Starting phenix.real_space_refine on Thu Jul 2 22:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mae_63750/07_2026/9mae_63750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mae_63750/07_2026/9mae_63750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mae_63750/07_2026/9mae_63750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mae_63750/07_2026/9mae_63750.map" model { file = "/net/cci-nas-00/data/ceres_data/9mae_63750/07_2026/9mae_63750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mae_63750/07_2026/9mae_63750.cif" } resolution = 3.13 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= 0.040 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 48 5.16 5 C 6588 2.51 5 N 1710 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10163 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 7, 'TRANS': 312} Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2484 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain: "C" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 7, 'TRANS': 312} Chain: "D" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2484 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.20 Number of scatterers: 10163 At special positions: 0 Unit cell: (93.79, 88.81, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 48 16.00 O 1814 8.00 N 1710 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 140 " distance=2.03 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: 0.73 Conformation dependent library (CDL) restraints added in 362.2 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 22 sheets defined 35.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 60 through 69 removed outlier: 4.114A pdb=" N LYS A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 98 Processing helix chain 'A' and resid 99 through 104 removed outlier: 6.403A pdb=" N LEU A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 143 through 174 removed outlier: 3.604A pdb=" N MET A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'B' and resid 47 through 61 removed outlier: 3.762A pdb=" N TRP B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 94 Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.963A pdb=" N PHE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 171 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 68 through 98 removed outlier: 4.155A pdb=" N HIS C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 removed outlier: 6.435A pdb=" N LEU C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 143 through 174 removed outlier: 3.562A pdb=" N MET C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 325 through 328 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'D' and resid 47 through 61 removed outlier: 3.713A pdb=" N TRP D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 94 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 115 through 127 removed outlier: 4.008A pdb=" N PHE D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 171 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.609A pdb=" N ALA A 188 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.720A pdb=" N VAL A 212 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A 213 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A 285 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.720A pdb=" N VAL A 212 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 315 " --> pdb=" O MET A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 310 Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.405A pdb=" N TYR A 321 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU B 42 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A 323 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.823A pdb=" N TYR B 135 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.392A pdb=" N ALA B 185 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 228 through 235 removed outlier: 5.267A pdb=" N ARG B 230 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N HIS B 221 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 249 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 228 through 235 removed outlier: 5.267A pdb=" N ARG B 230 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N HIS B 221 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY B 210 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR B 286 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AB4, first strand: chain 'B' and resid 323 through 325 removed outlier: 3.816A pdb=" N ILE B 315 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU C 213 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 285 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 244 through 