Starting phenix.real_space_refine on Fri Sep 19 01:12:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnp_50601/09_2025/9fnp_50601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnp_50601/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fnp_50601/09_2025/9fnp_50601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnp_50601/09_2025/9fnp_50601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fnp_50601/09_2025/9fnp_50601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnp_50601/09_2025/9fnp_50601.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 3.46, per 1000 atoms: 0.16 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 B 159 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.04 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.71 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: 4.14 Time building geometry restraints manager: 2.90 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 5.170 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.005 0.001 ARG D 28 TYR 0.019 0.003 TYR G 357 PHE 0.029 0.003 PHE D 321 TRP 0.014 0.002 TRP C 329 HIS 0.005 0.002 HIS G 186 Details of bonding type rmsd covalent geometry : bond 0.00578 (22582) covalent geometry : angle 0.88400 (30835) SS BOND : bond 0.00790 ( 7) SS BOND : angle 2.24680 ( 14) hydrogen bonds : bond 0.18950 ( 819) hydrogen bonds : angle 6.94705 ( 2373) *********************** 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 : 0.872 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: 0.8311 time to fit residues: 274.6628 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 : 0.836 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0170 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.105736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.077930 restraints weight = 28594.346| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.87 r_work: 0.2810 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22589 Z= 0.158 Angle : 0.577 6.640 30849 Z= 0.328 Chirality : 0.047 0.151 3234 Planarity : 0.005 0.035 4025 Dihedral : 5.358 46.145 3039 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.32 % Allowed : 5.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 2751 helix: 0.87 (0.22), residues: 490 sheet: 1.40 (0.15), residues: 1127 loop : -0.21 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.021 0.002 TYR D 61 PHE 0.010 0.001 PHE F 321 TRP 0.010 0.001 TRP A 370 HIS 0.003 0.001 HIS G 186 Details of bonding type rmsd covalent geometry : bond 0.00274 (22582) covalent geometry : angle 0.57702 (30835) SS BOND : bond 0.00230 ( 7) SS BOND : angle 1.04788 ( 14) hydrogen bonds : bond 0.05351 ( 819) hydrogen bonds : angle 5.20244 ( 2373) *********************** 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 245 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.788 Fit side-chains REVERT: A 8 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7971 (mm-40) REVERT: A 57 MET cc_start: 0.8130 (mtp) cc_final: 0.7781 (mtp) REVERT: A 185 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8361 (mttp) REVERT: A 233 TYR cc_start: 0.7356 (m-80) cc_final: 0.6697 (t80) REVERT: A 258 GLU cc_start: 0.8502 (tt0) cc_final: 0.8247 (tt0) REVERT: B 57 MET cc_start: 0.8153 (mtp) cc_final: 0.7851 (mtp) REVERT: B 185 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8462 (mttm) REVERT: B 233 TYR cc_start: 0.7320 (m-80) cc_final: 0.6729 (t80) REVERT: B 258 GLU cc_start: 0.8506 (tt0) cc_final: 0.8275 (tt0) REVERT: C 8 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7948 (mm-40) REVERT: C 57 MET cc_start: 0.8212 (mtm) cc_final: 0.7952 (mtp) REVERT: C 116 THR cc_start: 0.9190 (m) cc_final: 0.8835 (p) REVERT: C 233 TYR cc_start: 0.7359 (m-80) cc_final: 0.6635 (t80) REVERT: C 258 GLU cc_start: 0.8480 (tt0) cc_final: 0.8231 (tt0) REVERT: C 311 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: D 185 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8510 (mttm) REVERT: D 233 TYR cc_start: 0.7468 (m-80) cc_final: 0.6784 (t80) REVERT: D 258 GLU cc_start: 0.8451 (tt0) cc_final: 0.8175 (tt0) REVERT: E 45 TRP cc_start: 0.6374 (m100) cc_final: 0.6150 (m100) REVERT: E 116 THR cc_start: 0.9172 (m) cc_final: 0.8853 (p) REVERT: E 140 MET cc_start: 0.8977 (mmm) cc_final: 0.8648 (mmm) REVERT: E 233 TYR cc_start: 0.7307 (m-80) cc_final: 0.6751 (t80) REVERT: F 185 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8481 (mttm) REVERT: F 233 TYR