Starting phenix.real_space_refine on Fri Aug 22 20:39:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjx_18453/08_2025/8qjx_18453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjx_18453/08_2025/8qjx_18453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qjx_18453/08_2025/8qjx_18453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjx_18453/08_2025/8qjx_18453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qjx_18453/08_2025/8qjx_18453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjx_18453/08_2025/8qjx_18453.map" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4963 2.51 5 N 1301 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7868 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1619 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 196} Chain breaks: 2 Chain: "E" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1605 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 2 Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Time building chain proxies: 1.72, per 1000 atoms: 0.22 Number of scatterers: 7868 At special positions: 0 Unit cell: (97.5, 101.4, 98.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1571 8.00 N 1301 7.00 C 4963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 303.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 18 sheets defined 7.7% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.904A pdb=" N GLU C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.303A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.893A pdb=" N LEU B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 246 through 252 removed outlier: 5.464A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AA2, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.852A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.645A pdb=" N LEU D 128 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR D 173 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.676A pdb=" N VAL D 285 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG D 243 " --> pdb=" O GLY D 283 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY D 283 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.660A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.688A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.987A pdb=" N LEU E 128 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 173 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 222 through 223 removed outlier: 5.694A pdb=" N GLU E 240 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 287 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 229 through 232 removed outlier: 6.640A pdb=" N SER E 302 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AB2, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.578A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 218 through 220 removed outlier: 4.456A pdb=" N HIS C 218 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AB5, first strand: chain 'A' and resid 190 through 199 removed outlier: 6.148A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.565A pdb=" N HIS A 218 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AB8, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.568A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 219 through 220 246 hydrogen bonds defined for protein. 