247 removed outlier: 3.713A pdb=" N VAL C 212 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU C 213 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 285 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AB7, first strand: chain 'C' and resid 183 through 184 removed outlier: 6.586A pdb=" N ALA C 188 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 308 through 310 Processing sheet with id=AB9, first strand: chain 'C' and resid 314 through 316 removed outlier: 6.481A pdb=" N TYR C 321 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 179 through 181 removed outlier: 3.598A pdb=" N ARG D 180 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 179 through 181 removed outlier: 3.598A pdb=" N ARG D 180 " --> pdb=" O ALA D 201 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA D 185 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 228 through 235 removed outlier: 5.378A pdb=" N ARG D 230 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N HIS D 221 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY D 210 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR D 286 " --> pdb=" O GLY D 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 309 through 311 501 hydrogen bonds defined for protein. 1431 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: 1.59 Time building geometry restraints manager: 0.99 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: 3210 1.34 - 1.46: 1878 1.46 - 1.57: 5248 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 10406 Sorted by residual: bond pdb=" C VAL B 112 " pdb=" O VAL B 112 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.56e-01 bond pdb=" C ILE D 250 " pdb=" O ILE D 250 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.96e-01 bond pdb=" CB VAL A 91 " pdb=" CG1 VAL A 91 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.73e-01 bond pdb=" CG LEU A 189 " pdb=" CD2 LEU A 189 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.58e-01 bond pdb=" CG LEU C 189 " pdb=" CD2 LEU C 189 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.54e-01 ... (remaining 10401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 13976 1.73 - 3.46: 137 3.46 - 5.19: 13 5.19 - 6.92: 2 6.92 - 8.65: 2 Bond angle restraints: 14130 Sorted by residual: angle pdb=" CA LEU D 99 " pdb=" CB LEU D 99 " pdb=" CG LEU D 99 " ideal model delta sigma weight residual 116.30 124.95 -8.65 3.50e+00 8.16e-02 6.11e+00 angle pdb=" CA LEU B 99 " pdb=" CB LEU B 99 " pdb=" CG LEU B 99 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 angle pdb=" CA ILE D 250 " pdb=" C ILE D 250 " pdb=" N LEU D 251 " ideal model delta sigma weight residual 116.60 119.52 -2.92 1.45e+00 4.76e-01 4.05e+00 angle pdb=" CA PRO B 101 " pdb=" C PRO B 101 " pdb=" N PRO B 102 " ideal model delta sigma weight residual 117.93 120.16 -2.23 1.20e+00 6.94e-01 3.44e+00 angle pdb=" CA LEU B 146 " pdb=" CB LEU B 146 " pdb=" CG LEU B 146 " ideal model delta sigma weight residual 116.30 122.69 -6.39 3.50e+00 8.16e-02 3.33e+00 ... (remaining 14125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5399 17.94 - 35.87: 564 35.87 - 53.81: 120 53.81 - 71.75: 36 71.75 - 89.68: 7 Dihedral angle restraints: 6126 sinusoidal: 2428 harmonic: 3698 Sorted by residual: dihedral pdb=" CA ASP A 40 " pdb=" CB ASP A 40 " pdb=" CG ASP A 40 " pdb=" OD1 ASP A 40 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA VAL B 109 " pdb=" C VAL B 109 " pdb=" N VAL B 110 " pdb=" CA VAL B 110 " ideal model delta harmonic sigma weight residual 180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU C 315 " pdb=" CG GLU C 315 " pdb=" CD GLU C 315 " pdb=" OE1 GLU C 315 " ideal model delta sinusoidal sigma weight residual 0.00 89.68 -89.68 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1096 0.031 - 0.063: 348 0.063 - 0.094: 101 0.094 - 0.125: 81 0.125 - 0.156: 2 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CA ILE D 179 " pdb=" N ILE D 179 " pdb=" C ILE D 179 " pdb=" CB ILE D 179 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE B 179 " pdb=" N ILE B 179 " pdb=" C ILE B 179 " pdb=" CB ILE B 179 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE B 282 " pdb=" N ILE B 282 " pdb=" C ILE B 282 " pdb=" CB ILE B 282 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1625 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 101 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO D 102 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 100 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 101 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 249 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 250 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " -0.018 