cc_start: 0.7321 (m-80) cc_final: 0.6765 (t80) REVERT: F 258 GLU cc_start: 0.8509 (tt0) cc_final: 0.8246 (tt0) REVERT: F 311 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: G 57 MET cc_start: 0.8069 (mtm) cc_final: 0.7787 (mtp) REVERT: G 116 THR cc_start: 0.9135 (m) cc_final: 0.8817 (p) REVERT: G 233 TYR cc_start: 0.7427 (m-80) cc_final: 0.6689 (t80) REVERT: G 258 GLU cc_start: 0.8446 (tt0) cc_final: 0.8174 (tt0) outliers start: 31 outliers final: 7 residues processed: 234 average time/residue: 0.6567 time to fit residues: 174.1100 Evaluate side-chains 180 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 367 GLU 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 311 ASP 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 114 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 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 195 GLN G 231 ASN G 263 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.073972 restraints weight = 28517.825| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.83 r_work: 0.2737 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2060 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= 0.177 Angle : 0.594 4.726 30849 Z= 0.339 Chirality : 0.048 0.143 3234 Planarity : 0.005 0.037 4025 Dihedral : 4.711 16.004 3024 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.70 % Allowed : 5.87 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 2751 helix: 1.19 (0.23), residues: 497 sheet: 1.40 (0.15), residues: 1099 loop : -0.39 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.018 0.002 TYR F 61 PHE 0.012 0.002 PHE D 308 TRP 0.011 0.001 TRP G 359 HIS 0.005 0.001 HIS G 186 Details of bonding type rmsd covalent geometry : bond 0.00343 (22582) covalent geometry : angle 0.59362 (30835) SS BOND : bond 0.00175 ( 7) SS BOND : angle 0.74171 ( 14) hydrogen bonds : bond 0.06037 ( 819) hydrogen bonds : angle 4.73006 ( 2373) *********************** 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 217 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.891 Fit side-chains REVERT: A 8 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7969 (mm-40) REVERT: A 57 MET cc_start: 0.8130 (mtp) cc_final: 0.7835 (mtp) REVERT: A 185 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8348 (mttp) REVERT: A 233 TYR cc_start: 0.7446 (m-80) cc_final: 0.6605 (t80) REVERT: A 258 GLU cc_start: 0.8418 (tt0) cc_final: 0.8172 (tt0) REVERT: B 57 MET cc_start: 0.8199 (mtp) cc_final: 0.7926 (mtp) REVERT: B 76 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.5773 (t80) REVERT: B 233 TYR cc_start: 0.7390 (m-80) cc_final: 0.6673 (t80) REVERT: B 258 GLU cc_start: 0.8419 (tt0) cc_final: 0.8177 (tt0) REVERT: C 8 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7994 (mm-40) REVERT: C 116 THR cc_start: 0.9195 (m) cc_final: 0.8805 (p) REVERT: C 185 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8505 (mttp) REVERT: C 207 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8730 (t70) REVERT: C 233 TYR cc_start: 0.7458 (m-80) cc_final: 0.6618 (t80) REVERT: C 258 GLU cc_start: 0.8396 (tt0) cc_final: 0.8126 (tt0) REVERT: D 185 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8549 (mttm) REVERT: D 233 TYR cc_start: 0.7546 (m-80) cc_final: 0.6737 (t80) REVERT: D 258 GLU cc_start: 0.8375 (tt0) cc_final: 0.8101 (tt0) REVERT: E 116 THR cc_start: 0.9207 (m) cc_final: 0.8845 (p) REVERT: E 207 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8716 (t0) REVERT: E 233 TYR cc_start: 0.7436 (m-80) cc_final: 0.6670 (t80) REVERT: F 185 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8430 (mttp) REVERT: F 233 TYR cc_start: 0.7393 (m-80) cc_final: 0.6657 (t80) REVERT: F 258 GLU cc_start: 0.8457 (tt0) cc_final: 0.8204 (tt0) REVERT: G 76 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.5648 (t80) REVERT: G 185 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8586 (mttm) REVERT: G 233 TYR cc_start: 0.7514 (m-80) cc_final: 0.6642 (t80) REVERT: G 258 GLU cc_start: 0.8354 (tt0) cc_final: 0.8104 (tt0) outliers start: 40 outliers final: 13 residues processed: 202 average time/residue: 0.6319 time to fit residues: 145.7305 Evaluate side-chains 185 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C 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 50 LEU Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 76 TYR 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 13 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 