Starting phenix.real_space_refine on Wed Jun 18 23:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnp_50601/06_2025/9fnp_50601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnp_50601/06_2025/9fnp_50601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fnp_50601/06_2025/9fnp_50601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnp_50601/06_2025/9fnp_50601.map" model { file = "/net/cci-nas-00/data/ceres_data/9fnp_50601/06_2025/9fnp_50601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnp_50601/06_2025/9fnp_50601.cif" } resolution = 2.2 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= 0.000 sd= 0.019 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 56 5.16 5 C 13853 2.51 5 N 3766 2.21 5 O 4291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21966 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3138 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 9.77, per 1000 atoms: 0.44 Number of scatterers: 21966 At special positions: 0 Unit cell: (175.13, 175.13, 114.54, 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 56 16.00 O 4291 8.00 N 3766 7.00 C 13853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.04 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.04 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.04 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: 5.29 Conformation dependent library (CDL) restraints added in 2.9 seconds 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 20.1% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.626A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.572A pdb=" N THR A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.627A pdb=" N VAL B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.572A pdb=" N THR B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 28 through 34 removed outlier: 3.626A pdb=" N VAL C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.572A pdb=" N THR C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 28 through 34 removed outlier: 3.627A pdb=" N VAL D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 372 through 381 removed outlier: 3.572A pdb=" N THR D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 28 through 34 removed outlier: 3.626A pdb=" N VAL E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.572A pdb=" N THR E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 28 through 34 removed outlier: 3.627A pdb=" N VAL F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.571A pdb=" N THR F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 28 through 34 removed outlier: 3.626A pdb=" N VAL G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 354 through 361 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.571A pdb=" N THR G 376 " --> pdb=" O ASP G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.381A pdb=" N ASN A 72 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 96 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 96 current: chain 'A' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 179 current: chain 'A' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 345 current: chain 'B' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 179 current: chain 'B' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 345 current: chain 'C' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 179 current: chain 'C' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 345 current: chain 'D' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 179 current: chain 'D' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 345 current: chain 'E' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 179 current: chain 'E' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 338 through 345 current: chain 'F' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 345 current: chain 'G' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 179 current: chain 'G' and resid 289 through 321 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 243 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.381A pdb=" N ASN B 72 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.381A pdb=" N ASN C 72 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.381A pdb=" N ASN D 72 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 65 through 67 removed outlier: 4.381A pdb=" N ASN E 72 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.380A pdb=" N ASN F 72 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.381A pdb=" N ASN G 72 " --> pdb=" O ILE G 47 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2373 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: 8.01 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6434 1.34 - 1.46: 5147 1.46 - 1.58: 10910 1.58 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 22582 Sorted by residual: bond pdb=" C ARG C 336 " pdb=" O ARG C 336 " ideal model delta sigma weight residual 1.235 1.216 0.019 4.70e-03 4.53e+04 1.57e+01 bond pdb=" C ARG B 336 " pdb=" O ARG B 336 " ideal model delta sigma weight residual 1.235 1.217 0.018 4.70e-03 4.53e+04 1.46e+01 bond pdb=" C ARG E 336 " pdb=" O ARG E 336 " ideal model delta sigma weight residual 1.235 1.217 0.018 4.70e-03 4.53e+04 1.45e+01 bond pdb=" C ARG D 336 " pdb=" O ARG D 336 " ideal model delta sigma weight residual 1.235 1.217 0.018 4.70e-03 4.53e+04 1.41e+01 bond pdb=" C ARG F 336 " pdb=" O ARG F 336 " ideal model delta sigma weight residual 1.235 1.217 0.018 4.70e-03 4.53e+04 1.40e+01 ... (remaining 22577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 26921 1.21 - 2.43: 3084 2.43 - 3.64: 699 3.64 - 4.85: 96 4.85 - 6.07: 35 Bond angle restraints: 30835 Sorted by residual: angle pdb=" N LYS B 309 " pdb=" CA LYS B 309 " pdb=" CB LYS B 309 " ideal model delta sigma weight residual 110.83 104.76 6.07 1.74e+00 3.30e-01 1.22e+01 angle pdb=" N LYS F 309 " pdb=" CA LYS F 309 " pdb=" CB LYS F 309 " ideal model delta sigma weight residual 110.83 104.76 6.07 1.74e+00 3.30e-01 1.22e+01 angle pdb=" N LYS A 309 " pdb=" CA LYS A 309 " pdb=" CB LYS A 309 " ideal model delta sigma weight residual 110.83 104.77 6.06 1.74e+00 3.30e-01 1.21e+01 angle pdb=" N LYS D 309 " pdb=" CA LYS D 309 " pdb=" CB LYS D 309 " ideal model delta sigma weight residual 110.83 104.78 6.05 1.74e+00 3.30e-01 1.21e+01 angle pdb=" N LYS G 309 " pdb=" CA LYS G 309 " pdb=" CB LYS G 309 " ideal model delta sigma weight residual 110.83 104.78 6.05 1.74e+00 3.30e-01 1.21e+01 ... (remaining 30830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 12321 17.60 - 35.19: 580 35.19 - 52.79: 105 52.79 - 70.39: 56 70.39 - 87.99: 7 Dihedral angle restraints: 13069 sinusoidal: 5089 harmonic: 7980 Sorted by residual: dihedral pdb=" CA TYR B 298 " pdb=" C TYR B 298 " pdb=" N LYS B 299 " pdb=" CA LYS B 299 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR C 298 " pdb=" C TYR C 298 " pdb=" N LYS C 299 " pdb=" CA LYS C 299 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR D 298 " pdb=" C TYR D 298 " pdb=" N LYS D 299 " pdb=" CA LYS D 299 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 13066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1659 0.038 - 0.075: 1032 0.075 - 0.113: 365 0.113 - 0.150: 141 0.150 - 0.188: 37 Chirality restraints: 3234 Sorted by residual: chirality pdb=" CA ILE G 259 " pdb=" N ILE G 259 " pdb=" C ILE G 259 " pdb=" CB ILE G 259 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CA ILE D 259 " pdb=" N ILE D 259 " pdb=" C ILE D 259 " pdb=" CB ILE D 259 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ILE A 259 " pdb=" N ILE A 259 " pdb=" C ILE A 259 " pdb=" CB ILE A 259 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 3231 not shown) Planarity restraints: 4025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 28 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.61e+00 pdb=" NE ARG B 28 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 28 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 28 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 28 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 28 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.60e+00 pdb=" NE ARG G 28 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 28 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 28 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 28 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 28 " 0.247 9.50e-02 1.11e+02 1.11e-01 7.59e+00 pdb=" NE ARG E 28 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 28 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 28 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 4022 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4415 2.80 - 3.32: 18545 3.32 - 3.85: 36635 3.85 - 4.37: 41807 4.37 - 4.90: 70875 Nonbonded interactions: 172277 Sorted by model distance: nonbonded pdb=" NH1 ARG E 220 " pdb=" OD2 ASP E 222 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG A 220 " pdb=" OD2 ASP A 222 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG F 220 " pdb=" OD2 ASP F 222 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG G 220 " pdb=" OD2 ASP G 222 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG D 220 " pdb=" OD2 ASP D 222 " model vdw 2.273 3.120 ... (remaining 172272 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 4.700 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: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 46.700 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.120 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:18.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 : 0.006 0.039 22589 Z= 0.365 Angle : 0.885 6.067 30849 Z= 0.530 Chirality : 0.057 0.188 3234 Planarity : 0.009 0.111 4025 Dihedral : 11.822 87.986 7980 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.19 % Allowed : 2.38 % Favored : 96.43 % 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: 0.59 (0.15), residues: 2751 helix: -0.27 (0.22), residues: 490 sheet: 1.55 (0.16), residues: 980 loop : -0.20 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 329 HIS 0.005 0.002 HIS G 186 PHE 0.029 0.003 PHE D 321 TYR 0.019 0.003 TYR G 357 ARG 0.005 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.18950 ( 819) hydrogen bonds : angle 6.94705 ( 2373) SS BOND : bond 0.00790 ( 7) SS BOND : angle 2.24680 ( 14) covalent geometry : bond 0.00578 (22582) covalent geometry : angle 0.88400 (30835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 2.372 Fit side-chains REVERT: A 8 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7886 (mm-40) REVERT: A 57 MET cc_start: 0.8100 (mtp) cc_final: 0.7695 (mtp) REVERT: A 76 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.5754 (t80) REVERT: A 171 LYS cc_start: 0.8881 (mttt) cc_final: 0.8661 (mttp) REVERT: A 185 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8232 (mttp) REVERT: A 233 TYR cc_start: 0.7370 (m-80) cc_final: 0.6875 (t80) REVERT: A 258 GLU cc_start: 0.8485 (tt0) cc_final: 