVERT: B 87 MET cc_start: 0.3994 (mtt) cc_final: 0.2828 (mtt) REVERT: B 310 ASP cc_start: 0.8339 (m-30) cc_final: 0.8054 (m-30) REVERT: B 387 MET cc_start: 0.8912 (mtm) cc_final: 0.8588 (mtm) REVERT: B 397 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 401 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 52 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7217 (pttp) REVERT: C 87 MET cc_start: 0.4024 (OUTLIER) cc_final: 0.2900 (mtt) REVERT: C 143 THR cc_start: 0.8349 (m) cc_final: 0.8057 (m) REVERT: C 151 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7874 (tt) REVERT: C 310 ASP cc_start: 0.8343 (m-30) cc_final: 0.8065 (m-30) REVERT: D 52 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7241 (pttp) REVERT: D 143 THR cc_start: 0.8364 (m) cc_final: 0.8072 (m) REVERT: D 296 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7961 (mtt-85) REVERT: D 310 ASP cc_start: 0.8348 (m-30) cc_final: 0.8123 (m-30) REVERT: D 385 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7760 (ttp-110) REVERT: D 427 MET cc_start: 0.8342 (ptt) cc_final: 0.8107 (ptt) outliers start: 33 outliers final: 28 residues processed: 208 average time/residue: 1.6288 time to fit residues: 364.1185 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 : 1.326 ------------------------------------------------------------------------------- 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 211 ARG 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 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 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: 0.5980 chunk 137 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 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 = 0.3701 r_free = 0.3701 target = 0.150460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123280 restraints weight = 12867.468| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.31 r_work: 0.3216 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2549 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= 0.155 Angle : 0.550 7.821 16736 Z= 0.284 Chirality : 0.038 0.175 2056 Planarity : 0.004 0.034 2020 Dihedral : 3.894 13.619 1688 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.44 % Allowed : 18.42 % Favored : 79.14 % 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: 3.00 (0.21), residues: 1520 helix: 2.84 (0.13), residues: 1236 sheet: 1.21 (0.59), residues: 40 loop : -2.86 (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 D 370 PHE 0.025 0.002 PHE B 444 TYR 0.023 0.002 TYR B 124 ARG 0.004 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 1040) hydrogen bonds : angle 3.44353 ( 3096) covalent geometry : bond 0.00364 (12340) covalent geometry : angle 0.54958 (16736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9557.57 seconds wall clock time: 165 minutes 57.52 seconds (9957.52 seconds total)