Starting phenix.real_space_refine on Sun May 11 08:28:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qjx_18453/05_2025/8qjx_18453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qjx_18453/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qjx_18453/05_2025/8qjx_18453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qjx_18453/05_2025/8qjx_18453.map" model { file = "/net/cci-nas-00/data/ceres_data/8qjx_18453/05_2025/8qjx_18453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qjx_18453/05_2025/8qjx_18453.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.11, per 1000 atoms: 0.65 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.92 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: 2.11 Time building geometry restraints manager: 2.37 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: 0.260 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.900 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (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 TRP 0.030 0.003 TRP C 296 HIS 0.005 0.001 HIS C 218 PHE 0.018 0.002 PHE C 172 TYR 0.020 0.002 TYR E 172 ARG 0.010 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.13502 ( 246) hydrogen bonds : angle 7.47743 ( 603) covalent geometry : bond 0.00495 ( 8022) covalent geometry : angle 0.58836 (10923) *********************** 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 : 1.044 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: 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: 0.3387 time to fit residues: 71.0181 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 : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 C 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.049884 restraints weight = 21799.451| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.27 r_work: 0.2660 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8022 Z= 0.161 Angle : 0.561 6.178 10923 Z= 0.301 Chirality : 0.046 0.146 1276 Planarity : 0.004 0.066 1406 Dihedral : 4.614 14.829 1070 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.69 % Allowed : 14.62 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.28), residues: 979 helix: -2.15 (0.72), residues: 36 sheet: -0.43 (0.26), residues: 382 loop : 0.23 (0.29), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 296 HIS 0.004 0.001 HIS C 218 PHE 0.016 0.002 PHE E 247 TYR 0.023 0.002 TYR E 293 ARG 0.005 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 246) hydrogen bonds : angle 6.34452 ( 603) covalent geometry : bond 0.00363 ( 8022) covalent geometry : angle 0.56126 (10923) *********************** 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 134 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.908 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: 0.9110 (mt-10) cc_final: 0.8868 (mt-10) REVERT: D 210 GLN cc_start: 0.9101 (mt0) cc_final: 0.8764 (mp10) REVERT: D 231 MET cc_start: 0.8648 (ttp) cc_final: 0.8402 (ttm) REVERT: D 255 ASP cc_start: 0.9210 (m-30) cc_final: 0.8552 (t70) REVERT: D 272 PHE cc_start: 0.8438 (m-80) cc_final: 0.8164 (m-80) REVERT: E 170 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8723 (mt-10) REVERT: C 138 VAL cc_start: 0.8935 (t) cc_final: 0.8570 (m) REVERT: C 184 MET cc_start: 0.8488 (ttt) cc_final: 0.8027 (tmm) REVERT: C 191 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8509 (mm) REVERT: C 246 ASP cc_start: 0.8951 (t0) cc_final: 0.8707 (t0) REVERT: C 276 MET cc_start: 0.8386 (ttm) cc_final: 0.8140 (ttp) REVERT: C 285 GLU cc_start: 0.8902 (tp30) cc_final: 0.8664 (tp30) REVERT: C 300 ASP cc_start: 0.8662 (t0) cc_final: 0.8217 (t0) REVERT: C 323 GLU cc_start: 0.8835 (tp30) cc_final: 0.8605 (tp30) REVERT: A 184 MET cc_start: 0.8818 (ppp) cc_final: 0.8574 (ppp) REVERT: A 250 GLU cc_start: 0.9043 (pt0) cc_final: 0.8452 (pm20) REVERT: B 276 MET cc_start: 0.8642 (ttm) cc_final: 0.8205 (ttp) REVERT: B 323 GLU cc_start: 0.8965 (tp30) cc_final: 0.8733 (mm-30) outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 0.2668 time to fit residues: 44.6474 Evaluate side-chains 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 C residue 272 