Starting phenix.real_space_refine on Sat Aug 3 09:40:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/08_2024/8qjx_18453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/08_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_18453/08_2024/8qjx_18453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/08_2024/8qjx_18453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/08_2024/8qjx_18453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/08_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-5409/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: 4.75, per 1000 atoms: 0.60 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: 2.61 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: 0.92 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: 2.04 Time building geometry restraints manager: 2.90 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 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- 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 : 0.892 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: 0.2790 time to fit residues: 57.4430 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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= 0.237 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 *********************** 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 fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.929 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 255 ASP cc_start: 0.8583 (m-30) cc_final: 0.8366 (t70) REVERT: D 272 PHE cc_start: 0.7625 (m-80) cc_final: 0.7416 (m-80) REVERT: C 138 VAL cc_start: 0.8927 (t) cc_final: 0.8589 (m) REVERT: C 300 ASP cc_start: 0.8749 (t0) cc_final: 0.8544 (t0) REVERT: B 276 MET cc_start: 0.8634 (ttm) cc_final: 0.8266 (ttp) outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 0.2641 time to fit residues: 44.4935 Evaluate side-chains 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 E 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8022 Z= 0.332 Angle : 0.564 6.860 10923 Z= 0.301 Chirality : 0.046 0.142 1276 Planarity : 0.004 0.061 1406 Dihedral : 4.677 16.965 1070 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.14 % Allowed : 14.06 % Favored : 83.80 % 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: -0.27 (0.28), residues: 979 helix: -1.88 (0.76), residues: 36 sheet: -0.37 (0.25), residues: 381 loop : 0.25 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 296 HIS 0.003 0.001 HIS C 218 PHE 0.019 0.002 PHE B 199 TYR 0.018 0.002 TYR E 293 ARG 0.007 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 129 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8619 (m-30) cc_final: 0.8370 (t70) REVERT: E 243 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8307 (mtp85) REVERT: C 284 ASP cc_start: 0.8084 (p0) cc_final: 0.6000 (p0) REVERT: C 300 ASP cc_start: 0.8800 (t0) cc_final: 0.8547 (t0) REVERT: A 250 GLU cc_start: 0.8295 (pm20) cc_final: 0.8035 (pm20) REVERT: B 276 MET cc_start: 0.8620 (ttm) cc_final: 0.8270 (ttp) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.2599 time to fit residues: 41.7795 Evaluate side-chains 114 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 296 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8022 Z= 0.283 Angle : 0.554 7.655 10923 Z= 0.294 Chirality : 0.045 0.146 1276 Planarity : 0.003 0.055 1406 Dihedral : 4.630 14.972 1070 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.25 % Allowed : 14.96 % 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: -0.32 (0.28), residues: 979 helix: -1.51 (0.82), residues: 36 sheet: -0.39 (0.25), residues: 381 loop : 0.17 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 296 HIS 0.003 0.001 HIS C 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 *********************** 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 128 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8613 (m-30) cc_final: 0.8364 (t70) REVERT: E 243 ARG cc_start: 0.8713 (mtp85) cc_final: 0.8317 (mtp85) REVERT: C 284 ASP cc_start: 0.7731 (p0) cc_final: 0.6665 (p0) REVERT: C 285 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 300 ASP cc_start: 0.8851 (t0) cc_final: 0.8591 (t0) REVERT: B 276 MET cc_start: 0.8608 (ttm) cc_final: 0.8243 (ttp) REVERT: B 300 ASP cc_start: 0.8917 (t0) cc_final: 