0.8252 (tt0) REVERT: B 57 MET cc_start: 0.8191 (mtp) cc_final: 0.7819 (mtp) REVERT: B 76 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6052 (t80) REVERT: B 185 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8334 (mttm) REVERT: B 233 TYR cc_start: 0.7341 (m-80) cc_final: 0.6962 (t80) REVERT: B 258 GLU cc_start: 0.8518 (tt0) cc_final: 0.8273 (tt0) REVERT: C 8 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7789 (mm-40) REVERT: C 76 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 233 TYR cc_start: 0.7430 (m-80) cc_final: 0.6878 (t80) REVERT: C 258 GLU cc_start: 0.8391 (tt0) cc_final: 0.8118 (tt0) REVERT: D 76 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5969 (t80) REVERT: D 185 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8363 (mttm) REVERT: D 233 TYR cc_start: 0.7470 (m-80) cc_final: 0.6930 (t80) REVERT: D 258 GLU cc_start: 0.8368 (tt0) cc_final: 0.8091 (tt0) REVERT: E 45 TRP cc_start: 0.6063 (m100) cc_final: 0.5780 (m100) REVERT: E 57 MET cc_start: 0.8118 (mtp) cc_final: 0.7875 (mtp) REVERT: E 76 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7085 (t80) REVERT: E 233 TYR cc_start: 0.7345 (m-80) cc_final: 0.6828 (t80) REVERT: F 2 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7797 (mt-10) REVERT: F 185 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8200 (mttp) REVERT: F 233 TYR cc_start: 0.7362 (m-80) cc_final: 0.6825 (t80) REVERT: F 258 GLU cc_start: 0.8469 (tt0) cc_final: 0.8183 (tt0) REVERT: F 378 GLN cc_start: 0.8248 (mt0) cc_final: 0.7752 (mm110) REVERT: G 2 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7646 (mt-10) REVERT: G 233 TYR cc_start: 0.7464 (m-80) cc_final: 0.6955 (t80) REVERT: G 258 GLU cc_start: 0.8428 (tt0) cc_final: 0.8137 (tt0) REVERT: G 378 GLN cc_start: 0.8385 (mt0) cc_final: 0.7928 (mm110) outliers start: 28 outliers final: 4 residues processed: 298 average time/residue: 1.6809 time to fit residues: 558.6898 Evaluate side-chains 182 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain G residue 76 TYR Chi-restraints excluded: chain G residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 231 ASN B 8 GLN B 46 GLN B 134 GLN B 231 ASN C 46 GLN C 195 GLN C 231 ASN D 8 GLN D 134 GLN D 195 GLN D 231 ASN E 8 GLN E 195 GLN E 231 ASN F 8 GLN F 134 GLN F 195 GLN F 231 ASN G 8 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.073595 restraints weight = 28568.269| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.83 r_work: 0.2730 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22589 Z= 0.217 Angle : 0.663 6.653 30849 Z= 0.380 Chirality : 0.050 0.151 3234 Planarity : 0.005 0.040 4025 Dihedral : 5.669 48.783 3039 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.57 % Allowed : 5.70 % Favored : 92.73 % 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: 0.84 (0.15), residues: 2751 helix: 0.85 (0.22), residues: 490 sheet: 1.48 (0.15), residues: 1029 loop : -0.34 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 370 HIS 0.006 0.002 HIS G 186 PHE 0.012 0.002 PHE D 321 TYR 0.024 0.002 TYR D 61 ARG 0.003 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.06653 ( 819) hydrogen bonds : angle 5.15037 ( 2373) SS BOND : bond 0.00258 ( 7) SS BOND : angle 1.11177 ( 14) covalent geometry : bond 0.00423 (22582) covalent geometry : angle 0.66279 (30835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 2.657 Fit side-chains REVERT: A 8 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8071 (mm-40) REVERT: A 57 MET cc_start: 0.8188 (mtp) cc_final: 0.7896 (mtp) REVERT: A 76 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.5553 (t80) REVERT: A 171 LYS cc_start: 0.9124 (mttt) cc_final: 0.8912 (mttp) REVERT: A 185 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8356 (mttp) REVERT: A 233 TYR cc_start: 0.7507 (m-80) cc_final: 0.6746 (t80) REVERT: A 258 GLU cc_start: 0.8518 (tt0) cc_final: 0.8258 (tt0) REVERT: B 57 MET cc_start: 0.8203 (mtp) cc_final: 0.7909 (mtp) REVERT: B 76 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.5894 (t80) REVERT: B 233 TYR cc_start: 0.7446 (m-80) cc_final: 0.6803 (t80) REVERT: B 258 GLU cc_start: 0.8522 (tt0) cc_final: 0.8261 (tt0) REVERT: C 8 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8011 (mm-40) REVERT: C 57 MET cc_start: 0.8260 (mtm) cc_final: 0.8019 (mtp) REVERT: C 76 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.5786 (t80) REVERT: C 116 THR cc_start: 0.9218 (m) cc_final: 0.8836 (p) REVERT: C 233 TYR cc_start: 0.7490 (m-80) cc_final: 0.6688 (t80) REVERT: C 258 GLU cc_start: 0.8488 (tt0) cc_final: 0.8212 (tt0) REVERT: D 76 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.5667 (t80) REVERT: D 185 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8550 (mttm) REVERT: D 233 TYR cc_start: 0.7599 (m-80) cc_final: 0.6831 (t80) REVERT: D 258 GLU cc_start: 0.8453 (tt0) cc_final: 0.8174 (tt0) REVERT: E 45 TRP cc_start: 0.6648 (m100) cc_final: 0.6426 (m100) REVERT: E 116 THR cc_start: 0.9210 (m) cc_final: 0.8881 (p) REVERT: E 233 TYR cc_start: 0.7489 (m-80) cc_final: 0.6775 (t80) REVERT: F 185 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8450 (mttp) REVERT: F 233 TYR cc_start: 0.7467 (m-80) cc_final: 0.6783 (t80) REVERT: F 258 GLU cc_start: 0.8505 (tt0) cc_final: 0.8245 (tt0) REVERT: F 378 GLN cc_start: 0.8312 (mt0) cc_final: 0.7875 (mm110) REVERT: G 76 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.5711 (t80) REVERT: G 233 TYR cc_start: 0.7541 (m-80) cc_final: 