Starting phenix.real_space_refine on Fri Jul 19 11:42:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/07_2024/8qjx_18453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/07_2024/8qjx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/07_2024/8qjx_18453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/07_2024/8qjx_18453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/07_2024/8qjx_18453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/07_2024/8qjx_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 Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.64, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 2.88 Conformation dependent library (CDL) restraints added in 1.5 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: 0.91 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: 1.87 Time building geometry restraints manager: 3.19 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: 99.82 - 106.66: 194 106.66 - 113.51: 4478 113.51 - 120.35: 2821 120.35 - 127.19: 3356 127.19 - 134.04: 74 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 2.440 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 1.961 2.440 nonbonded pdb=" OD1 ASP A 265 " pdb=" OG1 THR A 267 " model vdw 2.153 2.440 nonbonded pdb=" OH TYR C 319 " pdb=" OH TYR A 319 " model vdw 2.170 2.440 nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 2.188 2.440 ... (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 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: 0.220 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.700 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- 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= 0.327 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.997 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: 0.2837 time to fit residues: 58.6114 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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: 2.9990 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8022 Z= 0.166 Angle : 0.540 6.529 10923 Z= 0.289 Chirality : 0.045 0.152 1276 Planarity : 0.004 0.065 1406 Dihedral : 4.435 14.486 1070 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.14 % Allowed : 13.84 % Favored : 84.03 % 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: -0.35 (0.28), residues: 979 helix: -2.19 (0.74), residues: 36 sheet: -0.41 (0.25), residues: 382 loop : 0.20 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 296 HIS 0.003 0.001 HIS C 218 PHE 0.017 0.002 PHE E 247 TYR 0.020 0.001 TYR E 293 ARG 0.005 0.001 ARG A 208 *********************** 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 139 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.928 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: D 255 ASP cc_start: 0.8590 (m-30) cc_final: 0.8182 (t0) REVERT: C 300 ASP cc_start: 0.8693 (t0) cc_final: 0.8476 (t0) REVERT: B 276 MET cc_start: 0.8599 (ttm) cc_final: 0.8246 (ttp) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.2747 time to fit residues: 46.6482 Evaluate side-chains 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 272 ASP Chi-restraints excluded: chain A 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 296 TRP Chi-restraints excluded: chain B residue 324 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8022 Z= 0.217 Angle : 0.516 6.031 10923 Z= 0.274 Chirality : 0.044 0.145 1276 Planarity : 0.003 0.060 1406 Dihedral : 4.351 14.766 1070 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.36 % Allowed : 13.61 % Favored : 84.03 % 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: -0.21 (0.28), residues: 979 helix: -1.93 (0.77), residues: 36 sheet: -0.32 (0.25), residues: 384 loop : 0.28 (0.29), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 296 HIS 0.002 0.001 HIS C 218 PHE 0.014 0.002 PHE C 172 TYR 0.016 0.001 TYR E 293 ARG 0.008 0.001 ARG A 280 *********************** 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 132 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 MET cc_start: 0.8201 (ttp) cc_final: 0.7871 (tmm) REVERT: B 276 MET cc_start: 0.8572 (ttm) cc_final: 0.8225 (ttp) outliers start: 21 outliers final: 16 residues processed: 126 average time/residue: 0.2734 time to fit residues: 43.6315 Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A 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 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 87 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8022 Z= 0.357 Angle : 0.565 5.847 10923 Z= 0.299 Chirality : 0.045 0.146 1276 Planarity : 0.003 0.056 1406 Dihedral : 4.580 14.736 1070 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.04 % Allowed : 14.62 % Favored : 82.34 % 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: -0.21 (0.28), residues: 979 helix: -1.77 (0.79), residues: 36 sheet: -0.26 (0.25), residues: 381 loop : 0.21 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.020 0.002 PHE B 199 TYR 0.016 0.002 TYR E 293 ARG 0.006 0.001 ARG A 208 *********************** 