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.77: 1763 2.77 - 3.36: 10982 3.36 - 3.95: 18953 3.95 - 4.55: 26168 4.55 - 5.14: 41396 Nonbonded interactions: 99262 Sorted by model distance: nonbonded pdb=" O LEU B 151 " pdb=" OG1 THR B 155 " model vdw 2.176 3.040 nonbonded pdb=" O LEU C 126 " pdb=" OG1 THR C 130 " model vdw 2.181 3.040 nonbonded pdb=" O LEU D 151 " pdb=" OG1 THR D 155 " model vdw 2.201 3.040 nonbonded pdb=" OG SER A 227 " pdb=" OE1 GLU A 228 " model vdw 2.210 3.040 nonbonded pdb=" O SER D 182 " pdb=" OH TYR D 300 " model vdw 2.213 3.040 ... (remaining 99257 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 351) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 27 through 339) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.650 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.760 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10410 Z= 0.114 Angle : 0.459 8.651 14138 Z= 0.248 Chirality : 0.040 0.156 1628 Planarity : 0.003 0.044 1758 Dihedral : 15.820 89.682 3722 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.36 % Allowed : 20.57 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1258 helix: 2.69 (0.24), residues: 414 sheet: -0.50 (0.33), residues: 272 loop : -0.52 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.007 0.001 TYR B 87 PHE 0.016 0.001 PHE B 327 TRP 0.017 0.001 TRP C 85 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (10406) covalent geometry : angle 0.45920 / 0.25 (14130) SS BOND : bond 0.00096 / 0.05 ( 4) SS BOND : angle 0.33126 / 0.17 ( 8) hydrogen bonds : bond 0.18230 / 11.91 ( 479) hydrogen bonds : angle 6.81687 / 4.92 ( 1431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: D 62 MET cc_start: 0.4800 (mmm) cc_final: 0.4278 (mtp) REVERT: D 180 ARG cc_start: 0.7695 (ptm160) cc_final: 0.6954 (ptt180) REVERT: D 204 ARG cc_start: 0.6783 (mmp80) cc_final: 0.6247 (mmm-85) REVERT: D 303 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6696 (pm20) outliers start: 4 outliers final: 0 residues processed: 116 average time/residue: 0.1372 time to fit residues: 20.8549 Evaluate side-chains 111 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 259 HIS C 308 HIS D 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.213410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137780 restraints weight = 9154.676| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.55 r_work: 0.3267 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10410 Z= 0.138 Angle : 0.507 12.462 14138 Z= 0.261 Chirality : 0.042 0.166 1628 Planarity : 0.004 0.048 1758 Dihedral : 4.200 42.990 1379 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.97 % Allowed : 18.60 % Favored : 79.43 % 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 are not related in a simple way. whole: 0.94 (0.24), residues: 1258 helix: 2.64 (0.24), residues: 422 sheet: -0.24 (0.31), residues: 284 loop : -0.47 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.009 0.001 TYR C 223 PHE 0.015 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10406) covalent geometry : angle 0.50726 / 0.26 (14130) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.71699 / 0.38 ( 8) hydrogen bonds : bond 0.03902 / 2.58 ( 479) hydrogen bonds : angle 4.67990 / 3.43 ( 1431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6784 (tpp-160) REVERT: A 172 MET cc_start: 0.5670 (tpp) cc_final: 0.5094 (tpp) REVERT: A 228 GLU cc_start: 0.7101 (mp0) cc_final: 0.6520 (mt-10) REVERT: B 212 GLN cc_start: 0.7341 (pt0) cc_final: 0.6513 (tt0) REVERT: C 129 GLN cc_start: 0.7852 (tt0) cc_final: 0.7519 (tt0) REVERT: C 172 MET cc_start: 0.5595 (tpp) cc_final: 0.5040 (tpp) REVERT: C 274 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7263 (t0) REVERT: D 204 ARG cc_start: 0.6688 (mmp80) cc_final: 0.6048 (mmt90) REVERT: D 303 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7282 (pm20) outliers start: 22 outliers final: 9 residues processed: 138 average time/residue: 0.1216 time to fit residues: 22.2241 Evaluate side-chains 126 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.214501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138485 restraints weight = 9154.856| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.60 r_work: 0.3274 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10410 Z= 0.129 Angle : 0.490 12.113 14138 Z= 0.251 Chirality : 0.041 0.162 1628 Planarity : 0.004 0.048 1758 Dihedral : 4.171 49.065 1379 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.22 % Allowed : 18.52 % Favored : 78.26 % 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 are not related in a simple way. whole: 1.10 (0.24), residues: 1258 helix: 2.75 (0.24), residues: 