0.6752 (t80) outliers start: 37 outliers final: 9 residues processed: 228 average time/residue: 1.3356 time to fit residues: 348.8605 Evaluate side-chains 183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 76 TYR Chi-restraints excluded: chain G residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 207 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 46 GLN B 134 GLN B 231 ASN C 46 GLN C 195 GLN C 263 GLN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 134 GLN G 195 GLN G 231 ASN G 263 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.076222 restraints weight = 28294.215| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.86 r_work: 0.2779 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22589 Z= 0.137 Angle : 0.528 4.621 30849 Z= 0.299 Chirality : 0.046 0.142 3234 Planarity : 0.004 0.034 4025 Dihedral : 5.042 43.455 3035 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.49 % Allowed : 6.21 % Favored : 92.30 % 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: 1.01 (0.15), residues: 2751 helix: 1.33 (0.23), residues: 497 sheet: 1.36 (0.15), residues: 1064 loop : -0.22 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 370 HIS 0.003 0.001 HIS G 186 PHE 0.014 0.001 PHE B 321 TYR 0.019 0.001 TYR E 61 ARG 0.003 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 819) hydrogen bonds : angle 4.69474 ( 2373) SS BOND : bond 0.00082 ( 7) SS BOND : angle 0.55569 ( 14) covalent geometry : bond 0.00245 (22582) covalent geometry : angle 0.52774 (30835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 2.641 Fit side-chains REVERT: A 8 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7958 (mm-40) REVERT: A 57 MET cc_start: 0.8099 (mtp) cc_final: 0.7804 (mtp) REVERT: A 185 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8350 (mttp) REVERT: A 233 TYR cc_start: 0.7356 (m-80) cc_final: 0.6483 (t80) REVERT: A 258 GLU cc_start: 0.8404 (tt0) cc_final: 0.8183 (tt0) REVERT: B 57 MET cc_start: 0.8190 (mtp) cc_final: 0.7916 (mtm) REVERT: B 233 TYR cc_start: 0.7298 (m-80) cc_final: 0.6593 (t80) REVERT: B 258 GLU cc_start: 0.8371 (tt0) cc_final: 0.8125 (tt0) REVERT: B 263 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7556 (mp-120) REVERT: C 8 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8020 (mm-40) REVERT: C 57 MET cc_start: 0.8213 (mtm) cc_final: 0.7995 (mtp) REVERT: C 116 THR cc_start: 0.9177 (m) cc_final: 0.8784 (p) REVERT: C 185 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8509 (mttm) REVERT: C 207 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8788 (t70) REVERT: C 233 TYR cc_start: 0.7359 (m-80) cc_final: 0.6501 (t80) REVERT: C 258 GLU cc_start: 0.8375 (tt0) cc_final: 0.8099 (tt0) REVERT: D 185 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8549 (mttm) REVERT: D 233 TYR cc_start: 0.7387 (m-80) cc_final: 0.6661 (t80) REVERT: D 258 GLU cc_start: 0.8362 (tt0) cc_final: 0.8084 (tt0) REVERT: E 76 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.5528 (t80) REVERT: E 116 THR cc_start: 0.9193 (m) cc_final: 0.8845 (p) REVERT: E 140 MET cc_start: 0.9015 (mmm) cc_final: 0.8606 (mmm) REVERT: E 207 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8771 (t0) REVERT: E 233 TYR cc_start: 0.7298 (m-80) cc_final: 0.6641 (t80) REVERT: F 185 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8425 (mttp) REVERT: F 233 TYR cc_start: 0.7277 (m-80) cc_final: 0.6602 (t80) REVERT: F 258 GLU cc_start: 0.8429 (tt0) cc_final: 0.8182 (tt0) REVERT: F 378 GLN cc_start: 0.8256 (mt0) cc_final: 0.7822 (mm110) REVERT: G 185 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8594 (mttm) REVERT: G 233 TYR cc_start: 0.7374 (m-80) cc_final: 0.6562 (t80) outliers start: 35 outliers final: 12 residues processed: 200 average time/residue: 1.2370 time to fit residues: 286.6628 Evaluate side-chains 183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 81 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 134 GLN B 231 ASN C 231 ASN C 263 GLN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 134 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.076213 restraints weight = 28598.821| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.88 r_work: 0.2777 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 22589 Z= 0.129 Angle : 0.506 4.697 30849 Z= 0.286 Chirality : 0.045 0.140 3234 Planarity : 0.004 0.031 4025 Dihedral : 4.345 15.240 3024 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.53 % Allowed : 6.51 % Favored : 91.96 % 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: 1.05 (0.15), residues: 2751 helix: 1.46 (0.23), residues: 497 sheet: 1.37 (0.15), residues: 1071 loop : -0.24 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.003 0.001 HIS G 186 PHE 0.013 0.001 PHE A 321 TYR 0.012 0.001 TYR G 61 ARG 0.002 0.000 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 819) hydrogen bonds : angle 4.46936 ( 2373) SS BOND : bond 0.00066 ( 7) SS BOND : angle 0.40302 ( 14) covalent geometry : bond 0.00233 (22582) covalent geometry : angle 0.50582 (30835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 2.915 Fit side-chains REVERT: A 8 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8034 (mm-40) REVERT: A 57 MET cc_start: 0.8290 (mtp) cc_final: 0.7983 (mtp) REVERT: A 185 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8360 (mttp) REVERT: A 233 TYR cc_start: 0.7345 (m-80) cc_final: 0.6454 (t80) REVERT: A 258 GLU cc_start: 0.8368 (tt0) cc_final: 0.8154 (tt0) REVERT: B 57 MET cc_start: 0.8247 (mtp) cc_final: 0.7987 (mtp) REVERT: B 233 TYR cc_start: 0.7328 (m-80) cc_final: 0.6582 (t80) REVERT: B 258 GLU cc_start: 0.8356 (tt0) cc_final: 0.8104 (tt0) REVERT: C 8 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7925 (mm-40) REVERT: C 116 THR cc_start: 0.9161 (m) cc_final: 0.8756 (p) REVERT: C 185 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8517 (mttm) REVERT: C 207 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8720 (t70) REVERT: C 233 TYR cc_start: 0.7317 (m-80) cc_final: 0.6421 (t80) REVERT: D 185 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8550 (mttm) REVERT: D 233 TYR cc_start: 0.7410 (m-80) cc_final: 0.6625 (t80) REVERT: D 258 GLU cc_start: 0.8356 (tt0) cc_final: 0.8085 (tt0) REVERT: E 116 THR cc_start: 0.9180 (m) cc_final: 0.8824 (p) REVERT: E 140 MET cc_start: 0.8970 (mmm) cc_final: 0.8647 (mmm) REVERT: E 207 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8712 (t0) REVERT: E 233 TYR cc_start: 0.7317 (m-80) cc_final: 0.6612 (t80) REVERT: F 185 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8424 (mttp) REVERT: F 233 TYR cc_start: 0.7295 (m-80) cc_final: 0.6518 (t80) REVERT: F 258 GLU cc_start: 0.8385 (tt0) cc_final: 0.8127 (tt0) REVERT: F 378 GLN cc_start: 0.8269 (mt0) cc_final: 0.7829 (mm110) REVERT: G 50 LEU cc_start: 0.7312 (pt) cc_final: 0.7096 (pp) REVERT: G 185 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8609 (mttm) REVERT: G 233 TYR cc_start: 0.7392 (m-80) cc_final: 0.6520 (t80) outliers start: 36 outliers final: 13 residues processed: 194 average time/residue: 1.4361 time to fit residues: 321.9556 Evaluate side-chains 177 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 127 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 134 GLN B 231 ASN C 231 ASN C 263 GLN D 8 GLN D 134 GLN D 231 ASN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 134 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.070815 restraints weight = 28303.501| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.86 r_work: 0.2680 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 22589 Z= 0.265 Angle : 0.694 6.031 30849 Z= 0.397 Chirality : 0.053 0.205 3234 Planarity : 0.006 0.039 4025 Dihedral : 4.993 16.379 3024 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.21 % Allowed : 6.46 % Favored : 91.33 % 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: 0.61 (0.15), residues: 2751 helix: 1.13 (0.23), residues: 497 sheet: 1.57 (0.17), residues: 882 loop : -0.67 (0.14), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 370 HIS 0.007 0.002 HIS G 186 PHE 0.013 0.002 PHE A 308 TYR 0.025 0.002 TYR E 61 ARG 0.005 0.001 ARG C 220 Details of bonding type rmsd hydrogen bonds : bond 0.07580 ( 819) hydrogen bonds : angle 4.68145 ( 2373) SS BOND : bond 0.00239 ( 7) SS BOND : angle 0.78069 ( 14) covalent geometry : bond 0.00583 (22582) covalent geometry : angle 0.69413 (30835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 3.426 Fit side-chains REVERT: A 8 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8081 (mm-40) REVERT: A 57 MET cc_start: 0.8301 (mtp) cc_final: 0.8074 (mtp) REVERT: A 233 TYR cc_start: 0.7706 (m-80) cc_final: 0.6760 (t80) REVERT: A 258 GLU cc_start: 0.8441 (tt0) cc_final: 0.8195 (tt0) REVERT: B 76 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.5650 (t80) REVERT: B 233 TYR cc_start: 0.7676 (m-80) cc_final: 0.6758 (t80) REVERT: B 258 GLU cc_start: 0.8451 (tt0) cc_final: 0.8205 (tt0) REVERT: C 8 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8042 (mm-40) REVERT: C 76 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.5617 (t80) REVERT: C 116 THR cc_start: 0.9222 (m) cc_final: 0.8856 (p) REVERT: C 185 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8558 (mttm) REVERT: C 207 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8634 (t0) REVERT: C 233 TYR cc_start: 0.7653 (m-80) cc_final: 0.6666 (t80) REVERT: D 76 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.5519 (t80) REVERT: D 185 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8604 (mttp) REVERT: D 233 TYR cc_start: 0.7772 (m-80) cc_final: 0.6783 (t80) REVERT: D 258 GLU cc_start: 0.8438 (tt0) cc_final: 0.8160 (tt0) REVERT: E 50 LEU cc_start: 0.7570 (pt) cc_final: 0.7334 (pp) REVERT: E 76 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.5591 (t80) REVERT: E 116 THR cc_start: 0.9230 (m) cc_final: 0.8894 (p) REVERT: E 140 MET cc_start: 0.8965 (mmm) cc_final: 0.8723 (mmm) REVERT: E 207 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8546 (t0) REVERT: E 233 TYR cc_start: 0.7681 (m-80) cc_final: 0.6768 (t80) REVERT: F 185 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8432 (mttp) REVERT: F 233 TYR cc_start: 0.7688 (m-80) cc_final: 0.6746 (t80) REVERT: F 258 GLU cc_start: 0.8464 (tt0) cc_final: 0.8231 (tt0) REVERT: F 378 GLN cc_start: 0.8475 (mt0) cc_final: 0.7967 (mm-40) REVERT: G 233 TYR cc_start: 0.7689 (m-80) cc_final: 0.6729 (t80) outliers start: 52 outliers final: 26 residues processed: 192 average time/residue: 1.6912 time to fit residues: 378.5097 Evaluate side-chains 184 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 69 optimal weight: 0.0670 chunk 258 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 134 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.073284 restraints weight = 28173.757| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.85 r_work: 0.2727 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22589 