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 133 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 276 MET cc_start: 0.8559 (ttm) cc_final: 0.8220 (ttp) REVERT: B 300 ASP cc_start: 0.8982 (t0) cc_final: 0.8735 (t0) outliers start: 27 outliers final: 22 residues processed: 126 average time/residue: 0.2538 time to fit residues: 41.0652 Evaluate side-chains 122 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 232 VAL 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 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR 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 272 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 HIS E 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8022 Z= 0.192 Angle : 0.514 6.773 10923 Z= 0.273 Chirality : 0.044 0.148 1276 Planarity : 0.003 0.050 1406 Dihedral : 4.333 14.332 1070 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.81 % Allowed : 16.20 % Favored : 80.99 % 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: -0.19 (0.28), residues: 979 helix: -1.55 (0.84), residues: 36 sheet: -0.18 (0.25), residues: 390 loop : 0.17 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.015 0.001 TYR E 293 ARG 0.006 0.001 ARG A 208 *********************** 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 129 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8436 (ttm170) cc_final: 0.7650 (ttm170) REVERT: E 243 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8329 (mtt-85) REVERT: B 276 MET cc_start: 0.8498 (ttm) cc_final: 0.8182 (ttp) REVERT: B 300 ASP cc_start: 0.8948 (t0) cc_final: 0.8741 (t0) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.2882 time to fit residues: 44.6716 Evaluate side-chains 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 232 VAL 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 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 309 THR 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 272 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 90 optimal weight: 0.0470 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN E 208 GLN B 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8022 Z= 0.395 Angle : 0.575 6.932 10923 Z= 0.303 Chirality : 0.046 0.138 1276 Planarity : 0.004 0.050 1406 Dihedral : 4.640 14.843 1070 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.26 % Allowed : 16.42 % 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: -0.33 (0.27), residues: 979 helix: -1.41 (0.84), residues: 36 sheet: -0.26 (0.25), residues: 381 loop : 0.03 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.022 0.002 PHE B 199 TYR 0.016 0.002 TYR D 172 ARG 0.007 0.001 ARG A 208 *********************** 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 127 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8523 (ttm170) cc_final: 0.7655 (ttm170) REVERT: E 243 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8361 (mtt-85) REVERT: B 276 MET cc_start: 0.8612 (ttm) cc_final: 0.8277 (ttp) outliers start: 29 outliers final: 23 residues processed: 117 average time/residue: 0.2437 time to fit residues: 36.9119 Evaluate side-chains 119 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain E residue 231 MET 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 C residue 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR 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 272 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 79 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8022 Z= 0.242 Angle : 0.526 6.182 10923 Z= 0.279 Chirality : 0.044 0.142 1276 Planarity : 0.003 0.046 1406 Dihedral : 4.461 15.108 1070 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.04 % Allowed : 16.31 % Favored : 80.65 % 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: -0.30 (0.27), residues: 979 helix: -1.10 (0.89), residues: 36 sheet: -0.22 (0.25), residues: 389 loop : 0.02 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.021 0.001 TYR D 293 ARG 0.008 0.001 ARG A 208 *********************** 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 127 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8532 (ttm170) cc_final: 0.7772 (ttm170) REVERT: E 243 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8257 (mtt-85) REVERT: A 184 MET cc_start: 0.8707 (ppp) cc_final: 0.8487 (ppp) REVERT: B 276 MET cc_start: 0.8502 (ttm) cc_final: 0.8182 (ttp) outliers start: 27 outliers final: 21 residues processed: 118 average time/residue: 0.2679 time to fit residues: 41.0537 Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 C residue 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR 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 272 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 7.9990 chunk 28 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8022 Z= 0.226 Angle : 0.530 6.650 10923 Z= 0.280 Chirality : 0.044 0.139 1276 Planarity : 0.003 0.043 1406 Dihedral : 4.417 16.765 1070 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.81 % Allowed : 16.76 % 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 (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: -0.32 (0.27), residues: 979 helix: -0.98 (0.91), residues: 36 sheet: -0.19 (0.25), residues: 389 loop : -0.04 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.002 PHE C 172 TYR 0.028 0.001 TYR D 293 ARG 0.008 0.001 ARG A 208 *********************** 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 124 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8433 (ttm170) cc_final: 0.7755 (ttm170) REVERT: E 238 ASN cc_start: 0.8542 (t0) cc_final: 0.8134 (t0) REVERT: E 243 ARG cc_start: 0.8726 (mtp85) cc_final: 0.8204 (mtt-85) REVERT: E 279 GLN cc_start: 0.8532 (pp30) cc_final: 0.8330 (pm20) REVERT: B 276 MET cc_start: 0.8484 (ttm) cc_final: 0.8158 (ttp) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.2496 time to fit residues: 37.8415 Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 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 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 C residue 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 309 THR 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 272 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 208 GLN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8022 Z= 0.169 Angle : 0.516 7.745 10923 Z= 0.273 Chirality : 0.044 0.140 1276 Planarity : 0.003 0.041 1406 Dihedral : 4.236 15.994 1070 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.36 % Allowed : 17.55 % Favored : 80.09 % 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: -0.31 (0.27), residues: 979 helix: -0.82 (0.93), residues: 36 sheet: -0.24 (0.25), residues: 404 loop : 0.01 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.014 0.001 TYR A 260 ARG 0.009 0.001 ARG A 208 *********************** 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 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8404 (ttm170) cc_final: 0.7743 (ttm170) REVERT: E 238 ASN cc_start: 0.8747 (t0) cc_final: 0.8433 (t0) REVERT: E 243 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8253 (mtt-85) REVERT: E 279 GLN cc_start: 0.8506 (pp30) cc_final: 0.8250 (pm20) REVERT: B 276 MET cc_start: 0.8446 (ttm) cc_final: 0.8144 (ttp) outliers start: 21 outliers final: 20 residues processed: 114 average time/residue: 0.2503 time to fit residues: 36.7846 Evaluate side-chains 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 175 VAL Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A 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 194 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 272 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8022 Z= 0.299 Angle : 0.561 7.759 10923 Z= 0.296 Chirality : 0.045 0.138 1276 Planarity : 0.003 0.042 1406 Dihedral : 4.466 15.942 1070 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.36 % Allowed : 18.00 % Favored : 79.64 % 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: -0.39 (0.27), residues: 979 helix: -0.82 (0.91), residues: 36 sheet: -0.24 (0.25), residues: 404 loop : -0.10 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 296 HIS 0.002 0.001 HIS A 188 PHE 0.020 0.002 PHE B 199 TYR 0.023 0.002 TYR D 293 ARG 0.009 0.001 ARG A 208 ********************** 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 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8473 (ttm170) cc_final: 0.7792 (ttm170) REVERT: E 238 ASN cc_start: 0.8822 (t0) cc_final: 0.8368 (t0) REVERT: E 243 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8312 (mtt-85) REVERT: E 279 GLN cc_start: 0.8564 (pp30) cc_final: 0.8352 (pm20) REVERT: B 276 MET cc_start: 0.8571 (ttm) cc_final: 0.8220 (ttp) outliers start: 21 outliers final: 21 residues processed: 110 average time/residue: 0.2525 time to fit residues: 35.8361 Evaluate side-chains 114 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 175 VAL Chi-restraints excluded: chain C residue 259 CYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 309 THR 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 272 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 0.0170 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.071583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.049087 restraints weight = 21874.777| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.22 r_work: 0.2629 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8022 Z= 0.210 Angle : 0.558 10.800 10923 Z= 0.290 Chirality : 0.044 0.139 1276 Planarity : 0.003 0.041 1406 Dihedral : 4.363 15.906 1070 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.59 % Allowed : 17.77 % Favored : 79.64 % 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: -0.40 (0.27), residues: 979 helix: -0.76 (0.92), residues: 36 sheet: -0.24 (0.25), residues: 404 loop : -0.12 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.014 0.001 TYR A 260 ARG 0.009 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.45 seconds wall clock time: 34 minutes 41.19 seconds (2081.19 seconds total)