Starting phenix.real_space_refine on Fri Dec 8 08:47:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/12_2023/8qjx_18453.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/12_2023/8qjx_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_18453/12_2023/8qjx_18453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/12_2023/8qjx_18453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/12_2023/8qjx_18453.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qjx_18453/12_2023/8qjx_18453.pdb" } 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-1.21rc1-5172/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: 4.38, per 1000 atoms: 0.56 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: 2.71 Conformation dependent library (CDL) restraints added in 1.4 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: 1.03 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: 1.91 Time building geometry restraints manager: 2.96 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: 0.010 Normalize map: mean=0, sd=1: 0.160 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: 1.300 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.820 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- 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 : 0.942 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 outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2868 time to fit residues: 59.1701 Evaluate side-chains 107 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2238 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 39 optimal weight: 0.0060 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8022 Z= 0.225 Angle : 0.560 6.918 10923 Z= 0.297 Chirality : 0.045 0.147 1276 Planarity : 0.004 0.066 1406 Dihedral : 4.511 17.369 1070 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.02 % Allowed : 14.62 % Favored : 83.35 % 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: -0.37 (0.28), residues: 979 helix: -2.18 (0.72), residues: 36 sheet: -0.43 (0.26), residues: 382 loop : 0.18 (0.28), 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 0.019 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 136 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 132 average time/residue: 0.2662 time to fit residues: 44.4150 Evaluate side-chains 119 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0734 time to fit residues: 2.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8022 Z= 0.404 Angle : 0.583 6.930 10923 Z= 0.309 Chirality : 0.046 0.137 1276 Planarity : 0.004 0.060 1406 Dihedral : 4.729 16.590 1070 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.80 % Allowed : 15.07 % Favored : 83.13 % 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 (0.28), residues: 979 helix: -1.84 (0.74), residues: 36 sheet: -0.36 (0.26), residues: 381 loop : 0.17 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 296 HIS 0.003 0.001 HIS C 218 PHE 0.021 0.002 PHE B 199 TYR 0.015 0.002 TYR D 172 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 124 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 121 average time/residue: 0.2680 time to fit residues: 41.2204 Evaluate side-chains 111 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0792 time to fit residues: 2.9078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 0.0770 chunk 93 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8022 Z= 0.143 Angle : 0.515 6.810 10923 Z= 0.275 Chirality : 0.044 0.143 1276 Planarity : 0.003 0.054 1406 Dihedral : 4.318 15.297 1070 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.79 % Allowed : 16.20 % Favored : 83.01 % 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: -0.26 (0.27), residues: 979 helix: -1.54 (0.83), residues: 36 sheet: -0.26 (0.25), residues: 390 loop : 0.13 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.012 0.001 TYR D 186 ARG 0.008 0.001 ARG A 280 *********************** 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 119 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 117 average time/residue: 0.3446 time to fit residues: 52.6931 Evaluate side-chains 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1095 time to fit residues: 2.2079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 8022 Z= 0.432 Angle : 0.586 7.109 10923 Z= 0.311 Chirality : 0.046 0.147 1276 Planarity : 0.004 0.052 1406 Dihedral : 4.732 16.893 1070 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.01 % Allowed : 17.10 % Favored : 81.89 % 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 (0.28), residues: 979 helix: -1.50 (0.81), residues: 36 sheet: -0.29 (0.25), residues: 381 loop : 0.06 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 296 HIS 0.003 0.001 HIS C 218 PHE 0.022 0.002 PHE B 199 TYR 0.016 0.002 TYR D 172 ARG 0.009 0.001 ARG A 280 *********************** 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 108 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.2662 time to fit residues: 36.0812 Evaluate side-chains 103 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0715 time to fit residues: 2.1550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 