Z= 0.162 Angle : 0.565 4.747 30849 Z= 0.320 Chirality : 0.047 0.144 3234 Planarity : 0.004 0.034 4025 Dihedral : 4.673 16.290 3024 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.62 % Allowed : 7.27 % Favored : 91.11 % 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: 0.85 (0.15), residues: 2751 helix: 1.23 (0.23), residues: 497 sheet: 1.31 (0.15), residues: 1057 loop : -0.38 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 370 HIS 0.004 0.001 HIS F 186 PHE 0.016 0.002 PHE F 321 TYR 0.014 0.001 TYR F 61 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 819) hydrogen bonds : angle 4.55223 ( 2373) SS BOND : bond 0.00087 ( 7) SS BOND : angle 0.39981 ( 14) covalent geometry : bond 0.00307 (22582) covalent geometry : angle 0.56493 (30835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 3.220 Fit side-chains REVERT: A 8 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8045 (mm-40) REVERT: A 57 MET cc_start: 0.8266 (mtp) cc_final: 0.8060 (mtp) REVERT: A 76 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.5242 (t80) REVERT: A 233 TYR cc_start: 0.7555 (m-80) cc_final: 0.6577 (t80) REVERT: B 29 GLU cc_start: 0.7444 (mp0) cc_final: 0.7241 (mp0) REVERT: B 233 TYR cc_start: 0.7517 (m-80) cc_final: 0.6667 (t80) REVERT: B 258 GLU cc_start: 0.8413 (tt0) cc_final: 0.8165 (tt0) REVERT: C 8 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8048 (mm-40) REVERT: C 116 THR cc_start: 0.9182 (m) cc_final: 0.8797 (p) REVERT: C 185 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8555 (mttm) REVERT: C 207 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8578 (t0) REVERT: C 233 TYR cc_start: 0.7487 (m-80) cc_final: 0.6494 (t80) REVERT: D 185 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8590 (mttp) REVERT: D 233 TYR cc_start: 0.7632 (m-80) cc_final: 0.6661 (t80) REVERT: D 258 GLU cc_start: 0.8380 (tt0) cc_final: 0.8122 (tt0) REVERT: E 76 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.5442 (t80) REVERT: E 116 THR cc_start: 0.9197 (m) cc_final: 0.8849 (p) REVERT: E 207 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8542 (t0) REVERT: E 233 TYR cc_start: 0.7556 (m-80) cc_final: 0.6708 (t80) REVERT: F 185 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8453 (mttp) REVERT: F 233 TYR cc_start: 0.7561 (m-80) cc_final: 0.6668 (t80) REVERT: F 258 GLU cc_start: 0.8436 (tt0) cc_final: 0.8207 (tt0) REVERT: F 378 GLN cc_start: 0.8394 (mt0) cc_final: 0.7910 (mm110) REVERT: G 76 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.5482 (t80) REVERT: G 233 TYR cc_start: 0.7630 (m-80) cc_final: 0.6669 (t80) outliers start: 38 outliers final: 15 residues processed: 184 average time/residue: 1.4315 time to fit residues: 307.9477 Evaluate side-chains 174 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 76 TYR Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 249 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.0010 chunk 187 optimal weight: 0.0040 chunk 217 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 234 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 134 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 134 GLN F 231 ASN G 8 GLN G 134 GLN G 231 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077375 restraints weight = 28399.793| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.86 r_work: 0.2802 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 22589 Z= 0.109 Angle : 0.479 7.153 30849 Z= 0.267 Chirality : 0.044 0.137 3234 Planarity : 0.004 0.029 4025 Dihedral : 4.239 15.000 3024 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.06 % Allowed : 8.08 % Favored : 90.86 % 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: 1.02 (0.15), residues: 2751 helix: 1.53 (0.23), residues: 497 sheet: 1.31 (0.15), residues: 1071 loop : -0.27 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 45 HIS 0.003 0.001 HIS E 186 PHE 0.018 0.001 PHE A 321 TYR 0.013 0.001 TYR B 61 ARG 0.002 0.000 ARG E 397 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 819) hydrogen bonds : angle 4.39277 ( 2373) SS BOND : bond 0.00017 ( 7) SS BOND : angle 0.14622 ( 14) covalent geometry : bond 0.00192 (22582) covalent geometry : angle 0.47912 (30835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 2.544 Fit side-chains REVERT: A 57 MET cc_start: 0.8260 (mtp) cc_final: 0.8029 (mtp) REVERT: A 185 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8358 (mttp) REVERT: A 233 TYR cc_start: 0.7349 (m-80) cc_final: 0.6380 (t80) REVERT: B 29 GLU cc_start: 0.7381 (mp0) cc_final: 0.7148 (mp0) REVERT: B 233 TYR cc_start: 0.7311 (m-80) cc_final: 0.6557 (t80) REVERT: B 258 GLU cc_start: 0.8308 (tt0) cc_final: 0.8030 (tt0) REVERT: C 8 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7965 (mm-40) REVERT: C 116 THR cc_start: 0.9132 (m) cc_final: 0.8723 (p) REVERT: C 185 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8545 (mttm) REVERT: C 207 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8694 (t0) REVERT: C 233 TYR cc_start: 0.7279 (m-80) cc_final: 0.6359 (t80) REVERT: D 185 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8566 (mttp) REVERT: D 233 TYR cc_start: 0.7428 (m-80) cc_final: 0.6574 (t80) REVERT: D 258 GLU cc_start: 0.8308 (tt0) cc_final: 0.8051 (tt0) REVERT: E 116 THR cc_start: 0.9147 (m) cc_final: 0.8792 (p) REVERT: E 233 TYR cc_start: 0.7311 (m-80) cc_final: 0.6560 (t80) REVERT: F 185 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8442 (mttp) REVERT: F 233 TYR