Starting phenix.real_space_refine on Sun Apr 5 12:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mae_63750/04_2026/9mae_63750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mae_63750/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mae_63750/04_2026/9mae_63750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mae_63750/04_2026/9mae_63750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mae_63750/04_2026/9mae_63750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mae_63750/04_2026/9mae_63750.map" } 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-2.1rc1-6017/lib/python3.9/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, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.23 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: 0.74 Conformation dependent library (CDL) restraints added in 473.8 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: 0.34 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: 1.62 Time building geometry restraints manager: 1.00 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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.940 Find NCS groups from input model: 0.190 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 covalent geometry : bond 0.00254 (10406) covalent geometry : angle 0.45920 (14130) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.33126 ( 8) hydrogen bonds : bond 0.18230 ( 479) hydrogen bonds : angle 6.81687 ( 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 : 0.364 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: 0.1430 time to fit residues: 21.5776 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 : 0.349 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4239 r_free = 0.4239 target = 0.213739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143826 restraints weight = 9127.167| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.37 r_work: 0.3302 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0886 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= 0.137 Angle : 0.504 12.275 14138 Z= 0.259 Chirality : 0.042 0.166 1628 Planarity : 0.004 0.048 1758 Dihedral : 4.169 43.171 1379 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.97 % Allowed : 18.87 % Favored : 79.16 % 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 are not related in a simple way. whole: 0.88 (0.24), residues: 1258 helix: 2.64 (0.24), residues: 422 sheet: -0.25 (0.31), residues: 284 loop : -0.57 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 35 TYR 0.009 0.001 TYR C 223 PHE 0.016 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00321 (10406) covalent geometry : angle 0.50339 (14130) SS BOND : bond 0.00091 ( 4) SS BOND : angle 0.72427 ( 8) hydrogen bonds : bond 0.03896 ( 479) hydrogen bonds : angle 4.64730 ( 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 140 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.5794 (tpp) cc_final: 0.5213 (tpp) REVERT: B 41 MET cc_start: 0.7987 (tpt) cc_final: 0.7766 (tpt) REVERT: B 212 GLN cc_start: 0.7416 (pt0) cc_final: 0.6602 (tt0) REVERT: C 172 MET cc_start: 0.5686 (tpp) cc_final: 0.5130 (tpp) REVERT: C 274 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7284 (t0) REVERT: D 204 ARG cc_start: 0.6596 (mmp80) cc_final: 0.5930 (mmt90) REVERT: D 303 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7347 (pm20) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 0.1379 time to fit residues: 24.6468 Evaluate side-chains 127 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 224 THR 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: 0.6980 chunk 71 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 76 optimal weight: 8.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4240 r_free = 0.4240 target = 0.213938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.147814 restraints weight = 9155.002| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.21 r_work: 0.3313 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1108 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= 0.128 Angle : 0.488 12.110 14138 Z= 0.250 Chirality : 0.041 0.164 1628 Planarity : 0.004 0.048 1758 Dihedral : 4.146 49.099 1379 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.31 % Allowed : 18.60 % Favored : 78.09 % 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: 1.00 (0.24), residues: 1258 helix: 2.74 (0.24), residues: 424 sheet: -0.11 (0.31), residues: 284 loop : -0.56 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.010 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 C 259 Details of bonding type rmsd covalent geometry : bond 0.00302 (10406) covalent geometry : angle 0.48755 (14130) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.72104 ( 8) hydrogen bonds : bond 0.03538 ( 479) hydrogen bonds : angle 4.32305 ( 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 161 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.383 Fit side-chains REVERT: A 172 MET cc_start: 0.5837 (tpp) cc_final: 0.5277 (tpp) REVERT: A 196 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.5041 (ptpt) REVERT: A 228 GLU cc_start: 0.6996 (mp0) cc_final: 