603 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: 0.74 Time building geometry restraints manager: 0.60 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: 2570 1.34 - 1.46: 1431 1.46 - 1.57: 3967 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8022 Sorted by residual: bond pdb=" C LEU D 154 " pdb=" N GLU D 155 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.44e-02 4.82e+03 3.24e+00 bond pdb=" C PRO D 325 " pdb=" O PRO D 325 " ideal model delta sigma weight residual 1.235 1.219 0.017 1.30e-02 5.92e+03 1.63e+00 bond pdb=" N PRO D 325 " pdb=" CA PRO D 325 " ideal model delta sigma weight residual 1.469 1.454 0.015 1.28e-02 6.10e+03 1.41e+00 bond pdb=" CA GLN A 146 " pdb=" CB GLN A 146 " ideal model delta sigma weight residual 1.527 1.507 0.020 1.75e-02 3.27e+03 1.28e+00 bond pdb=" N VAL E 227 " pdb=" CA VAL E 227 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.19e+00 ... (remaining 8017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 10267 1.10 - 2.21: 537 2.21 - 3.31: 85 3.31 - 4.42: 31 4.42 - 5.52: 3 Bond angle restraints: 10923 Sorted by residual: angle pdb=" CA TRP B 296 " pdb=" CB TRP B 296 " pdb=" CG TRP B 296 " ideal model delta sigma weight residual 113.60 119.12 -5.52 1.90e+00 2.77e-01 8.44e+00 angle pdb=" N THR C 309 " pdb=" CA THR C 309 " pdb=" C THR C 309 " ideal model delta sigma weight residual 113.43 110.35 3.08 1.26e+00 6.30e-01 5.97e+00 angle pdb=" C LEU C 134 " pdb=" N TRP C 135 " pdb=" CA TRP C 135 " ideal model delta sigma weight residual 122.36 118.55 3.81 1.60e+00 3.91e-01 5.66e+00 angle pdb=" CA PRO E 160 " pdb=" C PRO E 160 " pdb=" O PRO E 160 " ideal model delta sigma weight residual 123.16 120.00 3.16 1.49e+00 4.50e-01 4.49e+00 angle pdb=" C TYR E 158 " pdb=" N PRO E 159 " pdb=" CD PRO E 159 " ideal model delta sigma weight residual 120.60 115.94 4.66 2.20e+00 2.07e-01 4.48e+00 ... (remaining 10918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4432 17.97 - 35.94: 270 35.94 - 53.91: 64 53.91 - 71.87: 13 71.87 - 89.84: 10 Dihedral angle restraints: 4789 sinusoidal: 1850 harmonic: 2939 Sorted by residual: dihedral pdb=" CA ILE D 315 " pdb=" C ILE D 315 " pdb=" N ARG D 316 " pdb=" CA ARG D 316 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER E 317 " pdb=" C SER E 317 " pdb=" N LYS E 318 " pdb=" CA LYS E 318 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA VAL C 173 " pdb=" C VAL C 173 " pdb=" N TYR C 174 " pdb=" CA TYR C 174 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 4786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 707 0.031 - 0.063: 385 0.063 - 0.094: 97 0.094 - 0.125: 62 0.125 - 0.157: 25 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CA VAL E 285 " pdb=" N VAL E 285 " pdb=" C VAL E 285 " pdb=" CB VAL E 285 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ILE C 255 " pdb=" N ILE C 255 " pdb=" C ILE C 255 " pdb=" CB ILE C 255 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1273 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 324 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO E 325 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 325 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO E 325 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 158 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO E 159 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 159 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 159 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 208 " -0.149 9.50e-02 1.11e+02 6.71e-02 3.08e+00 pdb=" NE ARG C 208 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 208 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 208 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 208 " -0.002 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 32 2.48 - 3.08: 5619 3.08 - 3.69: 11318 3.69 - 4.29: 17956 4.29 - 4.90: 29962 Nonbonded interactions: 64887 Sorted by model distance: nonbonded pdb=" OH TYR C 319 " pdb=" OH TYR B 319 " model vdw 1.871 3.040 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 1.961 3.040 nonbonded pdb=" OD1 ASP A 