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 = 0.3271 r_free = 0.3271 target = 0.099196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.071092 restraints weight = 28397.285| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.86 r_work: 0.2684 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22589 Z= 0.246 Angle : 0.681 6.134 30849 Z= 0.389 Chirality : 0.052 0.193 3234 Planarity : 0.006 0.040 4025 Dihedral : 5.042 16.648 3024 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.34 % Allowed : 5.91 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 2751 helix: 1.06 (0.23), residues: 497 sheet: 1.45 (0.16), residues: 945 loop : -0.70 (0.15), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 362 TYR 0.026 0.002 TYR E 61 PHE 0.012 0.002 PHE D 321 TRP 0.013 0.002 TRP B 370 HIS 0.007 0.002 HIS G 186 Details of bonding type rmsd covalent geometry : bond 0.00528 (22582) covalent geometry : angle 0.68109 (30835) SS BOND : bond 0.00218 ( 7) SS BOND : angle 0.85722 ( 14) hydrogen bonds : bond 0.07301 ( 819) hydrogen bonds : angle 4.75786 ( 2373) *********************** 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 212 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 0.880 Fit side-chains REVERT: A 8 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8009 (mm-40) REVERT: A 57 MET cc_start: 0.8295 (mtp) cc_final: 0.8038 (mtp) REVERT: A 76 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.5385 (t80) REVERT: A 233 TYR cc_start: 0.7686 (m-80) cc_final: 0.6756 (t80) REVERT: A 258 GLU cc_start: 0.8436 (tt0) cc_final: 0.8181 (tt0) REVERT: B 57 MET cc_start: 0.8234 (mtp) cc_final: 0.7980 (mtp) REVERT: B 76 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.5675 (t80) REVERT: B 233 TYR cc_start: 0.7659 (m-80) cc_final: 0.6759 (t80) REVERT: B 258 GLU cc_start: 0.8448 (tt0) cc_final: 0.8197 (tt0) REVERT: C 8 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8067 (mm-40) REVERT: C 76 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.5768 (t80) REVERT: C 116 THR cc_start: 0.9220 (m) cc_final: 0.8834 (p) REVERT: C 185 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8556 (mttm) REVERT: C 207 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8596 (t0) REVERT: C 233 TYR cc_start: 0.7638 (m-80) cc_final: 0.6724 (t80) REVERT: C 258 GLU cc_start: 0.8458 (tt0) cc_final: 0.8180 (tt0) REVERT: D 76 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.5666 (t80) REVERT: D 185 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8605 (mttp) REVERT: D 233 TYR cc_start: 0.7722 (m-80) cc_final: 0.6776 (t80) REVERT: D 258 GLU cc_start: 0.8426 (tt0) cc_final: 0.8147 (tt0) REVERT: E 76 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6213 (t80) REVERT: E 116 THR cc_start: 0.9228 (m) cc_final: 0.8878 (p) REVERT: E 207 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8578 (t0) REVERT: E 233 TYR cc_start: 0.7667 (m-80) cc_final: 0.6757 (t80) REVERT: F 185 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8474 (mttp) REVERT: F 233 TYR cc_start: 0.7610 (m-80) cc_final: 0.6729 (t80) REVERT: F 258 GLU cc_start: 0.8473 (tt0) cc_final: 0.8225 (tt0) REVERT: G 76 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.5708 (t80) REVERT: G 233 TYR cc_start: 0.7635 (m-80) cc_final: 0.6721 (t80) outliers start: 55 outliers final: 21 residues processed: 198 average time/residue: 0.6166 time to fit residues: 140.2903 Evaluate side-chains 183 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 A residue 350 ASP Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 97 ASP 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 241 THR 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 F residue 50 LEU 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 76 TYR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 106 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 143 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.071805 restraints weight = 28389.609| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.81 r_work: 0.2701 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22589 Z= 0.208 Angle : 0.625 5.693 30849 Z= 0.356 Chirality : 0.049 0.150 3234 Planarity : 0.005 0.036 4025 Dihedral : 4.891 16.477 3024 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.08 % Allowed : 6.68 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.15), residues: 2751 helix: 1.08 (0.22), residues: 497 