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050674 restraints weight = 22533.854| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.24 r_work: 0.2681 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8022 Z= 0.123 Angle : 0.517 6.721 10923 Z= 0.277 Chirality : 0.045 0.139 1276 Planarity : 0.003 0.059 1406 Dihedral : 4.396 14.684 1070 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.25 % Allowed : 13.50 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.28), residues: 979 helix: -1.86 (0.78), residues: 36 sheet: -0.30 (0.25), residues: 390 loop : 0.29 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 296 HIS 0.003 0.001 HIS A 218 PHE 0.015 0.002 PHE C 172 TYR 0.025 0.002 TYR E 293 ARG 0.008 0.001 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 246) hydrogen bonds : angle 6.06732 ( 603) covalent geometry : bond 0.00277 ( 8022) covalent geometry : angle 0.51748 (10923) *********************** 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 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8809 (mt-10) REVERT: D 210 GLN cc_start: 0.9174 (mt0) cc_final: 0.8926 (mp10) REVERT: D 231 MET cc_start: 0.8492 (ttp) cc_final: 0.8175 (ttm) REVERT: D 255 ASP cc_start: 0.9188 (m-30) cc_final: 0.8555 (t70) REVERT: E 150 ARG cc_start: 0.8785 (mtm110) cc_final: 0.8581 (mtm110) REVERT: E 301 PHE cc_start: 0.8918 (p90) cc_final: 0.8620 (p90) REVERT: C 184 MET cc_start: 0.8369 (ttt) cc_final: 0.8064 (tmm) REVERT: C 191 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8532 (mm) REVERT: C 246 ASP cc_start: 0.8751 (t0) cc_final: 0.8475 (t0) REVERT: C 276 MET cc_start: 0.8494 (ttm) cc_final: 0.8175 (ttp) REVERT: C 285 GLU cc_start: 0.8927 (tp30) cc_final: 0.8630 (tp30) REVERT: C 300 ASP cc_start: 0.8650 (t0) cc_final: 0.8209 (t0) REVERT: B 276 MET cc_start: 0.8616 (ttm) cc_final: 0.8192 (ttp) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.2590 time to fit residues: 44.7464 Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain C residue 191 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 3 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.071512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.050133 restraints weight = 22743.024| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.22 r_work: 0.2648 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8022 Z= 0.163 Angle : 0.527 6.578 10923 Z= 0.280 Chirality : 0.045 0.147 1276 Planarity : 0.003 0.054 1406 Dihedral : 4.449 14.791 1070 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.36 % Allowed : 14.85 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.28), residues: 979 helix: -1.54 (0.83), residues: 36 sheet: -0.25 (0.25), residues: 390 loop : 0.19 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 296 HIS 0.003 0.001 HIS A 218 PHE 0.017 0.002 PHE B 199 TYR 0.019 0.002 TYR E 293 ARG 0.005 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 246) hydrogen bonds : angle 5.97912 ( 603) covalent geometry : bond 0.00371 ( 8022) covalent geometry : angle 0.52657 (10923) *********************** 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 131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.8444 (mtm) cc_final: 0.8240 (mtt) REVERT: D 170 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8783 (mt-10) REVERT: D 210 GLN cc_start: 0.9118 (mt0) cc_final: 0.8853 (mp10) REVERT: D 255 ASP cc_start: 0.9173 (m-30) cc_final: 0.8537 (t70) REVERT: E 150 ARG cc_start: 0.8735 (mtm110) cc_final: 0.8508 (mtm110) REVERT: E 231 MET cc_start: 0.8109 (ptm) cc_final: 0.7583 (ttp) REVERT: E 243 ARG cc_start: 0.9252 (mtp85) cc_final: 0.8623 (mtp85) REVERT: E 271 TYR cc_start: 0.8556 (m-10) cc_final: 0.8323 (m-10) REVERT: C 184 MET cc_start: 0.8382 (ttt) cc_final: 0.8077 (tmm) REVERT: C 191 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8517 (mm) REVERT: C 246 ASP cc_start: 0.8788 (t0) cc_final: 0.8493 (t0) REVERT: C 276 MET cc_start: 0.8420 (ttm) cc_final: 0.8147 (ttp) REVERT: C 285 GLU cc_start: 0.8932 (tp30) cc_final: 0.8557 (tp30) REVERT: C 300 ASP cc_start: 0.8669 (t0) cc_final: 0.8212 (t0) REVERT: A 250 GLU cc_start: 0.9000 (pt0) cc_final: 0.8392 (pm20) REVERT: B 142 