265 " pdb=" OG1 THR A 267 " model vdw 2.153 3.040 nonbonded pdb=" OH TYR C 319 " pdb=" OH TYR A 319 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 2.188 3.040 ... (remaining 64882 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 110 through 135 or resid 147 through 331)) selection = (chain 'E' and resid 110 through 331) } 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 : 0.005 0.033 8022 Z= 0.234 Angle : 0.588 5.519 10923 Z= 0.339 Chirality : 0.047 0.157 1276 Planarity : 0.005 0.101 1406 Dihedral : 13.623 89.843 2881 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 12.49 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.27), residues: 979 helix: -2.88 (0.61), residues: 39 sheet: -0.59 (0.25), residues: 402 loop : -0.19 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 208 TYR 0.020 0.002 TYR E 172 PHE 0.018 0.002 PHE C 172 TRP 0.030 0.003 TRP C 296 HIS 0.005 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8022) covalent geometry : angle 0.58836 (10923) hydrogen bonds : bond 0.13502 ( 246) hydrogen bonds : angle 7.47743 ( 603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 231 MET cc_start: 0.7881 (ptm) cc_final: 0.7122 (ppp) REVERT: C 138 VAL cc_start: 0.9020 (t) cc_final: 0.8712 (m) REVERT: C 300 ASP cc_start: 0.8686 (t0) cc_final: 0.8468 (t0) REVERT: C 324 ASP cc_start: 0.8040 (m-30) cc_final: 0.7817 (m-30) REVERT: A 273 ILE cc_start: 0.9273 (mt) cc_final: 0.8442 (mt) REVERT: B 276 MET cc_start: 0.8632 (ttm) cc_final: 0.8240 (ttp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1288 time to fit residues: 26.4479 Evaluate side-chains 108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 ASN D 307 ASN E 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051043 restraints weight = 21809.168| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.27 r_work: 0.2687 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8022 Z= 0.124 Angle : 0.550 6.305 10923 Z= 0.295 Chirality : 0.046 0.144 1276 Planarity : 0.004 0.066 1406 Dihedral : 4.544 14.538 1070 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.57 % Allowed : 14.29 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.28), residues: 979 helix: -2.22 (0.73), residues: 36 sheet: -0.43 (0.25), residues: 382 loop : 0.23 (0.29), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.023 0.001 TYR E 293 PHE 0.017 0.002 PHE E 247 TRP 0.022 0.002 TRP B 296 HIS 0.004 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8022) covalent geometry : angle 0.55016 (10923) hydrogen bonds : bond 0.03487 ( 246) hydrogen bonds : angle 6.37229 ( 603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8873 (mt-10) REVERT: D 210 GLN cc_start: 0.9058 (mt0) cc_final: 0.8735 (mp10) REVERT: D 231 MET cc_start: 0.8587 (ttp) cc_final: 0.8328 (ttm) REVERT: D 255 ASP cc_start: 0.9216 (m-30) cc_final: 0.8339 (t0) REVERT: D 272 PHE cc_start: 0.8415 (m-80) cc_final: 0.8182 (m-80) REVERT: E 170 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8713 (mt-10) REVERT: C 184 MET cc_start: 0.8465 (ttt) cc_final: 0.8184 (tmm) REVERT: C 191 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (mm) REVERT: C 246 ASP cc_start: 0.8882 (t0) cc_final: 0.8639 (t0) REVERT: C 276 MET cc_start: 0.8371 (ttm) cc_final: 0.8084 (ttp) REVERT: C 300 ASP cc_start: 0.8591 (t0) cc_final: 0.8101 (t0) REVERT: C 323 GLU cc_start: 0.8839 (tp30) cc_final: 0.8637 (tp30) REVERT: A 184 MET cc_start: 0.8804 (ppp) cc_final: 0.8565 (ppp) REVERT: A 250 GLU cc_start: 0.9021 (pt0) cc_final: 0.8431 (pm20) REVERT: A 260 TYR cc_start: 0.9105 (m-80) cc_final: 0.8769 (m-80) REVERT: B 226 THR cc_start: 0.9443 (m) cc_final: 0.9240 (p) REVERT: B 276 MET cc_start: 0.8638 (ttm) cc_final: 0.8187 (ttp) REVERT: B 323 GLU cc_start: 0.8944 (tp30) cc_final: 0.8713 (mm-30) outliers start: 14 outliers final: 6 residues processed: 137 average time/residue: 0.1131 time to fit residues: 19.6780 Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 217 ASN E 307 ASN C 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049754 restraints weight = 22426.317| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.21 r_work: 0.2659 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8022 Z= 0.167 Angle : 0.533 6.767 10923 Z= 0.285 Chirality : 0.045 0.142 1276 Planarity : 0.004 0.060 1406 Dihedral : 4.487 16.078 1070 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.25 % Allowed : 13.84 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.28), residues: 979 helix: -1.84 (0.78), residues: 36 sheet: -0.35 (0.25), residues: 383 loop : 0.28 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 280 TYR 0.024 0.002 TYR E 293 PHE 0.016 0.002 PHE C 172 TRP 0.020 0.002 TRP C 296 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8022) covalent geometry : angle 0.53289 (10923) hydrogen bonds : bond 0.03278 ( 246) hydrogen bonds : angle 6.11140 ( 603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8822 (mt-10) REVERT: D 210 GLN cc_start: 0.9287 (mt0) cc_final: 0.9014 (mp10) REVERT: D 231 MET cc_start: 0.8486 (ttp) cc_final: 0.8183 (ttm) REVERT: D 255 ASP cc_start: 0.9181 (m-30) cc_final: 0.8542 (t70) REVERT: C 184 MET cc_start: 0.8356 (ttt) cc_final: 0.8007 (tmm) REVERT: C 191 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8540 (mm) REVERT: C 246 ASP cc_start: 0.8837 (t0) cc_final: 0.8514 (t0) REVERT: C 250 GLU cc_start: 0.8776 (pt0) cc_final: 0.8252 (pm20) REVERT: C 276 MET cc_start: 0.8419 (ttm) cc_final: 0.8144 (ttp) REVERT: C 284 ASP cc_start: 0.8659 (p0) cc_final: 0.6565 (p0) REVERT: C 300 ASP cc_start: 0.8694 (t0) cc_final: 0.8258 (t0) REVERT: C 323 GLU cc_start: 0.8866 (tp30) cc_final: 0.8604 (tp30) REVERT: A 184 MET cc_start: 0.8849 (ppp) cc_final: 0.8623 (ppp) REVERT: A 250 GLU cc_start: 0.9052 (pt0) cc_final: 0.8568 (pm20) REVERT: A 260 TYR cc_start: 0.9090 (m-80) cc_final: 0.8866 (m-80) REVERT: B 184 MET cc_start: 0.9209 (ttp) cc_final: 0.8989 (tmm) REVERT: B 276 MET cc_start: 0.8640 (ttm) cc_final: 0.8209 (ttp) REVERT: B 323 GLU cc_start: 0.8938 (tp30) cc_final: 0.8728 (mm-30) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.1080 time to fit residues: 18.4138 Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 172 TYR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 296 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.046874 restraints weight = 22700.660| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.25 r_work: 0.2572 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8022 Z= 0.277 Angle : 0.589 7.706 10923 Z= 0.311 Chirality : 0.047 0.142 1276 Planarity : 0.004 0.056 1406 Dihedral : 4.763 14.934 1070 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.92 % Allowed : 14.62 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.28), residues: 979 helix: -1.63 (0.79), residues: 36 sheet: -0.35 (0.25), residues: 381 loop : 0.16 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.018 0.002 TYR D 172 PHE 0.023 0.002 PHE B 199 TRP 0.030 0.003 TRP C 296 HIS 0.002 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 8022) covalent geometry : angle 0.58934 (10923) hydrogen bonds : bond 0.03386 ( 246) hydrogen bonds : angle 6.14091 ( 603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8511 (mtm) cc_final: 0.8292 (mtt) REVERT: D 170 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8735 (mt-10) REVERT: D 210 GLN cc_start: 0.9223 (mt0) cc_final: 0.8921 (mp10) REVERT: D 243 ARG