0.6535 (mt-10) REVERT: B 34 ASP cc_start: 0.7326 (t70) cc_final: 0.7056 (t0) REVERT: B 41 MET cc_start: 0.8049 (tpt) cc_final: 0.7810 (tpt) REVERT: B 212 GLN cc_start: 0.7462 (pt0) cc_final: 0.6663 (tt0) REVERT: B 278 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: B 303 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: C 129 GLN cc_start: 0.8014 (tt0) cc_final: 0.7652 (tt0) REVERT: C 172 MET cc_start: 0.5695 (tpp) cc_final: 0.5131 (tpp) REVERT: C 196 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.5253 (ptpt) REVERT: C 274 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7281 (t0) REVERT: C 279 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8006 (mt) REVERT: D 204 ARG cc_start: 0.6697 (mmp80) cc_final: 0.6027 (mmt90) REVERT: D 303 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7479 (pm20) outliers start: 37 outliers final: 15 residues processed: 157 average time/residue: 0.1357 time to fit residues: 27.9595 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 : 0.388 ------------------------------------------------------------------------------- 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 284 SER 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: 2.9990 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 53 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 0.0070 chunk 110 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.213475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.142435 restraints weight = 9119.415| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.33 r_work: 0.3297 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10410 Z= 0.120 Angle : 0.481 11.796 14138 Z= 0.245 Chirality : 0.041 0.162 1628 Planarity : 0.003 0.048 1758 Dihedral : 4.168 55.281 1379 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.04 % Allowed : 19.05 % Favored : 77.91 % 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: 1.07 (0.24), residues: 1258 helix: 2.77 (0.23), residues: 424 sheet: 0.03 (0.31), residues: 284 loop : -0.56 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.010 0.001 TYR C 223 PHE 0.017 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.005 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00282 (10406) covalent geometry : angle 0.48094 (14130) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.71145 ( 8) hydrogen bonds : bond 0.03321 ( 479) hydrogen bonds : angle 4.13636 ( 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 159 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.448 Fit side-chains REVERT: A 172 MET cc_start: 0.5798 (tpp) cc_final: 0.5254 (tpp) REVERT: A 196 LYS cc_start: 0.5312 (OUTLIER) cc_final: 0.5066 (ptpt) REVERT: A 228 GLU cc_start: 0.7001 (mp0) cc_final: 0.6560 (mt-10) REVERT: B 42 GLU cc_start: 0.5873 (mm-30) cc_final: 0.5630 (mt-10) REVERT: B 212 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: B 278 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: B 303 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: C 196 LYS cc_start: 0.5528 (OUTLIER) cc_final: 0.5299 (ptpt) REVERT: C 274 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7264 (t0) REVERT: C 279 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8064 (mt) REVERT: D 204 ARG cc_start: 0.6812 (mmp80) cc_final: 0.6158 (mmt90) REVERT: D 303 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7504 (pm20) outliers start: 34 outliers final: 15 residues processed: 155 average time/residue: 0.1280 time to fit residues: 26.5066 Evaluate side-chains 144 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 C residue 279 LEU 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: 0.1980 chunk 120 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 259 HIS C 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.211877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142566 restraints weight = 9117.374| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.30 r_work: 0.3286 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10410 Z= 0.173 Angle : 0.528 11.335 14138 Z= 0.271 Chirality : 0.043 0.175 1628 Planarity : 0.004 0.048 1758 Dihedral : 4.284 48.518 1379 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.76 % Allowed : 18.96 % Favored : 77.28 % 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 are not related in a simple way. whole: 0.99 (0.23), residues: 1258 helix: 2.71 (0.24), residues: 426 sheet: -0.04 (0.30), residues: 284 loop : -0.62 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.013 0.001 TYR C 223 PHE 0.017 0.001 PHE D 327 TRP 0.008 0.001 TRP A 201 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00422 (10406) covalent geometry : angle 0.52821 (14130) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.64334 ( 8) hydrogen bonds : bond 0.03492 ( 479) hydrogen bonds : angle 4.24531 ( 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 155 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.364 Fit side-chains REVERT: A 172 MET cc_start: 0.5833 (tpp) cc_final: 0.5254 (tpp) REVERT: A 196 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.5104 (ptpt) REVERT: A 228 GLU