sheet: 1.31 (0.15), residues: 1092 loop : -0.59 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 220 TYR 0.020 0.002 TYR F 61 PHE 0.016 0.002 PHE D 321 TRP 0.011 0.002 TRP B 370 HIS 0.005 0.001 HIS G 186 Details of bonding type rmsd covalent geometry : bond 0.00433 (22582) covalent geometry : angle 0.62456 (30835) SS BOND : bond 0.00115 ( 7) SS BOND : angle 0.53782 ( 14) hydrogen bonds : bond 0.06441 ( 819) hydrogen bonds : angle 4.66864 ( 2373) *********************** 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 205 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.905 Fit side-chains REVERT: A 8 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8102 (mm-40) REVERT: A 57 MET cc_start: 0.8274 (mtp) cc_final: 0.8060 (mtp) REVERT: A 76 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.5303 (t80) REVERT: A 233 TYR cc_start: 0.7629 (m-80) cc_final: 0.6645 (t80) REVERT: A 258 GLU cc_start: 0.8443 (tt0) cc_final: 0.8194 (tt0) REVERT: B 57 MET cc_start: 0.8202 (mtp) cc_final: 0.7967 (mtm) REVERT: B 76 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.5665 (t80) REVERT: B 233 TYR cc_start: 0.7599 (m-80) cc_final: 0.6694 (t80) REVERT: B 258 GLU cc_start: 0.8434 (tt0) cc_final: 0.8179 (tt0) REVERT: C 8 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8074 (mm-40) REVERT: C 76 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.5508 (t80) REVERT: C 116 THR cc_start: 0.9200 (m) cc_final: 0.8819 (p) REVERT: C 185 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8563 (mttm) REVERT: C 207 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8595 (t0) REVERT: C 233 TYR cc_start: 0.7559 (m-80) cc_final: 0.6571 (t80) REVERT: C 258 GLU cc_start: 0.8421 (tt0) cc_final: 0.8159 (tt0) REVERT: D 76 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.5446 (t80) REVERT: D 185 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8604 (mttp) REVERT: D 233 TYR cc_start: 0.7743 (m-80) cc_final: 0.6749 (t80) REVERT: D 258 GLU cc_start: 0.8426 (tt0) cc_final: 0.8156 (tt0) REVERT: E 76 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.5595 (t80) REVERT: E 116 THR cc_start: 0.9216 (m) cc_final: 0.8872 (p) REVERT: E 207 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8592 (t0) REVERT: E 233 TYR cc_start: 0.7627 (m-80) cc_final: 0.6716 (t80) REVERT: F 185 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8470 (mttp) REVERT: F 233 TYR cc_start: 0.7644 (m-80) cc_final: 0.6717 (t80) REVERT: F 258 GLU cc_start: 0.8445 (tt0) cc_final: 0.8199 (tt0) REVERT: G 76 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.5584 (t80) REVERT: G 233 TYR cc_start: 0.7671 (m-80) cc_final: 0.6705 (t80) outliers start: 49 outliers final: 16 residues processed: 194 average time/residue: 0.6137 time to fit residues: 137.1010 Evaluate side-chains 179 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 56 ILE 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 C residue 56 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 TYR 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 F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 76 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 240 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 211 optimal weight: 0.0570 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 166 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- 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 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 231 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.073496 restraints weight = 28559.974| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.81 r_work: 0.2731 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22589 Z= 0.159 Angle : 0.558 5.296 30849 Z= 0.316 Chirality : 0.047 0.141 3234 Planarity : 0.004 0.034 4025 Dihedral : 4.654 16.017 3024 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.53 % Allowed : 7.19 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 2751 helix: 1.20 (0.22), residues: 497 sheet: 1.31 (0.15), residues: 1057 loop : -0.41 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.013 0.001 TYR E 61 PHE 0.018 0.002 PHE D 321 TRP 0.009 0.001 TRP D 370 HIS 0.004 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00304 (22582) covalent geometry : angle 0.55844 (30835) SS BOND : bond 0.00072 ( 7) SS BOND : angle 0.35502 ( 14) hydrogen bonds : bond 0.05390 ( 819) hydrogen bonds : angle 4.53364 ( 2373) *********************** 