424 sheet: -0.08 (0.31), residues: 284 loop : -0.41 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 302 TYR 0.010 0.001 TYR C 223 PHE 0.018 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.004 0.000 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10406) covalent geometry : angle 0.48957 / 0.25 (14130) SS BOND : bond 0.00340 / 0.17 ( 4) SS BOND : angle 0.63596 / 0.32 ( 8) hydrogen bonds : bond 0.03518 / 2.33 ( 479) hydrogen bonds : angle 4.31375 / 3.17 ( 1431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.369 Fit side-chains REVERT: A 172 MET cc_start: 0.5803 (tpp) cc_final: 0.5241 (tpp) REVERT: A 196 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5213 (ptpt) REVERT: A 228 GLU cc_start: 0.7051 (mp0) cc_final: 0.6584 (mt-10) REVERT: B 34 ASP cc_start: 0.7201 (t70) cc_final: 0.6973 (t0) REVERT: B 212 GLN cc_start: 0.7443 (pt0) cc_final: 0.6637 (tt0) REVERT: B 278 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: B 303 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6701 (pm20) REVERT: C 129 GLN cc_start: 0.7904 (tt0) cc_final: 0.7699 (tt0) REVERT: C 172 MET cc_start: 0.5659 (tpp) cc_final: 0.5088 (tpp) REVERT: C 196 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5410 (ptpt) REVERT: C 274 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7283 (t0) REVERT: C 279 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7960 (mt) REVERT: D 204 ARG cc_start: 0.6786 (mmp80) cc_final: 0.6135 (mmt90) REVERT: D 303 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7460 (pm20) outliers start: 36 outliers final: 14 residues processed: 155 average time/residue: 0.1234 time to fit residues: 25.2144 Evaluate side-chains 136 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 56 optimal weight: 0.0270 chunk 63 optimal weight: 0.0030 chunk 110 optimal weight: 2.9990 overall best weight: 0.4248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.215327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143783 restraints weight = 9126.655| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.44 r_work: 0.3347 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10410 Z= 0.107 Angle : 0.468 11.846 14138 Z= 0.240 Chirality : 0.041 0.162 1628 Planarity : 0.003 0.048 1758 Dihedral : 4.097 51.896 1379 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.95 % Allowed : 19.41 % Favored : 77.64 % 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 are not related in a simple way. whole: 1.23 (0.24), residues: 1258 helix: 2.80 (0.23), residues: 424 sheet: 0.07 (0.31), residues: 284 loop : -0.33 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.008 0.001 TYR C 223 PHE 0.016 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.004 0.000 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10406) covalent geometry : angle 0.46830 / 0.24 (14130) SS BOND : bond 0.00131 / 0.06 ( 4) SS BOND : angle 0.69524 / 0.35 ( 8) hydrogen bonds : bond 0.03246 / 2.16 ( 479) hydrogen bonds : angle 4.07071 / 2.99 ( 1431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.399 Fit side-chains REVERT: A 172 MET cc_start: 0.5783 (tpp) cc_final: 0.5219 (tpp) REVERT: A 196 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.5008 (ptpt) REVERT: A 228 GLU cc_start: 0.6947 (mp0) cc_final: 0.6508 (mt-10) REVERT: B 212 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: B 278 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: B 303 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6777 (pm20) REVERT: C 196 LYS cc_start: 0.5449 (OUTLIER) cc_final: 0.5223 (ptpt) REVERT: C 274 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7205 (t0) REVERT: D 204 ARG cc_start: 0.6754 (mmp80) cc_final: 0.6082 (mmt90) REVERT: D 303 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7478 (pm20) outliers start: 33 outliers final: 15 residues processed: 153 average time/residue: 0.1180 time to fit residues: 24.3441 Evaluate side-chains 139 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.213927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.144167 restraints weight = 9098.242| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.32 r_work: 0.3305 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10410 Z= 0.130 Angle : 0.492 11.479 14138 Z= 0.253 Chirality : 0.041 0.172 1628 Planarity : 0.003 0.048 1758 Dihedral : 4.209 59.807 1379 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.04 % Allowed : 20.30 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1258 helix: 2.83 (0.24), residues: 424 sheet: 0.08 (0.30), residues: 284 loop : -0.30 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 302 TYR 0.011 0.001 TYR C 223 PHE 0.016 0.001 PHE D 327 TRP 0.008 0.001 TRP C 