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8952 (mm-30) REVERT: B 233 LYS cc_start: 0.9358 (ttmm) cc_final: 0.9144 (tttp) REVERT: B 276 MET cc_start: 0.8628 (ttm) cc_final: 0.8139 (ttp) REVERT: B 300 ASP cc_start: 0.8859 (t0) cc_final: 0.8471 (t0) outliers start: 21 outliers final: 15 residues processed: 129 average time/residue: 0.2567 time to fit residues: 42.5416 Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 188 LEU 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 C residue 191 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.047861 restraints weight = 22298.403| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.26 r_work: 0.2605 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8022 Z= 0.201 Angle : 0.552 7.430 10923 Z= 0.292 Chirality : 0.045 0.146 1276 Planarity : 0.003 0.051 1406 Dihedral : 4.553 15.512 1070 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.47 % Allowed : 15.86 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.28), residues: 979 helix: -1.25 (0.88), residues: 36 sheet: -0.36 (0.25), residues: 405 loop : 0.12 (0.30), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.021 0.002 PHE B 199 TYR 0.015 0.002 TYR D 172 ARG 0.006 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 246) hydrogen bonds : angle 5.94877 ( 603) covalent geometry : bond 0.00455 ( 8022) covalent geometry : angle 0.55195 (10923) *********************** 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 128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8660 (mt-10) REVERT: D 210 GLN cc_start: 0.9064 (mt0) cc_final: 0.8829 (mp10) REVERT: D 233 GLU cc_start: 0.8618 (mp0) cc_final: 0.8031 (tm-30) REVERT: D 255 ASP cc_start: 0.9161 (m-30) cc_final: 0.8495 (t70) REVERT: E 233 GLU cc_start: 0.8087 (tt0) cc_final: 0.7771 (tm-30) REVERT: E 243 ARG cc_start: 0.9314 (mtp85) cc_final: 0.8650 (mtt-85) REVERT: E 271 TYR cc_start: 0.8590 (m-10) cc_final: 0.8316 (m-10) REVERT: C 184 MET cc_start: 0.8446 (ttt) cc_final: 0.8151 (tmm) REVERT: C 246 ASP cc_start: 0.8835 (t0) cc_final: 0.8490 (t0) REVERT: C 276 MET cc_start: 0.8487 (ttm) cc_final: 0.8243 (ttp) REVERT: C 285 GLU cc_start: 0.8975 (tp30) cc_final: 0.8581 (tp30) REVERT: A 184 MET cc_start: 0.8786 (ppp) cc_final: 0.8387 (ppp) REVERT: A 250 GLU cc_start: 0.9014 (pt0) cc_final: 0.8271 (pm20) REVERT: B 142 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8953 (mm-30) REVERT: B 233 LYS cc_start: 0.9390 (ttmm) cc_final: 0.9148 (tttp) REVERT: B 276 MET cc_start: 0.8647 (ttm) cc_final: 0.8176 (ttp) REVERT: B 300 ASP cc_start: 0.8977 (t0) cc_final: 0.8574 (t0) outliers start: 22 outliers final: 18 residues processed: 125 average time/residue: 0.2493 time to fit residues: 40.2287 Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 118 SER 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 285 VAL 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 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 73 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 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 = 0.3260 r_free = 0.3260 target = 0.068038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.045662 restraints weight = 22464.151| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.21 r_work: 0.2538 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 8022 Z= 0.359 Angle : 0.640 8.557 10923 Z= 0.338 Chirality : 0.048 0.142 1276 Planarity : 0.004 0.050 1406 Dihedral : 5.010 19.676 1070 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.36 % Allowed : 15.41 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 979 helix: -1.46 (0.84), residues: 36 sheet: -0.42 (0.25), residues: 381 loop : -0.04 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 296 HIS 0.003 0.001 HIS A 218 PHE 0.029 0.002 PHE B 199 TYR 0.019 0.002 TYR D 172 ARG 0.007 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 246) hydrogen bonds : angle 6.16117 ( 603) covalent geometry : bond 0.00811 ( 8022) covalent geometry : angle 0.64039 (10923) *********************** 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 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8664 (mt-10) REVERT: D 210 GLN cc_start: 0.9173 (mt0) cc_final: 0.8890 (mp10) REVERT: D 255 ASP cc_start: 0.9119 (m-30) cc_final: 0.8346 (t0) REVERT: E 231 MET cc_start: 0.8300 (ttp) cc_final: 0.7971 (ttp) REVERT: E 243 ARG cc_start: 0.9323 (mtp85) cc_final: 0.8622 (mtt-85) REVERT: C 184 MET cc_start: 0.8506 (ttt) cc_final: 0.8155 (tmm) REVERT: C 246 ASP cc_start: 0.8967 (t0) cc_final: 0.8593 (t0) REVERT: C 276 MET cc_start: 0.8603 (ttm) cc_final: 0.8339 (ttp) REVERT: C 285 GLU cc_start: 0.9040 (tp30) cc_final: 0.8645 (tp30) REVERT: A 250 GLU cc_start: 0.9061 (pt0) cc_final: 0.8299 (pm20) REVERT: B 142 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8930 (mm-30) REVERT: B 276 MET cc_start: 0.8701 (ttm) cc_final: 0.8288 (ttp) REVERT: B 300 ASP cc_start: 0.9018 (t0) cc_final: 0.8621 (t0) outliers start: 21 outliers final: 19 residues processed: 119 average time/residue: 0.2469 time to fit residues: 37.7862 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain E residue 118 SER 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 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 208 ARG 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 87 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.069909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.047657 restraints weight = 22218.541| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.21 r_work: 0.2593 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8022 Z= 0.174 Angle : 0.549 8.456 10923 Z= 0.293 Chirality : 0.045 0.142 1276 Planarity : 0.003 0.047 1406 Dihedral : 4.652 16.179 1070 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.59 % Allowed : 15.64 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 979 helix: -1.28 (0.88), residues: 36 sheet: -0.39 (0.25), residues: 388 loop : -0.02 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 296 HIS 0.002 0.001 HIS A 218 PHE 0.015 0.002 PHE C 172 TYR 0.018 0.002 TYR D 293 ARG 0.008 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 246) hydrogen bonds : angle 5.94480 ( 603) covalent geometry : bond 0.00392 ( 8022) covalent geometry : angle 0.54937 (10923) *********************** 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 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8619 (mt-10) REVERT: D 210 GLN cc_start: 0.9181 (mt0) cc_final: 0.8959 (mp10) REVERT: D 243 ARG cc_start: 0.9052 (ttm170) cc_final: 0.7916 (ttm170) REVERT: D 255 ASP cc_start: 0.9164 (m-30) cc_final: 0.8421 (t0) REVERT: D 275 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8572 (mp0) REVERT: E 193 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7668 (tpt90) REVERT: E 238 ASN cc_start: 0.9271 (t0) cc_final: 0.8936 (t0) REVERT: E 243 ARG cc_start: 0.9300 (mtp85) cc_final: 0.9094 (ptp-110) REVERT: C 184 MET cc_start: 0.8487 (ttt) cc_final: 0.8185 (tmm) REVERT: C 246 ASP cc_start: 0.8986 (t0) cc_final: 0.8474 (t0) REVERT: C 250 GLU cc_start: 0.8934 (pm20) cc_final: 0.8294 (pm20) REVERT: C 276 MET cc_start: 0.8478 (ttm) cc_final: 0.8258 (ttp) REVERT: C 285 GLU cc_start: 0.9039 (tp30) cc_final: 0.8624 (tp30) REVERT: A 184 MET cc_start: 0.8703 (ppp) cc_final: 0.8362 (ppp) REVERT: A 250 GLU cc_start: 0.9031 (pt0) cc_final: 0.8265 (pm20) REVERT: B 142 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8977 (mm-30) REVERT: B 276 MET cc_start: 0.8591 (ttm) cc_final: 0.8158 (ttp) REVERT: B 300 ASP cc_start: 0.8932 (t0) cc_final: 0.8535 (t0) outliers start: 23 outliers final: 20 residues processed: 120 average time/residue: 0.2574 time to fit residues: 39.7189 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 : 0.859 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain E residue 118 SER 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 C residue 272 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.047849 restraints weight = 22318.316| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.20 r_work: 0.2596 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8022 Z= 0.170 Angle : 0.549 8.362 10923 Z= 0.291 Chirality : 0.045 0.142 1276 Planarity : 0.003 0.044 1406 Dihedral : 4.578 15.939 1070 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.81 % Allowed : 15.52 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 979 helix: -1.22 (0.89), residues: 36 sheet: -0.49 (0.25), residues: 403 loop : -0.01 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.016 0.002 PHE B 199 TYR 0.021 0.001 TYR D 293 ARG 0.008 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 246) hydrogen bonds : angle 5.87278 ( 603) covalent geometry : bond 0.00384 ( 8022) covalent geometry : angle 0.54901 (10923) *********************** 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 127 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 GLN cc_start: 0.9195 (mt0) cc_final: 0.8991 (mp10) REVERT: D 233 GLU cc_start: 0.8682 (mp0) cc_final: 0.8002 (tm-30) REVERT: D 243 ARG cc_start: 0.9043 (ttm170) cc_final: 0.7926 (ttm170) REVERT: D 255 ASP cc_start: 0.9165 (m-30) cc_final: 0.8423 (t0) REVERT: D 275 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8564 (mp0) REVERT: E 238 ASN cc_start: 0.9315 (t0) cc_final: 0.8982 (t0) REVERT: E 243 ARG cc_start: 0.9309 (mtp85) cc_final: 0.9101 (ptp-110) REVERT: E 296 MET cc_start: 0.7189 (tpt) cc_final: 0.6509 (mmm) REVERT: C 184 MET cc_start: 0.8481 (ttt) cc_final: 0.8174 (tmm) REVERT: C 246 ASP cc_start: 0.8978 (t0) cc_final: 0.8537 (t0) REVERT: C 250 GLU cc_start: 0.8961 (pm20) cc_final: 0.8541 (pm20) REVERT: C 276 MET cc_start: 0.8456 (ttm) cc_final: 0.8236 (ttp) REVERT: C 285 GLU cc_start: 0.9045 (tp30) cc_final: 0.8674 (tp30) REVERT: A 184 MET cc_start: 0.8748 (ppp) cc_final: 0.8371 (ppp) REVERT: A 250 GLU cc_start: 0.9036 (pt0) cc_final: 0.8264 (pm20) REVERT: B 142 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8991 (mm-30) REVERT: B 276 MET cc_start: 0.8593 (ttm) cc_final: 0.8149 (ttp) REVERT: B 300 ASP cc_start: 0.8933 (t0) cc_final: 0.8550 (t0) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.2480 time to fit residues: 38.7784 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 : 0.902 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain E residue 118 SER 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 C residue 289 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 85 optimal weight: 0.0040 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.0040 chunk 41 optimal weight: 0.0470 chunk 20 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.071439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.049233 restraints weight = 22219.775| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.21 r_work: 0.2635 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8022 Z= 0.120 Angle : 0.549 8.154 10923 Z= 0.292 Chirality : 0.044 0.142 1276 Planarity : 0.003 0.042 1406 Dihedral : 4.396 15.993 1070 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.47 % Allowed : 16.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.28), residues: 979 helix: -1.13 (0.90), residues: 36 sheet: -0.43 (0.25), residues: 403 loop : 0.01 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 296 HIS 0.002 0.000 HIS A 218 PHE 0.016 0.001 PHE D 301 TYR 0.022 0.001 TYR D 293 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 246) hydrogen bonds : angle 5.76527 ( 603) covalent geometry : bond 0.00279 ( 8022) covalent geometry : angle 0.54853 (10923) *********************** 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 129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 GLN cc_start: 0.7909 (tt0) cc_final: 0.7405 (tm-30) REVERT: D 233 GLU cc_start: 0.8663 (mp0) cc_final: 0.8141 (tm-30) REVERT: D 243 ARG cc_start: 0.9068 (ttm170) cc_final: 0.7876 (ttm170) REVERT: D 255 ASP cc_start: 0.9175 (m-30) cc_final: 0.8395 (t70) REVERT: D 275 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8563 (mp0) REVERT: E 238 ASN cc_start: 0.9279 (t0) cc_final: 0.9016 (t0) REVERT: E 243 ARG cc_start: 0.9314 (mtp85) cc_final: 0.9112 (ptp-110) REVERT: E 296 MET cc_start: 0.7025 (tpt) cc_final: 0.6559 (mmm) REVERT: C 189 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7952 (mtp180) REVERT: C 224 MET cc_start: 0.8692 (mtt) cc_final: 0.8294 (mmm) REVERT: C 246 ASP cc_start: 0.8994 (t0) cc_final: 0.8518 (t0) REVERT: C 250 GLU cc_start: 0.9007 (pm20) cc_final: 