cc_start: 0.7334 (m-80) cc_final: 0.6479 (t80) REVERT: F 242 LYS cc_start: 0.7609 (tttt) cc_final: 0.7348 (ttmp) REVERT: F 258 GLU cc_start: 0.8384 (tt0) cc_final: 0.8166 (tt0) REVERT: F 378 GLN cc_start: 0.8360 (mt0) cc_final: 0.7863 (mm110) REVERT: G 233 TYR cc_start: 0.7368 (m-80) cc_final: 0.6451 (t80) outliers start: 25 outliers final: 13 residues processed: 200 average time/residue: 1.2030 time to fit residues: 281.6174 Evaluate side-chains 176 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 238 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 184 optimal weight: 0.2980 chunk 229 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 231 ASN B 8 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.074809 restraints weight = 28610.003| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.82 r_work: 0.2757 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22589 Z= 0.140 Angle : 0.527 7.405 30849 Z= 0.296 Chirality : 0.046 0.139 3234 Planarity : 0.004 0.031 4025 Dihedral : 4.383 15.160 3024 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.32 % Allowed : 8.04 % Favored : 90.65 % 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: 1.04 (0.15), residues: 2751 helix: 1.51 (0.23), residues: 497 sheet: 1.38 (0.15), residues: 1057 loop : -0.26 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 329 HIS 0.004 0.001 HIS G 186 PHE 0.014 0.001 PHE F 321 TYR 0.013 0.001 TYR B 61 ARG 0.002 0.000 ARG F 144 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 819) hydrogen bonds : angle 4.33716 ( 2373) SS BOND : bond 0.00068 ( 7) SS BOND : angle 0.29483 ( 14) covalent geometry : bond 0.00268 (22582) covalent geometry : angle 0.52728 (30835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 2.380 Fit side-chains REVERT: A 233 TYR cc_start: 0.7474 (m-80) cc_final: 0.6495 (t80) REVERT: B 29 GLU cc_start: 0.7385 (mp0) cc_final: 0.7163 (mp0) REVERT: B 233 TYR cc_start: 0.7431 (m-80) cc_final: 0.6586 (t80) REVERT: B 258 GLU cc_start: 0.8278 (tt0) cc_final: 0.8035 (tt0) REVERT: C 8 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8017 (mm-40) REVERT: C 116 THR cc_start: 0.9162 (m) cc_final: 0.8758 (p) REVERT: C 185 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8548 (mttm) REVERT: C 207 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8702 (t0) REVERT: C 233 TYR cc_start: 0.7396 (m-80) cc_final: 0.6465 (t80) REVERT: D 185 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8574 (mttp) REVERT: D 233 TYR cc_start: 0.7484 (m-80) cc_final: 0.6596 (t80) REVERT: D 258 GLU cc_start: 0.8359 (tt0) cc_final: 0.8096 (tt0) REVERT: E 50 LEU cc_start: 0.7235 (pt) cc_final: 0.7004 (pp) REVERT: E 116 THR cc_start: 0.9170 (m) cc_final: 0.8818 (p) REVERT: E 207 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8624 (t70) REVERT: E 233 TYR cc_start: 0.7442 (m-80) cc_final: 0.6634 (t80) REVERT: F 185 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8445 (mttp) REVERT: F 233 TYR cc_start: 0.7459 (m-80) cc_final: 0.6620 (t80) REVERT: F 242 LYS cc_start: 0.7609 (tttt) cc_final: 0.7347 (ttmp) REVERT: F 258 GLU cc_start: 0.8399 (tt0) cc_final: 0.8175 (tt0) REVERT: F 378 GLN cc_start: 0.8407 (mt0) cc_final: 0.7904 (mm110) REVERT: G 50 LEU cc_start: 0.7369 (tp) cc_final: 0.6863 (pp) REVERT: G 233 TYR cc_start: 0.7483 (m-80) cc_final: 0.6562 (t80) outliers start: 31 outliers final: 17 residues processed: 183 average time/residue: 1.2498 time to fit residues: 265.1647 Evaluate side-chains 179 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 69 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 241 optimal weight: 0.0980 chunk 102 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 249 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 231 ASN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 134 GLN G 231 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.077224 restraints weight = 28444.662| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.86 r_work: 0.2799 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22589 Z= 0.110 Angle : 0.482 6.771 30849 Z= 0.268 Chirality : 0.044 0.137 3234 Planarity : 0.004 0.030 4025 Dihedral : 4.182 14.618 3024 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.81 % Allowed : 8.46 % Favored : 90.73 % 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: 1.13 (0.15), residues: 2751 helix: 1.66 (0.23), residues: 497 sheet: 1.36 (0.15), residues: 1071 loop : -0.18 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.003 0.001 HIS C 186 PHE 0.017 0.001 PHE A 321 TYR 0.010 0.001 TYR A 61 ARG 0.002 0.000 ARG G 28 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 819) hydrogen bonds : angle 4.26662 ( 2373) SS BOND : bond 0.00027 ( 7) SS BOND : angle 0.17161 ( 14) covalent geometry : bond 0.00195 (22582) covalent geometry : angle 0.48227 (30835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 2.542 Fit side-chains REVERT: A 233 TYR cc_start: 0.7346 (m-80) cc_final: 0.6372 (t80) REVERT: B 233 TYR cc_start: 0.7336 (m-80) cc_final: 0.6560 (t80) REVERT: B 258 GLU cc_start: 0.8238 (tt0) cc_final: 0.7988 (tt0) REVERT: C 8 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8024 (mm-40) REVERT: C 116 THR cc_start: 0.9128 (m) cc_final: 0.8715 (p) REVERT: C 185 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8547 (mttm) REVERT: C 207 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8752 (t70) REVERT: C 233 TYR cc_start: 0.7279 (m-80) cc_final: 0.6359 (t80) REVERT: D 185 