85 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10406) covalent geometry : angle 0.49216 / 0.25 (14130) SS BOND : bond 0.00209 / 0.10 ( 4) SS BOND : angle 0.61669 / 0.31 ( 8) hydrogen bonds : bond 0.03263 / 2.17 ( 479) hydrogen bonds : angle 4.07095 / 2.99 ( 1431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.343 Fit side-chains REVERT: A 172 MET cc_start: 0.5723 (tpp) cc_final: 0.5157 (tpp) REVERT: A 196 LYS cc_start: 0.5271 (OUTLIER) cc_final: 0.5013 (ptpt) REVERT: A 228 GLU cc_start: 0.7031 (mp0) cc_final: 0.6599 (mt-10) REVERT: B 34 ASP cc_start: 0.7430 (t70) cc_final: 0.7129 (t70) REVERT: B 62 MET cc_start: 0.4285 (mmm) cc_final: 0.4074 (mmm) REVERT: B 212 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: B 278 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: B 303 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: C 196 LYS cc_start: 0.5478 (OUTLIER) cc_final: 0.5249 (ptpt) REVERT: C 274 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7287 (t0) REVERT: D 204 ARG cc_start: 0.6833 (mmp80) cc_final: 0.6157 (mmt90) outliers start: 34 outliers final: 22 residues processed: 148 average time/residue: 0.1172 time to fit residues: 23.2509 Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 278 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.215703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.149056 restraints weight = 9120.471| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.20 r_work: 0.3346 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10410 Z= 0.101 Angle : 0.466 11.227 14138 Z= 0.240 Chirality : 0.040 0.168 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.723 17.308 1376 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.31 % Allowed : 20.13 % Favored : 76.57 % 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 are not related in a simple way. whole: 1.40 (0.24), residues: 1258 helix: 2.83 (0.23), residues: 426 sheet: 0.22 (0.30), residues: 284 loop : -0.17 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.009 0.001 TYR C 223 PHE 0.016 0.001 PHE D 327 TRP 0.009 0.001 TRP C 85 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10406) covalent geometry : angle 0.46631 / 0.24 (14130) SS BOND : bond 0.00138 / 0.06 ( 4) SS BOND : angle 0.50018 / 0.25 ( 8) hydrogen bonds : bond 0.03101 / 2.07 ( 479) hydrogen bonds : angle 3.91673 / 2.88 ( 1431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.350 Fit side-chains REVERT: A 172 MET cc_start: 0.5698 (tpp) cc_final: 0.5104 (tpp) REVERT: A 196 LYS cc_start: 0.5306 (OUTLIER) cc_final: 0.4657 (ptpt) REVERT: B 34 ASP cc_start: 0.7370 (t70) cc_final: 0.7041 (t70) REVERT: B 62 MET cc_start: 0.4220 (mmm) cc_final: 0.3987 (mmm) REVERT: B 212 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: B 278 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: B 303 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: C 196 LYS cc_start: 0.5493 (OUTLIER) cc_final: 0.5267 (ptpt) REVERT: C 213 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 274 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7227 (t0) REVERT: D 204 ARG cc_start: 0.6840 (mmp80) cc_final: 0.6061 (mmm-85) REVERT: D 303 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6877 (pm20) outliers start: 37 outliers final: 20 residues processed: 148 average time/residue: 0.1237 time to fit residues: 24.4332 Evaluate side-chains 138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 67 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 chunk 53 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.215804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.149153 restraints weight = 9024.005| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.14 r_work: 0.3341 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10410 Z= 0.102 Angle : 0.468 11.145 14138 Z= 0.241 Chirality : 0.041 0.170 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.694 17.433 1376 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.31 % Allowed : 20.57 % Favored : 76.12 % 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 are not related in a simple way. whole: 1.51 (0.24), residues: 1258 helix: 2.88 (0.23), residues: 426 sheet: 0.32 (0.30), residues: 284 loop : -0.09 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 302 TYR 0.009 0.001 TYR C 223 PHE 0.017 0.001 PHE D 327 TRP 0.008 0.001 TRP C 85 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10406) covalent geometry : angle 0.46799 / 0.24 (14130) SS BOND : bond 0.00133 / 0.06 ( 4) SS BOND : angle 0.47193 / 0.24 ( 8) hydrogen bonds : bond 0.03060 / 2.04 ( 479) hydrogen bonds : angle 3.86455 / 2.85 ( 1431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.363 