0.8712 (t0) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.2632 time to fit residues: 42.5916 Evaluate side-chains 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 118 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 235 ASN E 307 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8022 Z= 0.381 Angle : 0.597 7.901 10923 Z= 0.315 Chirality : 0.046 0.144 1276 Planarity : 0.003 0.052 1406 Dihedral : 4.777 17.734 1070 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.70 % Allowed : 16.20 % 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: -0.41 (0.28), residues: 979 helix: -1.47 (0.83), residues: 36 sheet: -0.43 (0.25), residues: 381 loop : 0.08 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 296 HIS 0.002 0.001 HIS A 218 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.002 TYR D 172 ARG 0.007 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 127 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8642 (m-30) cc_final: 0.8360 (t70) REVERT: C 300 ASP cc_start: 0.8861 (t0) cc_final: 0.8610 (t0) REVERT: B 276 MET cc_start: 0.8621 (ttm) cc_final: 0.8283 (ttp) REVERT: B 300 ASP cc_start: 0.9010 (t0) cc_final: 0.8803 (t0) outliers start: 24 outliers final: 17 residues processed: 123 average time/residue: 0.2567 time to fit residues: 40.7533 Evaluate side-chains 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 HIS E 206 GLN E 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8022 Z= 0.339 Angle : 0.583 8.275 10923 Z= 0.309 Chirality : 0.046 0.151 1276 Planarity : 0.003 0.049 1406 Dihedral : 4.777 19.758 1070 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.47 % Allowed : 16.20 % Favored : 81.33 % 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: -0.50 (0.27), residues: 979 helix: -1.41 (0.85), residues: 36 sheet: -0.48 (0.25), residues: 381 loop : -0.01 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 296 HIS 0.003 0.001 HIS C 218 PHE 0.016 0.002 PHE C 172 TYR 0.015 0.002 TYR E 293 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 122 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8185 (ttm170) REVERT: D 255 ASP cc_start: 0.8610 (m-30) cc_final: 0.8345 (t70) REVERT: E 238 ASN cc_start: 0.8593 (t0) cc_final: 0.8220 (t0) REVERT: E 243 ARG cc_start: 0.8668 (mtp85) cc_final: 0.8214 (mtt-85) REVERT: C 224 MET cc_start: 0.9210 (mmt) cc_final: 0.8183 (mmm) REVERT: A 184 MET cc_start: 0.8754 (ppp) cc_final: 0.8477 (ppp) REVERT: B 276 MET cc_start: 0.8621 (ttm) cc_final: 0.8272 (ttp) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.2394 time to fit residues: 36.8175 Evaluate side-chains 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8022 Z= 0.322 Angle : 0.586 8.272 10923 Z= 0.310 Chirality : 0.045 0.143 1276 Planarity : 0.003 0.046 1406 Dihedral : 4.747 20.521 1070 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 16.87 % Favored : 80.20 % 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: -0.54 (0.27), residues: 979 helix: -1.39 (0.86), residues: 36 sheet: -0.53 (0.25), residues: 382 loop : -0.02 (0.28), residues: 561 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 0.019 0.002 PHE B 199 TYR 0.017 0.002 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 123 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8641 (m-30) cc_final: 0.8296 (t0) REVERT: E 238 ASN cc_start: 0.8671 (t0) cc_final: 0.8388 (t0) REVERT: E 243 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8171 (mtt-85) REVERT: C 284 ASP cc_start: 0.8043 (p0) cc_final: 0.7789 (p0) REVERT: B 276 MET cc_start: 0.8615 (ttm) cc_final: 0.8270 (ttp) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 0.2416 time to fit residues: 36.9700 Evaluate side-chains 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 55 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8022 Z= 0.237 Angle : 0.576 8.235 10923 Z= 0.303 Chirality : 0.045 0.143 1276 Planarity : 0.003 0.044 1406 Dihedral : 4.635 20.607 1070 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.81 % Allowed : 17.10 % 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: -0.58 (0.28), residues: 979 helix: -1.23 (0.88), residues: 36 sheet: -0.58 (0.25), residues: 404 loop : -0.00 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 296 HIS 0.002 0.001 HIS C 218 PHE 0.016 0.002 PHE C 172 