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8558 (mttp) REVERT: D 233 TYR cc_start: 0.7432 (m-80) cc_final: 0.6583 (t80) REVERT: D 258 GLU cc_start: 0.8295 (tt0) cc_final: 0.8034 (tt0) REVERT: E 116 THR cc_start: 0.9139 (m) cc_final: 0.8783 (p) REVERT: E 207 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8692 (t0) REVERT: E 233 TYR cc_start: 0.7324 (m-80) cc_final: 0.6557 (t80) REVERT: F 185 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8445 (mttp) REVERT: F 233 TYR cc_start: 0.7343 (m-80) cc_final: 0.6481 (t80) REVERT: F 242 LYS cc_start: 0.7594 (tttt) cc_final: 0.7330 (ttmp) REVERT: F 258 GLU cc_start: 0.8367 (tt0) cc_final: 0.8145 (tt0) REVERT: F 378 GLN cc_start: 0.8370 (mt0) cc_final: 0.7884 (mm110) REVERT: G 233 TYR cc_start: 0.7346 (m-80) cc_final: 0.6433 (t80) outliers start: 19 outliers final: 9 residues processed: 183 average time/residue: 1.2697 time to fit residues: 268.6117 Evaluate side-chains 173 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 216 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 0.0010 chunk 184 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 148 optimal weight: 0.0270 chunk 221 optimal weight: 0.2980 overall best weight: 0.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079857 restraints weight = 28687.332| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.86 r_work: 0.2848 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22589 Z= 0.092 Angle : 0.455 11.151 30849 Z= 0.250 Chirality : 0.044 0.139 3234 Planarity : 0.003 0.029 4025 Dihedral : 3.938 13.884 3024 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.68 % Allowed : 8.67 % Favored : 90.65 % 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: 1.31 (0.15), residues: 2751 helix: 1.91 (0.23), residues: 490 sheet: 1.43 (0.15), residues: 1106 loop : -0.13 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 45 HIS 0.002 0.001 HIS E 186 PHE 0.017 0.001 PHE A 321 TYR 0.009 0.001 TYR A 61 ARG 0.001 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 819) hydrogen bonds : angle 4.14413 ( 2373) SS BOND : bond 0.00012 ( 7) SS BOND : angle 0.10741 ( 14) covalent geometry : bond 0.00170 (22582) covalent geometry : angle 0.45542 (30835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5502 Ramachandran restraints generated. 2751 Oldfield, 0 Emsley, 2751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 2.620 Fit side-chains REVERT: A 233 TYR cc_start: 0.7178 (m-80) cc_final: 0.6317 (t80) REVERT: B 233 TYR cc_start: 0.7177 (m-80) cc_final: 0.6453 (t80) REVERT: B 258 GLU cc_start: 0.8192 (tt0) cc_final: 0.7973 (tt0) REVERT: C 8 GLN cc_start: 0.8237 (mm-40) cc_final: 0.8013 (mm-40) REVERT: C 116 THR cc_start: 0.9099 (m) cc_final: 0.8659 (p) REVERT: C 185 LYS cc_start: 0.8925 (mtmt) cc_final: 0.8529 (mttm) REVERT: C 207 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8811 (t70) REVERT: C 233 TYR cc_start: 0.7152 (m-80) cc_final: 0.6331 (t80) REVERT: D 185 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8550 (mttm) REVERT: D 233 TYR cc_start: 0.7295 (m-80) cc_final: 0.6458 (t80) REVERT: D 258 GLU cc_start: 0.8258 (tt0) cc_final: 0.7998 (tt0) REVERT: E 116 THR cc_start: 0.9111 (m) cc_final: 0.8747 (p) REVERT: E 233 TYR cc_start: 0.7133 (m-80) cc_final: 0.6458 (t80) REVERT: F 185 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8453 (mttp) REVERT: F 233 TYR cc_start: 0.7193 (m-80) cc_final: 0.6393 (t80) REVERT: F 242 LYS cc_start: 0.7630 (tttt) cc_final: 0.7374 (ttmp) REVERT: F 258 GLU cc_start: 0.8287 (tt0) cc_final: 0.8064 (tt0) REVERT: G 50 LEU cc_start: 0.6876 (tp) cc_final: 0.6201 (pt) REVERT: G 233 TYR cc_start: 0.7217 (m-80) cc_final: 0.6341 (t80) outliers start: 16 outliers final: 8 residues processed: 193 average time/residue: 1.1885 time to fit residues: 268.8875 Evaluate side-chains 176 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 207 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 145 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 205 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 70 optimal weight: 0.0050 chunk 31 optimal weight: 0.0030 chunk 43 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 8 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 231 ASN D 263 GLN E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 GLN G 134 GLN G 195 GLN G 231 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.078768 restraints weight = 28734.610| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.86 r_work: 0.2827 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22589 Z= 0.100 Angle : 0.465 8.609 30849 Z= 0.256 Chirality : 0.044 0.138 3234 Planarity : 0.003 0.029 4025 Dihedral : 3.987 14.056 3024 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.72 % Allowed : 8.76 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.15), residues: 2751 helix: 1.84 (0.23), residues: 497 sheet: 1.46 (0.15), residues: 1106 loop : -0.06 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 45 HIS 0.003 0.001 HIS B 186 PHE 0.016 0.001 PHE F 321 TYR 0.011 0.001 TYR A 61 ARG 0.001 0.000 ARG E 362 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 819) hydrogen bonds : angle 4.07286 ( 2373) SS BOND : bond 0.00030 ( 7) SS BOND : angle 0.12536 ( 14) covalent geometry : bond 0.00182 (22582) covalent geometry : angle 0.46510 (30835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23646.40 seconds wall clock time: 414 minutes 28.15 seconds (24868.15 seconds total)