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 195 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.011 Fit side-chains REVERT: A 8 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8086 (mm-40) REVERT: A 76 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.5250 (t80) REVERT: A 185 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8397 (mttp) REVERT: A 233 TYR cc_start: 0.7551 (m-80) cc_final: 0.6545 (t80) REVERT: A 258 GLU cc_start: 0.8404 (tt0) cc_final: 0.8156 (tt0) REVERT: B 57 MET cc_start: 0.8230 (mtp) cc_final: 0.7996 (mtm) REVERT: B 76 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 233 TYR cc_start: 0.7511 (m-80) cc_final: 0.6639 (t80) REVERT: B 258 GLU cc_start: 0.8414 (tt0) cc_final: 0.8168 (tt0) REVERT: C 8 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8047 (mm-40) REVERT: C 76 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.5469 (t80) REVERT: C 116 THR cc_start: 0.9172 (m) cc_final: 0.8790 (p) REVERT: C 185 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8566 (mttm) REVERT: C 207 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8580 (t0) REVERT: C 233 TYR cc_start: 0.7488 (m-80) cc_final: 0.6458 (t80) REVERT: D 76 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.5497 (t80) REVERT: D 185 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8594 (mttp) REVERT: D 233 TYR cc_start: 0.7607 (m-80) cc_final: 0.6673 (t80) REVERT: D 258 GLU cc_start: 0.8373 (tt0) cc_final: 0.8108 (tt0) REVERT: E 76 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.5447 (t80) REVERT: E 116 THR cc_start: 0.9201 (m) cc_final: 0.8849 (p) REVERT: E 233 TYR cc_start: 0.7526 (m-80) cc_final: 0.6740 (t80) REVERT: F 185 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8469 (mttp) REVERT: F 233 TYR cc_start: 0.7573 (m-80) cc_final: 0.6658 (t80) REVERT: F 258 GLU cc_start: 0.8447 (tt0) cc_final: 0.8198 (tt0) REVERT: G 233 TYR cc_start: 0.7617 (m-80) cc_final: 0.6635 (t80) outliers start: 36 outliers final: 13 residues processed: 190 average time/residue: 0.6233 time to fit residues: 136.5882 Evaluate side-chains 172 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 241 THR 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 F residue 50 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE 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 37 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 E 8 GLN E 231 ASN F 8 GLN F 134 GLN F 231 ASN G 8 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 = 0.3290 r_free = 0.3290 target = 0.100488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.072628 restraints weight = 28327.655| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.85 r_work: 0.2715 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22589 Z= 0.176 Angle : 0.580 5.216 30849 Z= 0.329 Chirality : 0.048 0.144 3234 Planarity : 0.005 0.035 4025 Dihedral : 4.699 16.060 3024 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.70 % Allowed : 7.10 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 2751 helix: 1.23 (0.23), residues: 497 sheet: 1.28 (0.15), residues: 1092 loop : -0.57 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 282 TYR 0.017 0.002 TYR A 61 PHE 0.016 0.002 PHE C 321 TRP 0.010 0.001 TRP D 370 HIS 0.005 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00350 (22582) covalent geometry : angle 0.58053 (30835) SS BOND : bond 0.00088 ( 7) SS BOND : angle 0.37810 ( 14) hydrogen bonds : bond 0.05839 ( 819) hydrogen bonds : angle 4.51179 ( 2373) *********************** 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 194 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.952 Fit side-chains REVERT: A 8 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8157 (mm-40) REVERT: A 76 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.5329 (t80) REVERT: A 233 TYR cc_start: 0.7585 (m-80) cc_final: 0.6578 (t80) REVERT: A 258 GLU cc_start: 0.8395 (tt0) cc_final: 0.8150 (tt0) REVERT: B 8 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: B 57 MET cc_start: 0.8334 (mtp) cc_final: 0.8100 (mtp) REVERT: B 76 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.5535 (t80) REVERT: B 233 TYR cc_start: 0.7581 (m-80) cc_final: 0.6700 (t80) REVERT: B 258 GLU cc_start: 0.8427 (tt0) cc_final: 0.8181 (tt0) REVERT: C 8 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8084 (mm-40) REVERT: C 76 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.5380 (t80) REVERT: C 116 THR cc_start: 0.9173 (m) cc_final: 0.8790 (p) REVERT: C 185 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8574 (mttm) REVERT: C 207 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8612 (t0) REVERT: C 233 TYR cc_start: 0.7522 (m-80) cc_final: 0.6495 (t80) REVERT: D 76 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.5514 (t80) REVERT: D 185 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8601 (mttp) REVERT: D 233 TYR cc_start: 0.7702 (m-80) cc_final: 0.6742 (t80) REVERT: D 258 GLU cc_start: 0.8373 (tt0) cc_final: 0.8113 (tt0) REVERT: E 50 LEU cc_start: 0.7353 (pt) cc_final: 0.7111 (pp) REVERT: E 76 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.5495 (t80) REVERT: E 116 THR cc_start: 0.9200 (m) cc_final: 0.8845 (p) REVERT: E 207 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8540 (t0) REVERT: E 233 TYR cc_start: 0.7581 (m-80) cc_final: 0.6769 (t80) REVERT: F 185 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8476 (mttp) REVERT: F 233 TYR cc_start: 0.7616 (m-80) cc_final: 0.6678 (t80) REVERT: F 258 GLU cc_start: 0.8455 (tt0) cc_final: 0.8205 (tt0) REVERT: G 76 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.5486 (t80) REVERT: G 233 TYR cc_start: 0.7669 (m-80) cc_final: 0.6675 (t80) outliers start: 40 outliers final: 19 residues processed: 187 average time/residue: 0.6200 time to fit residues: 133.8117 Evaluate side-chains 180 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 207 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 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 241 THR 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 F residue 50 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 36 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 2 optimal weight: 0.0000 chunk 270 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 231 ASN B 8 GLN B 134 GLN B 231 ASN C 231 ASN D 8 GLN D 134 GLN D 195 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 231 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.074731 restraints weight = 28174.510| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.85 r_work: 0.2752 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 22589 Z= 0.135 Angle : 0.518 4.628 30849 Z= 0.292 Chirality : 0.045 0.138 3234 Planarity : 0.004 0.031 4025 Dihedral : 4.467 15.621 3024 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.40 % Allowed : 7.36 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 2751 helix: 1.36 (0.22), residues: 497 sheet: 1.32 (0.15), residues: 1057 loop : -0.38 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 282 TYR 0.012 0.001 TYR A 61 PHE 0.018 0.001 PHE D 321 TRP 0.009 0.001 TRP D 370 HIS 0.003 0.001 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00243 (22582) covalent geometry : angle 0.51850 (30835) SS BOND : bond 0.00039 ( 7) SS BOND : angle 0.22731 ( 14) hydrogen bonds : bond 0.04675 ( 819) hydrogen bonds : angle 4.42158 ( 2373) *********************** 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 195 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.957 Fit side-chains REVERT: A 76 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.5212 (t80) REVERT: A 185 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8378 (mttp) REVERT: A 233 TYR cc_start: 0.7498 (m-80) cc_final: 0.6489 (t80) REVERT: A 258 GLU cc_start: 0.8364 (tt0) cc_final: 0.8115 (tt0) REVERT: B 57 MET cc_start: 0.8296 (mtp) cc_final: 0.8069 (mtp) REVERT: B 76 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.5456 (t80) REVERT: B 233 TYR cc_start: 0.7482 (m-80) cc_final: 0.6630 (t80) REVERT: B 258 GLU cc_start: 0.8346 (tt0) cc_final: 0.8099 (tt0) REVERT: B 407 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 8 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8100 (mm-40) REVERT: C 116 THR cc_start: 0.9155 (m) cc_final: 0.8745 (p) REVERT: C 185 LYS cc_start: 0.8954 (mtmt) cc_final: 0.8568 (mttm) REVERT: C 207 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8622 (t0) REVERT: C 233 TYR cc_start: 0.7429 (m-80) cc_final: 0.6453 (t80) REVERT: D 76 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.5329 (t80) REVERT: D 185 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8590 (mttp) REVERT: D 233 TYR cc_start: 0.7569 (m-80) cc_final: 0.6650 (t80) REVERT: D 258 GLU cc_start: 0.8319 (tt0) cc_final: 0.8056 (tt0) REVERT: E 116 THR cc_start: 0.9173 (m) cc_final: 0.8813 (p) REVERT: E 140 MET cc_start: 0.8917 (mmm) cc_final: 0.8604 (mmm) REVERT: E 207 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8560 (t0) REVERT: E 233 TYR cc_start: 0.7468 (m-80) cc_final: 0.6654 (t80) REVERT: F 185 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8465 (mttp) REVERT: F 233 TYR cc_start: 0.7518 (m-80) cc_final: 0.6627 (t80) REVERT: F 242 LYS cc_start: 0.7613 (tttt) cc_final: 0.7338 (ttmp) REVERT: F 258 GLU cc_start: 0.8448 (tt0) cc_final: 0.8205 (tt0) REVERT: G 233 TYR cc_start: 0.7524 (m-80) cc_final: 0.6594 (t80) outliers start: 33 outliers final: 17 residues processed: 189 average time/residue: 0.6139 time to fit residues: 134.0143 Evaluate side-chains 176 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 56 ILE 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 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 76 TYR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 241 THR 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 241 THR 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 48 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 134 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 231 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.073278 restraints weight = 28260.696| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.85 r_work: 0.2727 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22589 Z= 0.162 Angle : 0.557 4.786 30849 Z= 0.315 Chirality : 0.047 0.142 3234 Planarity : 0.004 0.033 4025 Dihedral : 4.576 15.693 3024 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 7.48 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 2751 helix: 1.34 (0.23), residues: 497 sheet: 1.34 (0.15), residues: 1057 loop : -0.38 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 220 TYR 0.016 0.001 TYR A 61 PHE 0.016 0.002 PHE F 321 TRP 0.009 0.001 TRP G 359 HIS 0.004 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00316 (22582) covalent geometry : angle 0.55717 (30835) SS BOND : bond 0.00064 ( 7) SS BOND : angle 0.29577 ( 14) hydrogen bonds : bond 0.05500 ( 819) hydrogen bonds : angle 4.43000 ( 2373) *********************** 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 184 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.954 Fit side-chains REVERT: A 76 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.5249 (t80) REVERT: A 233 TYR cc_start: 0.7574 (m-80) cc_final: 0.6551 (t80) REVERT: A 258 GLU cc_start: 0.8373 (tt0) cc_final: 0.8140 (tt0) REVERT: B 57 MET cc_start: 0.8306 (mtp) cc_final: 0.8085 (mtp) REVERT: B 76 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.5611 (t80) REVERT: B 233 TYR cc_start: 0.7569 (m-80) cc_final: 0.6664 (t80) REVERT: B 258 GLU cc_start: 0.8411 (tt0) cc_final: 0.8167 (tt0) REVERT: B 407 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8674 (mt-10) REVERT: C 8 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8059 (mm-40) REVERT: C 116 THR cc_start: 0.9171 (m) cc_final: 0.8765 (p) REVERT: C 185 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8575 (mttm) REVERT: C 207 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8619 (t0) REVERT: C 233 TYR cc_start: 0.7491 (m-80) cc_final: 0.6529 (t80) REVERT: D 76 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.5435 (t80) REVERT: D 185 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8592 (mttp) REVERT: D 233 TYR cc_start: 0.7612 (m-80) cc_final: 0.6622 (t80) REVERT: D 258 GLU cc_start: 0.8362 (tt0) cc_final: 0.8102 (tt0) REVERT: E 116 THR cc_start: 0.9185 (m) cc_final: 0.8824 (p) REVERT: E 207 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8535 (t0) REVERT: E 233 TYR cc_start: 0.7550 (m-80) cc_final: 0.6754 (t80) REVERT: F 185 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8468 (mttp) REVERT: F 233 TYR cc_start: 0.7607 (m-80) cc_final: 0.6653 (t80) REVERT: F 242 LYS cc_start: 0.7609 (tttt) cc_final: 0.7343 (ttmp) REVERT: F 258 GLU cc_start: 0.8459 (tt0) cc_final: 0.8211 (tt0) REVERT: G 233 TYR cc_start: 0.7616 (m-80) cc_final: 0.6639 (t80) outliers start: 32 outliers final: 20 residues processed: 178 average time/residue: 0.6218 time to fit residues: 127.9064 Evaluate side-chains 176 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 56 ILE 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 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 76 TYR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 241 THR 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 241 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 114 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 231 ASN B 134 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 231 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.075170 restraints weight = 28497.208| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.85 r_work: 0.2763 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 22589 Z= 0.128 Angle : 0.507 4.638 30849 Z= 0.285 Chirality : 0.045 0.137 3234 Planarity : 0.004 0.031 4025 Dihedral : 4.376 15.197 3024 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.19 % Allowed : 7.