cc_start: 0.9144 (ttm170) cc_final: 0.8930 (ttm170) REVERT: D 255 ASP cc_start: 0.9150 (m-30) cc_final: 0.8467 (t70) REVERT: E 231 MET cc_start: 0.8268 (ptm) cc_final: 0.7873 (ttp) REVERT: C 184 MET cc_start: 0.8494 (ttt) cc_final: 0.8156 (tmm) REVERT: C 224 MET cc_start: 0.8783 (mtt) cc_final: 0.8485 (mmm) REVERT: C 246 ASP cc_start: 0.8971 (t0) cc_final: 0.8558 (t0) REVERT: C 250 GLU cc_start: 0.8810 (pt0) cc_final: 0.8281 (pm20) REVERT: C 276 MET cc_start: 0.8559 (ttm) cc_final: 0.8233 (ttp) REVERT: C 284 ASP cc_start: 0.8280 (p0) cc_final: 0.7557 (p0) REVERT: C 285 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8167 (mm-30) REVERT: C 300 ASP cc_start: 0.8743 (t0) cc_final: 0.8261 (t0) REVERT: A 250 GLU cc_start: 0.9097 (pt0) cc_final: 0.8319 (pm20) REVERT: B 276 MET cc_start: 0.8664 (ttm) cc_final: 0.8242 (ttp) REVERT: B 300 ASP cc_start: 0.8998 (t0) cc_final: 0.8571 (t0) REVERT: B 323 GLU cc_start: 0.8975 (tp30) cc_final: 0.8734 (mm-30) outliers start: 26 outliers final: 16 residues processed: 129 average time/residue: 0.0959 time to fit residues: 15.9719 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 183 HIS E 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.049026 restraints weight = 22300.547| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.22 r_work: 0.2638 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8022 Z= 0.132 Angle : 0.536 7.814 10923 Z= 0.284 Chirality : 0.045 0.142 1276 Planarity : 0.003 0.050 1406 Dihedral : 4.483 14.375 1070 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 16.09 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.28), residues: 979 helix: -1.21 (0.88), residues: 36 sheet: -0.32 (0.25), residues: 390 loop : 0.13 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.013 0.001 TYR D 172 PHE 0.016 0.001 PHE C 172 TRP 0.018 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8022) covalent geometry : angle 0.53615 (10923) hydrogen bonds : bond 0.03031 ( 246) hydrogen bonds : angle 5.91789 ( 603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8447 (mtm) cc_final: 0.8219 (mtp) REVERT: D 170 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8654 (mt-10) REVERT: D 210 GLN cc_start: 0.9072 (mt0) cc_final: 0.8869 (mp10) REVERT: D 233 GLU cc_start: 0.8572 (mp0) cc_final: 0.8035 (tm-30) REVERT: D 243 ARG cc_start: 0.9085 (ttm170) cc_final: 0.8100 (ttm170) REVERT: D 255 ASP cc_start: 0.9159 (m-30) cc_final: 0.8486 (t70) REVERT: E 233 GLU cc_start: 0.8029 (tt0) cc_final: 0.7731 (tm-30) REVERT: C 184 MET cc_start: 0.8403 (ttt) cc_final: 0.8099 (tmm) REVERT: C 224 MET cc_start: 0.8633 (mtt) cc_final: 0.8392 (mmm) REVERT: C 246 ASP cc_start: 0.8881 (t0) cc_final: 0.8461 (t0) REVERT: C 250 GLU cc_start: 0.8766 (pt0) cc_final: 0.8255 (pm20) REVERT: C 300 ASP cc_start: 0.8742 (t0) cc_final: 0.8285 (t0) REVERT: A 184 MET cc_start: 0.8738 (ppp) cc_final: 0.8386 (ppp) REVERT: A 250 GLU cc_start: 0.9074 (pt0) cc_final: 0.8279 (pm20) REVERT: A 260 TYR cc_start: 0.9210 (m-80) cc_final: 0.8956 (m-80) REVERT: B 276 MET cc_start: 0.8577 (ttm) cc_final: 0.8126 (ttp) REVERT: B 300 ASP cc_start: 0.8917 (t0) cc_final: 0.8515 (t0) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.1019 time to fit residues: 15.9384 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 297 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.046836 restraints weight = 22419.254| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.22 r_work: 0.2570 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8022 Z= 0.249 Angle : 0.577 8.248 10923 Z= 0.305 Chirality : 0.046 0.137 1276 Planarity : 0.003 0.049 1406 Dihedral : 4.680 15.534 1070 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.25 % Allowed : 16.65 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.28), residues: 979 helix: -1.28 (0.88), residues: 36 sheet: -0.35 (0.25), residues: 388 loop : 0.07 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.016 0.002 TYR D 172 PHE 0.019 0.002 PHE B 199 TRP 0.027 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8022) covalent geometry : angle 0.57686 (10923) hydrogen bonds : bond 0.03275 ( 246) hydrogen bonds : angle 5.96157 ( 603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8596 (mtm) cc_final: 0.8383 (mtt) REVERT: D 170 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8673 (mt-10) REVERT: D 210 GLN cc_start: 0.9189 (mt0) cc_final: 0.8886 (mp10) REVERT: D 233 GLU cc_start: 0.8584 (mp0) cc_final: 0.7993 (tm-30) REVERT: D 243 ARG cc_start: 0.9098 (ttm170) cc_final: 0.8830 (ttm170) REVERT: D 255 ASP cc_start: 0.9146 (m-30) cc_final: 0.8406 (t0) REVERT: D 296 MET cc_start: 0.7143 (mmm) cc_final: 0.6869 (mmm) REVERT: C 184 MET cc_start: 0.8495 (ttt) cc_final: 0.8185 (tmm) REVERT: C 246 ASP cc_start: 0.8961 (t0) cc_final: 0.8542 (t0) REVERT: C 250 GLU cc_start: 0.8793 (pt0) cc_final: 0.8288 (pm20) REVERT: A 250 GLU cc_start: 0.9105 (pt0) cc_final: 0.8314 (pm20) REVERT: B 142 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8922 (mm-30) REVERT: B 276 MET cc_start: 0.8655 (ttm) cc_final: 0.8195 (ttp) REVERT: B 300 ASP cc_start: 0.8948 (t0) cc_final: 0.8547 (t0) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1008 time to fit residues: 15.6123 Evaluate side-chains 113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.069127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.046878 restraints weight = 22519.160| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.21 r_work: 0.2573 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8022 Z= 0.228 Angle : 0.576 8.391 10923 Z= 0.305 Chirality : 0.045 0.144 1276 Planarity : 0.003 0.047 1406 Dihedral : 4.698 16.155 1070 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.59 % Allowed : 16.31 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.27), residues: 979 helix: -1.24 (0.88), residues: 36 sheet: -0.45 (0.25), residues: 382 loop : -0.01 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.015 0.002 TYR D 293 PHE 0.016 0.002 PHE B 199 TRP 0.024 0.002 TRP C 296 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8022) covalent geometry : angle 0.57620 (10923) hydrogen bonds : bond 0.03226 ( 246) hydrogen bonds : angle 5.93706 ( 603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8640 (mt-10) REVERT: D 210 GLN cc_start: 0.9176 (mt0) cc_final: 0.8958 (mp10) REVERT: D 233 GLU cc_start: 0.8653 (mp0) cc_final: 0.8040 (tm-30) REVERT: D 243 ARG cc_start: 0.9043 (ttm170) cc_final: 0.8791 (ttm170) REVERT: D 255 ASP cc_start: 0.9142 (m-30) cc_final: 0.8398 (t0) REVERT: D 296 MET cc_start: 0.7381 (mmm) cc_final: 0.7116 (mmm) REVERT: E 193 ARG cc_start: 0.7822 (tpt90) cc_final: 0.7585 (tpt90) REVERT: E 238 ASN cc_start: 0.9253 (t0) cc_final: 0.8902 (t0) REVERT: C 184 MET cc_start: 0.8487 (ttt) cc_final: 0.8166 (tmm) REVERT: C 246 ASP cc_start: 0.8994 (t0) cc_final: 0.8557 (t0) REVERT: C 250 GLU cc_start: 0.8782 (pt0) cc_final: 0.8269 (pm20) REVERT: A 250 GLU cc_start: 0.9112 (pt0) cc_final: 0.8307 (pm20) REVERT: B 142 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8931 (mm-30) REVERT: B 276 MET cc_start: 0.8644 (ttm) cc_final: 0.8208 (ttp) REVERT: B 300 ASP cc_start: 0.8943 (t0) cc_final: 0.8539 (t0) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.1151 time to fit residues: 17.8571 Evaluate side-chains 116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.045968 restraints weight = 