0.8345 (pm20) REVERT: C 285 GLU cc_start: 0.9036 (tp30) cc_final: 0.8713 (tp30) REVERT: A 152 GLU cc_start: 0.9213 (pm20) cc_final: 0.8877 (pm20) REVERT: A 184 MET cc_start: 0.8734 (ppp) cc_final: 0.8448 (ppp) REVERT: B 142 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8979 (mm-30) REVERT: B 276 MET cc_start: 0.8508 (ttm) cc_final: 0.8115 (ttp) REVERT: B 300 ASP cc_start: 0.8902 (t0) cc_final: 0.8534 (t0) outliers start: 22 outliers final: 19 residues processed: 124 average time/residue: 0.2514 time to fit residues: 40.0023 Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 118 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.070037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.047802 restraints weight = 22202.102| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.20 r_work: 0.2592 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8022 Z= 0.195 Angle : 0.580 8.085 10923 Z= 0.305 Chirality : 0.045 0.145 1276 Planarity : 0.003 0.043 1406 Dihedral : 4.523 15.254 1070 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 979 helix: -1.18 (0.90), residues: 36 sheet: -0.38 (0.25), residues: 403 loop : -0.05 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 296 HIS 0.002 0.001 HIS A 218 PHE 0.022 0.002 PHE B 199 TYR 0.022 0.002 TYR D 293 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 246) hydrogen bonds : angle 5.83551 ( 603) covalent geometry : bond 0.00444 ( 8022) covalent geometry : angle 0.57987 (10923) ********************** 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 121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 233 GLU cc_start: 0.8738 (mp0) cc_final: 0.8077 (tm-30) REVERT: D 243 ARG cc_start: 0.8961 (ttm170) cc_final: 0.7822 (ttm170) REVERT: D 255 ASP cc_start: 0.9166 (m-30) cc_final: 0.8433 (t0) REVERT: D 275 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8552 (mp0) REVERT: E 238 ASN cc_start: 0.9313 (t0) cc_final: 0.9027 (t0) REVERT: E 296 MET cc_start: 0.7025 (tpt) cc_final: 0.6436 (tpp) REVERT: C 246 ASP cc_start: 0.8972 (t0) cc_final: 0.8467 (t0) REVERT: C 250 GLU cc_start: 0.9024 (pm20) cc_final: 0.8347 (pm20) REVERT: C 285 GLU cc_start: 0.9090 (tp30) cc_final: 0.8768 (tp30) REVERT: A 152 GLU cc_start: 0.9242 (pm20) cc_final: 0.8947 (pm20) REVERT: A 184 MET cc_start: 0.8801 (ppp) cc_final: 0.8475 (ppp) REVERT: A 250 GLU cc_start: 0.9031 (pt0) cc_final: 0.8272 (pm20) REVERT: A 276 MET cc_start: 0.7454 (ttp) cc_final: 0.7136 (ttp) REVERT: B 142 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9017 (mm-30) REVERT: B 276 MET cc_start: 0.8603 (ttm) cc_final: 0.8160 (ttp) REVERT: B 300 ASP cc_start: 0.8933 (t0) cc_final: 0.8550 (t0) outliers start: 21 outliers final: 20 residues processed: 118 average time/residue: 0.2613 time to fit residues: 39.6303 Evaluate side-chains 119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 118 SER 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 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 C residue 289 CYS 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 229 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.069925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.047613 restraints weight = 22384.153| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.21 r_work: 0.2590 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3855 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= 0.207 Angle : 0.603 8.980 10923 Z= 0.316 Chirality : 0.045 0.143 1276 Planarity : 0.003 0.042 1406 Dihedral : 4.631 18.193 1070 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.47 % Allowed : 17.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 979 helix: -1.24 (0.88), residues: 36 sheet: -0.44 (0.25), residues: 405 loop : -0.05 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.025 0.002 PHE B 199 TYR 0.020 0.002 TYR D 293 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 246) hydrogen bonds : angle 5.88854 ( 603) covalent geometry : bond 0.00472 ( 8022) covalent geometry : angle 0.60276 (10923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.79 seconds wall clock time: 64 minutes 39.62 seconds (3879.62 seconds total)