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.15), residues: 2751 helix: 1.47 (0.23), residues: 497 sheet: 1.36 (0.15), residues: 1057 loop : -0.32 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 397 TYR 0.010 0.001 TYR A 61 PHE 0.019 0.001 PHE A 321 TRP 0.010 0.001 TRP G 45 HIS 0.003 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00234 (22582) covalent geometry : angle 0.50702 (30835) SS BOND : bond 0.00034 ( 7) SS BOND : angle 0.18849 ( 14) hydrogen bonds : bond 0.04449 ( 819) hydrogen bonds : angle 4.35871 ( 2373) ********************** 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 195 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.919 Fit side-chains REVERT: A 185 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8382 (mttp) REVERT: A 233 TYR cc_start: 0.7487 (m-80) cc_final: 0.6485 (t80) REVERT: A 258 GLU cc_start: 0.8303 (tt0) cc_final: 0.8067 (tt0) REVERT: B 57 MET cc_start: 0.8265 (mtp) cc_final: 0.8011 (mtm) REVERT: B 233 TYR cc_start: 0.7465 (m-80) cc_final: 0.6594 (t80) REVERT: B 258 GLU cc_start: 0.8327 (tt0) cc_final: 0.8080 (tt0) REVERT: C 8 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8045 (mm-40) REVERT: C 116 THR cc_start: 0.9148 (m) cc_final: 0.8736 (p) REVERT: C 185 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8565 (mttm) REVERT: C 207 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8678 (t0) REVERT: C 233 TYR cc_start: 0.7421 (m-80) cc_final: 0.6433 (t80) REVERT: D 185 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8583 (mttp) REVERT: D 233 TYR cc_start: 0.7517 (m-80) cc_final: 0.6617 (t80) REVERT: D 258 GLU cc_start: 0.8315 (tt0) cc_final: 0.8046 (tt0) REVERT: E 116 THR cc_start: 0.9160 (m) cc_final: 0.8795 (p) REVERT: E 207 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8621 (t70) REVERT: E 233 TYR cc_start: 0.7426 (m-80) cc_final: 0.6630 (t80) REVERT: F 185 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8454 (mttp) REVERT: F 233 TYR cc_start: 0.7493 (m-80) cc_final: 0.6618 (t80) REVERT: F 242 LYS cc_start: 0.7609 (tttt) cc_final: 0.7349 (ttmp) REVERT: F 258 GLU cc_start: 0.8432 (tt0) cc_final: 0.8190 (tt0) REVERT: G 233 TYR cc_start: 0.7473 (m-80) cc_final: 0.6562 (t80) outliers start: 28 outliers final: 17 residues processed: 187 average time/residue: 0.6074 time to fit residues: 131.5644 Evaluate side-chains 176 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 207 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 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 241 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 144 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 134 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 231 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.072462 restraints weight = 28266.000| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.84 r_work: 0.2713 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22589 Z= 0.182 Angle : 0.585 5.206 30849 Z= 0.332 Chirality : 0.048 0.146 3234 Planarity : 0.005 0.034 4025 Dihedral : 4.641 15.725 3024 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.28 % Allowed : 7.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 2751 helix: 1.33 (0.23), residues: 497 sheet: 1.38 (0.15), residues: 1057 loop : -0.37 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 282 TYR 0.016 0.002 TYR A 61 PHE 0.014 0.002 PHE G 321 TRP 0.010 0.001 TRP G 359 HIS 0.005 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00366 (22582) covalent geometry : angle 0.58531 (30835) SS BOND : bond 0.00084 ( 7) SS BOND : angle 0.32752 ( 14) hydrogen bonds : bond 0.05997 ( 819) hydrogen bonds : angle 4.43893 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10838.99 seconds wall clock time: 184 minutes 28.20 seconds (11068.20 seconds total)