Fit side-chains REVERT: A 172 MET cc_start: 0.5642 (tpp) cc_final: 0.5054 (tpp) REVERT: A 196 LYS cc_start: 0.5165 (OUTLIER) cc_final: 0.4924 (ptpt) REVERT: B 34 ASP cc_start: 0.7312 (t70) cc_final: 0.7005 (t70) REVERT: B 62 MET cc_start: 0.4233 (mmm) cc_final: 0.3963 (mmm) REVERT: B 212 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6511 (tt0) REVERT: B 278 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: B 303 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: C 196 LYS cc_start: 0.5513 (OUTLIER) cc_final: 0.5298 (ptpt) REVERT: C 274 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7203 (t0) REVERT: D 180 ARG cc_start: 0.7616 (ptm160) cc_final: 0.6885 (ptt180) REVERT: D 204 ARG cc_start: 0.6763 (mmp80) cc_final: 0.6052 (mmm-85) REVERT: D 303 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6827 (pm20) outliers start: 37 outliers final: 26 residues processed: 151 average time/residue: 0.1231 time to fit residues: 24.8655 Evaluate side-chains 144 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.214130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145200 restraints weight = 9090.589| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.29 r_work: 0.3321 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10410 Z= 0.138 Angle : 0.514 10.929 14138 Z= 0.261 Chirality : 0.042 0.172 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.852 17.544 1376 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.31 % Allowed : 20.84 % Favored : 75.85 % 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 are not related in a simple way. whole: 1.47 (0.24), residues: 1258 helix: 2.87 (0.23), residues: 426 sheet: 0.25 (0.30), residues: 284 loop : -0.12 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 302 TYR 0.012 0.001 TYR C 223 PHE 0.023 0.001 PHE D 327 TRP 0.010 0.001 TRP B 86 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10406) covalent geometry : angle 0.51374 / 0.26 (14130) SS BOND : bond 0.00138 / 0.06 ( 4) SS BOND : angle 0.46929 / 0.23 ( 8) hydrogen bonds : bond 0.03214 / 2.15 ( 479) hydrogen bonds : angle 3.99243 / 2.93 ( 1431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.400 Fit side-chains REVERT: A 172 MET cc_start: 0.5685 (tpp) cc_final: 0.5083 (tpp) REVERT: A 196 LYS cc_start: 0.5123 (OUTLIER) cc_final: 0.4878 (ptpt) REVERT: A 228 GLU cc_start: 0.7093 (mp0) cc_final: 0.6678 (mt-10) REVERT: A 315 GLU cc_start: 0.7868 (tt0) cc_final: 0.7604 (tt0) REVERT: B 34 ASP cc_start: 0.7459 (t70) cc_final: 0.7111 (t70) REVERT: B 62 MET cc_start: 0.4111 (mmm) cc_final: 0.3861 (mmm) REVERT: B 205 LYS cc_start: 0.7881 (tttp) cc_final: 0.6930 (mmtt) REVERT: B 212 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6530 (tt0) REVERT: B 278 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: B 303 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: C 196 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.5280 (ptpt) REVERT: C 274 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7262 (t0) REVERT: D 180 ARG cc_start: 0.7611 (ptm160) cc_final: 0.6821 (ptt180) REVERT: D 204 ARG cc_start: 0.6798 (mmp80) cc_final: 0.6093 (mmm-85) REVERT: D 303 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6916 (pm20) outliers start: 37 outliers final: 26 residues processed: 144 average time/residue: 0.1166 time to fit residues: 22.6169 Evaluate side-chains 144 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS B 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.213242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145996 restraints weight = 9097.966| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.31 r_work: 0.3305 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10410 Z= 0.143 Angle : 0.520 11.709 14138 Z= 0.264 Chirality : 0.042 0.171 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.915 17.661 1376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.40 % Allowed : 21.11 % Favored : 75.49 % 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 are not related in a simple way. whole: 1.43 (0.24), residues: 1258 helix: 2.83 (0.23), residues: 426 sheet: 0.24 (0.30), residues: 284 loop : -0.14 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 302 TYR 0.013 0.001 TYR C 223 PHE 0.025 0.001 PHE D 327 TRP 0.007 0.001 TRP C 85 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (10406) covalent geometry : angle 0.52030 / 0.26 (14130) SS BOND : bond 0.00122 / 0.06 ( 4) SS BOND : angle 0.46234 / 0.23 ( 8) hydrogen bonds : bond 0.03226 / 2.15 ( 479) hydrogen bonds : angle 4.01642 / 2.95 ( 1431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.361 Fit side-chains REVERT: A 139 VAL cc_start: 0.6643 (OUTLIER) cc_final: 0.6351 (m) REVERT: A 172 MET cc_start: 0.5769 (tpp) cc_final: 0.5148 (tpp) REVERT: A 196 LYS cc_start: 0.5202 (OUTLIER) cc_final: 0.4943 (ptpt) REVERT: A 228 GLU cc_start: 0.7106 (mp0) cc_final: 0.6688 (mt-10) REVERT: B 34 ASP cc_start: 0.7549 (t70) cc_final: 0.7203 (t70) REVERT: B 62 MET cc_start: 0.4208 (mmm) cc_final: 0.3871 (mmm) REVERT: B 205 LYS cc_start: 0.7968 (tttp) cc_final: 0.7038 (mmtt) REVERT: B 212 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: B 278 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: B 303 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6752 (pm20) REVERT: C 129 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 196 LYS cc_start: 0.5557 (OUTLIER) cc_final: 0.5302 (ptpt) REVERT: C 274 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7264 (t0) REVERT: D 204 ARG cc_start: 0.6874 (mmp80) cc_final: 0.6138 (mmm-85) REVERT: D 303 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6816 (pm20) outliers start: 38 outliers final: 26 residues processed: 143 average time/residue: 0.1162 time to fit residues: 22.5145 Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS C 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.212029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.146093 restraints weight = 8970.329| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.18 r_work: 0.3303 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10410 Z= 0.165 Angle : 0.546 11.975 14138 Z= 0.276 Chirality : 0.043 0.176 1628 Planarity : 0.004 0.048 1758 Dihedral : 4.030 18.266 1376 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.13 % Allowed : 21.47 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1258 helix: 2.79 (0.23), residues: 426 sheet: 0.19 (0.30), residues: 284 loop : -0.21 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.014 0.001 TYR C 223 PHE 0.027 0.001 PHE D 327 TRP 0.009 0.001 TRP B 86 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 (10406) covalent geometry : angle 0.54565 / 0.28 (14130) SS BOND : bond 0.00148 / 0.07 ( 4) SS BOND : angle 0.53640 / 0.26 ( 8) hydrogen bonds : bond 0.03337 / 2.23 ( 479) hydrogen bonds : angle 4.09377 / 3.00 ( 1431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.358 Fit side-chains REVERT: A 139 VAL cc_start: 0.6688 (OUTLIER) cc_final: 0.6420 (m) REVERT: A 172 MET cc_start: 0.5815 (tpp) cc_final: 0.5150 (tpp) REVERT: A 196 LYS cc_start: 0.5197 (OUTLIER) cc_final: 0.4919 (ptpt) REVERT: A 228 GLU cc_start: 0.7132 (mp0) cc_final: 0.6694 (mt-10) REVERT: B 34 ASP cc_start: 0.7468 (t70) cc_final: 0.7117 (t70) REVERT: B 62 MET cc_start: 0.4202 (mmm) cc_final: 0.3735 (mmm) REVERT: B 205 LYS cc_start: 0.8020 (tttp) cc_final: 0.7087 (mmtt) REVERT: B 212 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: B 278 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: B 303 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: C 129 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 196 LYS cc_start: 0.5565 (OUTLIER) cc_final: 0.5296 (ptpt) REVERT: C 274 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7330 (t0) REVERT: D 204 ARG cc_start: 0.6912 (mmp80) cc_final: 0.6180 (mmm-85) REVERT: D 303 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6841 (pm20) outliers start: 35 outliers final: 24 residues processed: 140 average time/residue: 0.1196 time to fit residues: 22.6024 Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 8 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 110 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.214500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.146881 restraints weight = 9016.935| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.26 r_work: 0.3336 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10410 Z= 0.118 Angle : 0.501 12.245 14138 Z= 0.254 Chirality : 0.041 0.171 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.861 17.829 1376 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.86 % Allowed : 21.65 % Favored : 75.49 % 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 are not related in a simple way. whole: 1.45 (0.24), residues: 1258 helix: 2.86 (0.23), residues: 424 sheet: 0.28 (0.30), residues: 284 loop : -0.14 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.011 0.001 TYR C 223 PHE 0.021 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10406) covalent geometry : angle 0.50081 / 0.25 (14130) SS BOND : bond 0.00135 / 0.06 ( 4) SS BOND : angle 0.45576 / 0.23 ( 8) hydrogen bonds : bond 0.03149 / 2.10 ( 479) hydrogen bonds : angle 3.94305 / 2.89 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.48 seconds wall clock time: 52 minutes 0.26 seconds (3120.26 seconds total)