TYR 0.020 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 121 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8634 (m-30) cc_final: 0.8318 (t0) REVERT: E 238 ASN cc_start: 0.8735 (t0) cc_final: 0.8490 (t0) REVERT: E 243 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8138 (mtt-85) REVERT: B 276 MET cc_start: 0.8543 (ttm) cc_final: 0.8222 (ttp) outliers start: 25 outliers final: 18 residues processed: 116 average time/residue: 0.2447 time to fit residues: 36.7406 Evaluate side-chains 113 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain A residue 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 87 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 E 235 ASN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8022 Z= 0.340 Angle : 0.623 8.273 10923 Z= 0.328 Chirality : 0.046 0.143 1276 Planarity : 0.003 0.044 1406 Dihedral : 4.798 21.613 1070 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 17.44 % 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: -0.63 (0.27), residues: 979 helix: -1.25 (0.88), residues: 36 sheet: -0.61 (0.25), residues: 405 loop : -0.05 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 296 HIS 0.003 0.001 HIS C 188 PHE 0.017 0.002 PHE C 172 TYR 0.019 0.002 TYR D 293 ARG 0.010 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 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8664 (m-30) cc_final: 0.8323 (t0) REVERT: E 238 ASN cc_start: 0.8854 (t0) cc_final: 0.8450 (t0) REVERT: E 243 ARG cc_start: 0.8678 (mtp85) cc_final: 0.8201 (mtt-85) REVERT: C 284 ASP cc_start: 0.8236 (p0) cc_final: 0.8004 (p0) REVERT: B 276 MET cc_start: 0.8604 (ttm) cc_final: 0.8260 (ttp) outliers start: 22 outliers final: 20 residues processed: 115 average time/residue: 0.2465 time to fit residues: 36.8929 Evaluate side-chains 114 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 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 232 VAL 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 194 THR Chi-restraints excluded: chain B residue 229 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 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: 0.8686 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8022 Z= 0.189 Angle : 0.593 11.078 10923 Z= 0.311 Chirality : 0.045 0.156 1276 Planarity : 0.003 0.043 1406 Dihedral : 4.515 19.908 1070 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.57 % Allowed : 18.22 % Favored : 80.20 % 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: -0.54 (0.27), residues: 979 helix: 0.70 (1.42), residues: 18 sheet: -0.55 (0.25), residues: 405 loop : -0.11 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 296 HIS 0.003 0.001 HIS A 218 PHE 0.020 0.001 PHE D 301 TYR 0.013 0.001 TYR A 260 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 111 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 255 ASP cc_start: 0.8617 (m-30) cc_final: 0.8376 (t70) REVERT: E 231 MET cc_start: 0.7291 (mmm) cc_final: 0.6390 (tpp) REVERT: E 238 ASN cc_start: 0.8809 (t0) cc_final: 0.8464 (t0) REVERT: E 243 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8130 (mtt-85) REVERT: A 319 TYR cc_start: 0.8196 (m-80) cc_final: 0.7800 (m-80) REVERT: B 276 MET cc_start: 0.8493 (ttm) cc_final: 0.8226 (ttp) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.2416 time to fit residues: 34.2276 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.068670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.046342 restraints weight = 22299.767| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.19 r_work: 0.2562 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8022 Z= 0.451 Angle : 0.671 10.647 10923 Z= 0.350 Chirality : 0.047 0.156 1276 Planarity : 0.004 0.044 1406 Dihedral : 4.888 21.372 1070 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.91 % Allowed : 18.34 % Favored : 79.75 % 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: -0.67 (0.27), residues: 979 helix: -1.22 (0.88), residues: 36 sheet: -0.60 (0.25), residues: 405 loop : -0.11 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 296 HIS 0.003 0.001 HIS C 188 PHE 0.030 0.002 PHE B 199 TYR 0.028 0.002 TYR D 293 ARG 0.010 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.36 seconds wall clock time: 32 minutes 44.69 seconds (1964.69 seconds total)