0.0770 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8022 Z= 0.228 Angle : 0.530 7.428 10923 Z= 0.282 Chirality : 0.045 0.147 1276 Planarity : 0.003 0.048 1406 Dihedral : 4.470 18.944 1070 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.01 % Allowed : 17.44 % Favored : 81.55 % 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: -1.23 (0.88), residues: 36 sheet: -0.26 (0.25), residues: 381 loop : 0.06 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 296 HIS 0.002 0.001 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.011 0.001 TYR D 186 ARG 0.008 0.001 ARG E 243 *********************** 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 109 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 0.2772 time to fit residues: 37.5112 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1335 time to fit residues: 2.7890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 68 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8022 Z= 0.230 Angle : 0.532 7.375 10923 Z= 0.282 Chirality : 0.045 0.178 1276 Planarity : 0.003 0.046 1406 Dihedral : 4.414 20.233 1070 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.67 % Allowed : 18.34 % 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: -0.33 (0.28), residues: 979 helix: -1.00 (0.91), residues: 36 sheet: -0.31 (0.25), residues: 404 loop : 0.07 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 296 HIS 0.002 0.000 HIS C 218 PHE 0.016 0.002 PHE C 172 TYR 0.017 0.001 TYR D 293 ARG 0.009 0.001 ARG D 243 *********************** 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 105 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 100 average time/residue: 0.2695 time to fit residues: 34.7656 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0709 time to fit residues: 1.4862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 208 GLN B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8022 Z= 0.297 Angle : 0.557 7.608 10923 Z= 0.294 Chirality : 0.045 0.154 1276 Planarity : 0.003 0.046 1406 Dihedral : 4.525 20.414 1070 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.01 % Allowed : 18.11 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.91), residues: 36 sheet: -0.35 (0.25), residues: 397 loop : -0.01 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 296 HIS 0.002 0.001 HIS C 218 PHE 0.015 0.002 PHE C 172 TYR 0.023 0.002 TYR D 293 ARG 0.009 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 106 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.2662 time to fit residues: 34.9841 Evaluate side-chains 97 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0704 time to fit residues: 1.7949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8022 Z= 0.228 Angle : 0.542 7.445 10923 Z= 0.287 Chirality : 0.044 0.145 1276 Planarity : 0.003 0.044 1406 Dihedral : 4.441 19.569 1070 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.67 % Allowed : 18.11 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 979 helix: -0.89 (0.92), residues: 36 sheet: -0.31 (0.25), residues: 404 loop : -0.04 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.001 PHE C 172 TYR 0.020 0.001 TYR D 293 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 103 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 101 average time/residue: 0.2636 time to fit residues: 34.6487 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0939 time to fit residues: 1.6992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8022 Z= 0.196 Angle : 0.536 7.981 10923 Z= 0.283 Chirality : 0.044 0.142 1276 Planarity : 0.003 0.042 1406 Dihedral : 4.324 19.421 1070 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.45 % Allowed : 18.11 % Favored : 81.44 % 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: -0.84 (0.92), residues: 36 sheet: -0.26 (0.25), residues: 404 loop : -0.07 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 296 HIS 0.002 0.000 HIS C 218 PHE 0.015 0.001 PHE D 301 TYR 0.014 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 98 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 96 average time/residue: 0.2569 time to fit residues: 32.4318 Evaluate side-chains 96 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0763 time to fit residues: 1.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.047590 restraints weight = 22154.343| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.20 r_work: 0.2590 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8022 Z= 0.356 Angle : 0.582 7.511 10923 Z= 0.306 Chirality : 0.045 0.144 1276 Planarity : 0.003 0.043 1406 Dihedral : 4.652 21.099 1070 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.22 % Allowed : 18.45 % 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: -0.49 (0.27), residues: 979 helix: -0.93 (0.89), residues: 36 sheet: -0.31 (0.25), residues: 397 loop : -0.17 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 296 HIS 0.002 0.001 HIS C 218 PHE 0.025 0.002 PHE B 199 TYR 0.023 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: 1813.57 seconds wall clock time: 34 minutes 32.95 seconds (2072.95 seconds total)