cc_start: 0.7060 (mp0) cc_final: 0.6575 (mt-10) REVERT: B 27 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.4499 (ttp80) REVERT: B 34 ASP cc_start: 0.7507 (t70) cc_final: 0.7217 (t70) REVERT: B 62 MET cc_start: 0.4264 (mmm) cc_final: 0.4063 (mmm) REVERT: B 212 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6640 (tt0) REVERT: B 278 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: B 303 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: C 196 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5303 (ptpt) REVERT: C 274 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7320 (t0) REVERT: C 279 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8087 (mt) REVERT: D 148 ILE cc_start: 0.7359 (mt) cc_final: 0.7081 (tt) REVERT: D 204 ARG cc_start: 0.6910 (mmp80) cc_final: 0.6257 (mmt90) outliers start: 42 outliers final: 21 residues processed: 148 average time/residue: 0.1356 time to fit residues: 26.4524 Evaluate side-chains 137 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 225 GLU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 27 ARG 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 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 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 Chi-restraints excluded: chain D residue 284 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.215592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143114 restraints weight = 9112.635| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.51 r_work: 0.3298 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1563 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= 0.104 Angle : 0.468 11.170 14138 Z= 0.242 Chirality : 0.041 0.169 1628 Planarity : 0.003 0.049 1758 Dihedral : 3.787 17.593 1376 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.13 % Allowed : 20.30 % 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: 1.12 (0.23), residues: 1258 helix: 2.76 (0.23), residues: 426 sheet: 0.07 (0.30), residues: 284 loop : -0.51 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 302 TYR 0.009 0.001 TYR C 223 PHE 0.017 0.001 PHE B 327 TRP 0.009 0.001 TRP A 201 HIS 0.003 0.000 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00238 (10406) covalent geometry : angle 0.46829 (14130) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.57225 ( 8) hydrogen bonds : bond 0.03180 ( 479) hydrogen bonds : angle 3.98910 ( 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 147 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.418 Fit side-chains REVERT: A 172 MET cc_start: 0.5736 (tpp) cc_final: 0.5139 (tpp) REVERT: A 196 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4980 (ptpt) REVERT: B 34 ASP cc_start: 0.7330 (t70) cc_final: 0.6998 (t70) REVERT: B 62 MET cc_start: 0.4141 (mmm) cc_final: 0.3913 (mmm) REVERT: B 212 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: B 278 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: B 303 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: C 196 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.5153 (ptpt) REVERT: C 274 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7154 (t0) REVERT: D 148 ILE cc_start: 0.7409 (mt) cc_final: 0.7134 (tt) REVERT: D 204 ARG cc_start: 0.6738 (mmp80) cc_final: 0.6059 (mmt90) REVERT: D 303 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6831 (pm20) outliers start: 35 outliers final: 17 residues processed: 143 average time/residue: 0.1339 time to fit residues: 25.3317 Evaluate side-chains 128 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4226 r_free = 0.4226 target = 0.212060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143085 restraints weight = 9069.718| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.27 r_work: 0.3301 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10410 Z= 0.146 Angle : 0.515 11.024 14138 Z= 0.263 Chirality : 0.042 0.178 1628 Planarity : 0.004 0.048 1758 Dihedral : 3.915 17.794 1376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.31 % Allowed : 20.75 % Favored : 75.94 % 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: 1.09 (0.23), residues: 1258 helix: 2.76 (0.23), residues: 426 sheet: 0.08 (0.30), residues: 284 loop : -0.57 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 302 TYR 0.012 0.001 TYR C 223 PHE 0.019 0.001 PHE D 327 TRP 0.009 0.001 TRP B 86 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00352 (10406) covalent geometry : angle 0.51534 (14130) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.54138 ( 8) hydrogen bonds : bond 0.03311 ( 479) hydrogen bonds : angle 4.07508 ( 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 147 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.394 Fit side-chains REVERT: A 139 VAL cc_start: 0.6622 (OUTLIER) cc_final: 0.6290 (m) REVERT: A 172 MET cc_start: 0.5812 (tpp) cc_final: 0.5174 (tpp) REVERT: A 196 LYS cc_start: 0.5425 (OUTLIER) cc_final: 0.5128 (ptpt) REVERT: A 228 GLU cc_start: 0.7111 (mp0) cc_final: 0.6665 (mt-10) REVERT: B 34 ASP cc_start: 0.7347 (t70) cc_final: 0.6989 (t70) REVERT: B 62 MET cc_start: 0.4177 (mmm) cc_final: 0.3903 (mmm) REVERT: B 212 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6636 (tt0) REVERT: B 278 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: B 303 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: C 196 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5298 (ptpt) REVERT: C 274 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7291 (t0) REVERT: C 279 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8090 (mt) REVERT: D 27 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.4380 (ttp80) REVERT: D 148 ILE cc_start: 0.7371 (mt) cc_final: 0.7095 (tt) REVERT: D 204 ARG cc_start: 0.6969 (mmp80) cc_final: 0.6285 (mmt90) REVERT: D 303 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6796 (pm20) outliers start: 37 outliers final: 21 residues processed: 145 average time/residue: 0.1376 time to fit residues: 26.4122 Evaluate side-chains 139 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL 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 281 LEU 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 C residue 279 LEU Chi-restraints excluded: chain D residue 27 ARG 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 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: 0.2980 chunk 60 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.213726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.138986 restraints weight = 9095.195| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.50 r_work: 0.3282 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1747 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 : 0.483 10.963 14138 Z= 0.248 Chirality : 0.041 0.171 1628 Planarity : 0.004 0.048 1758 Dihedral : 3.799 17.709 1376 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.22 % Allowed : 20.57 % Favored : 76.21 % 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: 1.18 (0.23), residues: 1258 helix: 2.80 (0.23), residues: 426 sheet: 0.17 (0.30), residues: 284 loop : -0.49 (0.26), residues: 548 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 0.020 0.001 PHE B 327 TRP 0.009 0.001 TRP A 201 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00267 (10406) covalent geometry : angle 0.48251 (14130) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.47659 ( 8) hydrogen bonds : bond 0.03153 ( 479) hydrogen bonds : angle 3.94877 ( 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 151 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.395 Fit side-chains REVERT: A 172 MET cc_start: 0.5729 (tpp) cc_final: 0.5094 (tpp) REVERT: A 196 LYS cc_start: 0.5099 (OUTLIER) cc_final: 0.4805 (ptpt) REVERT: A 228 GLU cc_start: 0.6944 (mp0) cc_final: 0.6530 (mt-10) REVERT: B 34 ASP cc_start: 0.7300 (t70) cc_final: 0.6906 (t70) REVERT: B 62 MET cc_start: 0.4136 (mmm) cc_final: 0.3877 (mmm) REVERT: B 205 LYS cc_start: 0.7746 (tttp) cc_final: 0.6739 (mmtt) REVERT: B 212 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: B 278 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: B 303 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: C 196 LYS cc_start: 0.5233 (OUTLIER) cc_final: 0.4970 (ptpt) REVERT: C 274 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7081 (t0) REVERT: C 279 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8022 (mt) REVERT: D 148 ILE cc_start: 0.7272 (mt) cc_final: 0.6990 (tt) REVERT: D 180 ARG cc_start: 0.7755 (ptm160) cc_final: 0.6859 (ptt180) REVERT: D 204 ARG cc_start: 0.6706 (mmp80) cc_final: 0.5965 (mmm-85) REVERT: D 303 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6720 (pm20) outliers start: 36 outliers final: 22 residues processed: 148 average time/residue: 0.1296 time to fit residues: 25.4368 Evaluate side-chains 142 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL 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 C residue 279 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.2980 chunk 113 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 chunk 123 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.214817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.149190 restraints weight = 9086.144| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.15 r_work: 0.3366 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1840 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= 0.103 Angle : 0.475 10.973 14138 Z= 0.244 Chirality : 0.041 0.174 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.725 17.584 1376 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.95 % Allowed : 21.11 % Favored : 75.94 % 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: 2.84 (0.23), residues: 424 sheet: 0.25 (0.30), residues: 284 loop : -0.42 (0.26), residues: 550 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 0.021 0.001 PHE B 327 TRP 0.009 0.001 TRP A 201 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00235 (10406) covalent geometry : angle 0.47506 (14130) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.43048 ( 8) hydrogen bonds : bond 0.03077 ( 479) hydrogen bonds : angle 3.88320 ( 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 148 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.5749 (tpp) cc_final: 0.5085 (tpp) REVERT: A 196 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.4738 (ptpt) REVERT: B 34 ASP cc_start: 0.7373 (t70) cc_final: 0.7019 (t70) REVERT: B 62 MET cc_start: 0.4259 (mmm) cc_final: 0.3915 (mmm) REVERT: B 205 LYS cc_start: 0.7884 (tttp) cc_final: 0.6944 (mmtt) REVERT: B 212 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: B 278 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: B 303 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6777 (pm20) REVERT: C 196 LYS cc_start: 0.5646 (OUTLIER) cc_final: 0.5399 (ptpt) REVERT: C 274 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7204 (t0) REVERT: D 148 ILE cc_start: 0.7418 (mt) cc_final: 0.7117 (tt) REVERT: D 204 ARG cc_start: 0.6894 (mmp80) cc_final: 0.6182 (mmm-85) REVERT: D 303 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6869 (pm20) outliers start: 33 outliers final: 25 residues processed: 144 average time/residue: 0.1247 time to fit residues: 24.0082 Evaluate side-chains 140 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 114 THR 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 C residue 279 LEU 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 205 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.211880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136764 restraints weight = 8969.292| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.36 r_work: 0.3268 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10410 Z= 0.159 Angle : 0.535 10.787 14138 Z= 0.272 Chirality : 0.043 0.186 1628 Planarity : 0.004 0.048 1758 Dihedral : 3.965 17.981 1376 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.40 % Allowed : 20.84 % Favored : 75.76 % 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: 1.18 (0.24), residues: 1258 helix: 2.81 (0.23), residues: 426 sheet: 0.17 (0.30), residues: 284 loop : -0.50 (0.26), 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 0.027 0.001 PHE D 327 TRP 0.008 0.001 TRP B 86 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00387 (10406) covalent geometry : angle 0.53518 (14130) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.53493 ( 8) hydrogen bonds : bond 0.03292 ( 479) hydrogen bonds : angle 4.04894 ( 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 143 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.5859 (tpp) cc_final: 0.5190 (tpp) REVERT: A 196 LYS cc_start: 0.4950 (OUTLIER) cc_final: 0.4658 (ptpt) REVERT: A 228 GLU cc_start: 0.7042 (mp0) cc_final: 0.6633 (mt-10) REVERT: B 32 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 34 ASP cc_start: 0.7327 (t70) cc_final: 0.6982 (t70) REVERT: B 62 MET cc_start: 0.4169 (mmm) cc_final: 0.3761 (mmm) REVERT: B 205 LYS cc_start: 0.7890 (tttp) cc_final: 0.6986 (mmtt) REVERT: B 212 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6549 (tt0) REVERT: B 278 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: B 303 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: C 196 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.5146 (ptpt) REVERT: C 274 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7302 (t0) REVERT: C 279 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8078 (mt) REVERT: D 204 ARG cc_start: 0.6756 (mmp80) cc_final: 0.6030 (mmm-85) REVERT: D 303 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6716 (pm20) outliers start: 38 outliers final: 26 residues processed: 138 average time/residue: 0.1318 time to fit residues: 24.3374 Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 211 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 89 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 C residue 279 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 VAL 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 205 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 125 optimal weight: 0.4980 chunk 65 optimal weight: 0.0970 chunk 8 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 110 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.214118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146607 restraints weight = 9040.243| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.15 r_work: 0.3341 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10410 Z= 0.109 Angle : 0.484 10.792 14138 Z= 0.249 Chirality : 0.041 0.179 1628 Planarity : 0.003 0.048 1758 Dihedral : 3.821 17.812 1376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.49 % Allowed : 20.75 % Favored : 75.76 % 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: 1.28 (0.24), residues: 1258 helix: 2.85 (0.23), residues: 424 sheet: 0.24 (0.30), residues: 284 loop : -0.41 (0.26), residues: 550 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 0.022 0.001 PHE D 327 TRP 0.013 0.001 TRP C 85 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00252 (10406) covalent geometry : angle 0.48417 (14130) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.45268 ( 8) hydrogen bonds : bond 0.03128 ( 479) hydrogen bonds : angle 3.91981 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3328.20 seconds wall clock time: 57 minutes 29.32 seconds (3449.32 seconds total)