22844.537| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.20 r_work: 0.2549 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8022 Z= 0.304 Angle : 0.619 8.721 10923 Z= 0.327 Chirality : 0.046 0.140 1276 Planarity : 0.004 0.046 1406 Dihedral : 4.981 20.785 1070 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.36 % Allowed : 16.42 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.27), residues: 979 helix: -1.27 (0.87), residues: 36 sheet: -0.64 (0.25), residues: 396 loop : -0.10 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.022 0.002 TYR D 293 PHE 0.026 0.002 PHE B 199 TRP 0.025 0.002 TRP C 296 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 8022) covalent geometry : angle 0.61872 (10923) hydrogen bonds : bond 0.03460 ( 246) hydrogen bonds : angle 6.05475 ( 603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.9170 (mt0) cc_final: 0.8889 (mp10) REVERT: D 243 ARG cc_start: 0.9111 (ttm170) cc_final: 0.8808 (ttm170) REVERT: D 255 ASP cc_start: 0.9126 (m-30) cc_final: 0.8376 (t0) REVERT: D 296 MET cc_start: 0.7333 (mmm) cc_final: 0.7110 (mmm) REVERT: E 238 ASN cc_start: 0.9289 (t0) cc_final: 0.8984 (t0) REVERT: E 243 ARG cc_start: 0.8955 (mtt-85) cc_final: 0.8603 (mtt-85) REVERT: C 184 MET cc_start: 0.8484 (ttt) cc_final: 0.8189 (tmm) REVERT: C 246 ASP cc_start: 0.9044 (t0) cc_final: 0.8579 (t0) REVERT: C 250 GLU cc_start: 0.8820 (pt0) cc_final: 0.8293 (pm20) REVERT: A 250 GLU cc_start: 0.9123 (pt0) cc_final: 0.8305 (pm20) REVERT: B 142 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8938 (mm-30) REVERT: B 276 MET cc_start: 0.8697 (ttm) cc_final: 0.8267 (ttp) REVERT: B 300 ASP cc_start: 0.8969 (t0) cc_final: 0.8558 (t0) outliers start: 21 outliers final: 17 residues processed: 117 average time/residue: 0.1164 time to fit residues: 17.6687 Evaluate side-chains 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.048143 restraints weight = 22193.616| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.20 r_work: 0.2604 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8022 Z= 0.149 Angle : 0.569 8.152 10923 Z= 0.301 Chirality : 0.045 0.146 1276 Planarity : 0.003 0.043 1406 Dihedral : 4.595 17.376 1070 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 16.76 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.28), residues: 979 helix: -1.03 (0.91), residues: 36 sheet: -0.57 (0.25), residues: 403 loop : -0.05 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.018 0.001 TYR D 293 PHE 0.018 0.002 PHE D 301 TRP 0.017 0.002 TRP C 296 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8022) covalent geometry : angle 0.56869 (10923) hydrogen bonds : bond 0.03031 ( 246) hydrogen bonds : angle 5.88722 ( 603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.9181 (mt0) cc_final: 0.8980 (mp10) REVERT: D 233 GLU cc_start: 0.8673 (mp0) cc_final: 0.8118 (tm-30) REVERT: D 243 ARG cc_start: 0.9005 (ttm170) cc_final: 0.8756 (ttm170) REVERT: D 255 ASP cc_start: 0.9151 (m-30) cc_final: 0.8417 (t0) REVERT: D 293 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: E 238 ASN cc_start: 0.9285 (t0) cc_final: 0.8979 (t0) REVERT: E 243 ARG cc_start: 0.8978 (mtt-85) cc_final: 0.8529 (mtt-85) REVERT: C 184 MET cc_start: 0.8507 (ttt) cc_final: 0.8182 (tmm) REVERT: C 246 ASP cc_start: 0.8973 (t0) cc_final: 0.8509 (t0) REVERT: C 250 GLU cc_start: 0.8782 (pt0) cc_final: 0.8386 (pm20) REVERT: C 284 ASP cc_start: 0.8377 (p0) cc_final: 0.7384 (p0) REVERT: C 285 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 152 GLU cc_start: 0.9171 (pm20) cc_final: 0.8832 (pm20) REVERT: A 184 MET cc_start: 0.8759 (ppp) cc_final: 0.8486 (ppp) REVERT: A 250 GLU cc_start: 0.9106 (pt0) cc_final: 0.8289 (pm20) REVERT: A 260 TYR cc_start: 0.9234 (m-80) cc_final: 0.8932 (m-80) REVERT: B 142 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8934 (mm-30) REVERT: B 184 MET cc_start: 0.9304 (tmm) cc_final: 0.9038 (tmm) REVERT: B 276 MET cc_start: 0.8592 (ttm) cc_final: 0.8207 (ttp) REVERT: B 300 ASP cc_start: 0.8923 (t0) cc_final: 0.8528 (t0) outliers start: 21 outliers final: 17 residues processed: 118 average time/residue: 0.1039 time to fit residues: 15.9264 Evaluate side-chains 118 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN E 208 GLN A 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.069496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.047202 restraints weight = 22353.966| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.20 r_work: 0.2583 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8022 Z= 0.208 Angle : 0.591 9.836 10923 Z= 0.312 Chirality : 0.045 0.144 1276 Planarity : 0.003 0.044 1406 Dihedral : 4.681 18.599 1070 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.36 % Allowed : 17.21 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.28), residues: 979 helix: -1.09 (0.90), residues: 36 sheet: -0.55 (0.25), residues: 405 loop : -0.04 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.021 0.002 TYR D 293 PHE 0.018 0.002 PHE B 199 TRP 0.021 0.002 TRP C 296 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8022) covalent geometry : angle 0.59106 (10923) hydrogen bonds : bond 0.03208 ( 246) hydrogen bonds : angle 5.91914 ( 603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.9196 (mt0) cc_final: 0.8917 (mp10) REVERT: D 233 GLU cc_start: 0.8717 (mp0) cc_final: 0.8053 (tm-30) REVERT: D 243 ARG cc_start: 0.8958 (ttm170) cc_final: 0.8687 (ttm170) REVERT: D 255 ASP cc_start: 0.9137 (m-30) cc_final: 0.8398 (t0) REVERT: E 238 ASN cc_start: 0.9300 (t0) cc_final: 0.9051 (t0) REVERT: E 243 ARG cc_start: 0.8981 (mtt-85) cc_final: 0.8529 (mtt-85) REVERT: C 184 MET cc_start: 0.8472 (ttt) cc_final: 0.8181 (tmm) REVERT: C 246 ASP cc_start: 0.8996 (t0) cc_final: 0.8522 (t0) REVERT: C 250 GLU cc_start: 0.8840 (pt0) cc_final: 0.8396 (pm20) REVERT: C 284 ASP cc_start: 0.8426 (p0) cc_final: 0.7412 (p0) REVERT: C 285 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 184 MET cc_start: 0.8808 (ppp) cc_final: 0.8514 (ppp) REVERT: A 250 GLU cc_start: 0.9107 (pt0) cc_final: 0.8291 (pm20) REVERT: B 142 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8957 (mm-30) REVERT: B 276 MET cc_start: 0.8620 (ttm) cc_final: 0.8209 (ttp) REVERT: B 300 ASP cc_start: 0.8943 (t0) cc_final: 0.8552 (t0) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.1073 time to fit residues: 16.2464 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 0.0370 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.048521 restraints weight = 22165.937| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.20 r_work: 0.2620 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8022 Z= 0.140 Angle : 0.577 9.713 10923 Z= 0.304 Chirality : 0.045 0.141 1276 Planarity : 0.003 0.042 1406 Dihedral : 4.516 17.470 1070 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.02 % Allowed : 17.66 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.28), residues: 979 helix: -0.99 (0.91), residues: 36 sheet: -0.49 (0.25), residues: 405 loop : -0.02 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.019 0.001 TYR D 293 PHE 0.018 0.001 PHE D 301 TRP 0.016 0.002 TRP C 296 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8022) covalent geometry : angle 0.57743 (10923) hydrogen bonds : bond 0.03061 ( 246) hydrogen bonds : angle 5.84916 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.95 seconds wall clock time: 30 minutes 55.53 seconds (1855.53 seconds total)