Starting phenix.real_space_refine (version: dev) on Fri Feb 17 15:04:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2023/7yi9_33854_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2023/7yi9_33854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2023/7yi9_33854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2023/7yi9_33854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2023/7yi9_33854_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi9_33854/02_2023/7yi9_33854_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.076 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 Process input model Symmetric amino acids flipped Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5226 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.59 Number of scatterers: 5226 At special positions: 0 Unit cell: (80.75, 68, 122.4, 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 27 16.00 O 972 8.00 N 892 7.00 C 3335 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: 1.62 Conformation dependent library (CDL) restraints added in 812.7 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 2 sheets defined 33.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 166 through 169 Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.590A pdb=" N LYS A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'B' and resid 141 through 166 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 255 through 267 removed outlier: 5.318A pdb=" N ARG B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.537A pdb=" N GLU C 157 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 170 through 182 removed outlier: 4.420A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 52 through 65 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 84 through 95 removed outlier: 4.639A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 114 through 117 No H-bonds generated for 'chain 'D' and resid 114 through 117' Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing sheet with id= A, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.227A pdb=" N ALA A 146 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 432 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 148 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 183 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE A 149 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 185 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 182 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 361 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 364 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 209 " --> pdb=" O MET A 364 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG A 366 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR A 207 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 177 through 180 removed outlier: 6.520A pdb=" N TYR B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU B 353 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 205 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE B 354 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET B 207 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 248 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N MET B 208 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B 250 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 306 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU B 272 " --> pdb=" O VAL B 306 " (cutoff:3.500A) 148 hydrogen bonds defined for protein. 387 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: 1.21 Time building geometry restraints manager: 1.79 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: 1686 1.34 - 1.46: 761 1.46 - 1.57: 2824 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5319 Sorted by residual: bond pdb=" C2 SAM B 401 " pdb=" N3 SAM B 401 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C8 SAM B 401 " pdb=" N7 SAM B 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C2 SAM B 401 " pdb=" N1 SAM B 401 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C6 SAM B 401 " pdb=" N1 SAM B 401 " ideal model delta sigma weight residual 1.337 1.377 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1' SAM B 401 " pdb=" N9 SAM B 401 " ideal model delta sigma weight residual 1.452 1.478 -0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 5314 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.13: 86 106.13 - 113.11: 2875 113.11 - 120.08: 1863 120.08 - 127.06: 2280 127.06 - 134.04: 45 Bond angle restraints: 7149 Sorted by residual: angle pdb=" N ILE A 337 " pdb=" CA ILE A 337 " pdb=" C ILE A 337 " ideal model delta sigma weight residual 111.90 107.94 3.96 8.10e-01 1.52e+00 2.38e+01 angle pdb=" C LEU D 87 " pdb=" N GLU D 88 " pdb=" CA GLU D 88 " ideal model delta sigma weight residual 122.38 115.48 6.90 1.81e+00 3.05e-01 1.45e+01 angle pdb=" CA GLU D 88 " pdb=" CB GLU D 88 " pdb=" CG GLU D 88 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 angle pdb=" O SAM B 401 " pdb=" C SAM B 401 " pdb=" OXT SAM B 401 " ideal model delta sigma weight residual 126.77 117.87 8.90 3.00e+00 1.11e-01 8.79e+00 angle pdb=" N1 SAM B 401 " pdb=" C2 SAM B 401 " pdb=" N3 SAM B 401 " ideal model delta sigma weight residual 128.51 120.01 8.50 3.00e+00 1.11e-01 8.02e+00 ... (remaining 7144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2892 17.48 - 34.95: 276 34.95 - 52.43: 53 52.43 - 69.90: 7 69.90 - 87.38: 8 Dihedral angle restraints: 3236 sinusoidal: 1381 harmonic: 1855 Sorted by residual: dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N MET A 179 " pdb=" CA MET A 179 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET A 402 " pdb=" C MET A 402 " pdb=" N LYS A 403 " pdb=" CA LYS A 403 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA HIS A 379 " pdb=" C HIS A 379 " pdb=" N GLN A 380 " pdb=" CA GLN A 380 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.218: 780 2.218 - 4.436: 0 4.436 - 6.654: 0 6.654 - 8.872: 0 8.872 - 11.090: 1 Chirality restraints: 781 Sorted by residual: chirality pdb=" SD SAM B 401 " pdb=" CG SAM B 401 " pdb=" CE SAM B 401 " pdb=" C5' SAM B 401 " both_signs ideal model delta sigma weight residual False 5.50 -5.59 11.09 2.00e-01 2.50e+01 3.07e+03 chirality pdb=" CA GLN B 161 " pdb=" N GLN B 161 " pdb=" C GLN B 161 " pdb=" CB GLN B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C2' SAM B 401 " pdb=" C1' SAM B 401 " pdb=" C3' SAM B 401 " pdb=" O2' SAM B 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.59 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 778 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 112 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 113 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 353 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 174 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 175 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.020 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 69 2.67 - 3.23: 4872 3.23 - 3.79: 7747 3.79 - 4.34: 11272 4.34 - 4.90: 17994 Nonbonded interactions: 41954 Sorted by model distance: nonbonded pdb=" O LEU C 164 " pdb=" OH TYR C 171 " model vdw 2.115 2.440 nonbonded pdb=" NE2 GLN A 380 " pdb=" O GLY B 292 " model vdw 2.193 2.520 nonbonded pdb=" OD1 ASN A 210 " pdb=" OG1 THR A 361 " model vdw 2.237 2.440 nonbonded pdb=" NE1 TRP A 153 " pdb=" O TRP A 187 " model vdw 2.255 2.520 nonbonded pdb=" OD2 ASP B 204 " pdb=" NH1 ARG B 314 " model vdw 2.260 2.520 ... (remaining 41949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3335 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.880 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: 3.680 Check model and map are aligned: 0.070 Process input model: 15.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.004 0.056 5319 Z= 0.229 Angle : 0.651 8.895 7149 Z= 0.340 Chirality : 0.399 11.090 781 Planarity : 0.004 0.054 909 Dihedral : 14.290 87.381 2030 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.33), residues: 620 helix: -0.03 (0.36), residues: 204 sheet: 0.53 (0.52), residues: 102 loop : -1.23 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.576 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.2833 time to fit residues: 134.8669 Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 334 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5319 Z= 0.178 Angle : 0.546 5.894 7149 Z= 0.293 Chirality : 0.041 0.142 781 Planarity : 0.004 0.052 909 Dihedral : 4.726 16.357 675 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.33), residues: 620 helix: 0.19 (0.37), residues: 204 sheet: 0.62 (0.50), residues: 102 loop : -1.24 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.708 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 85 average time/residue: 1.3533 time to fit residues: 119.7354 Evaluate side-chains 80 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.7208 time to fit residues: 3.8514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 38 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 5319 Z= 0.289 Angle : 0.605 5.875 7149 Z= 0.323 Chirality : 0.043 0.149 781 Planarity : 0.005 0.056 909 Dihedral : 5.037 17.174 675 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.33), residues: 620 helix: -0.13 (0.36), residues: 204 sheet: 0.49 (0.50), residues: 103 loop : -1.37 (0.34), residues: 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.713 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 84 average time/residue: 1.3740 time to fit residues: 119.9916 Evaluate side-chains 80 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.3627 time to fit residues: 2.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5319 Z= 0.160 Angle : 0.508 5.156 7149 Z= 0.274 Chirality : 0.040 0.135 781 Planarity : 0.004 0.053 909 Dihedral : 4.729 22.463 675 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.33), residues: 620 helix: 0.10 (0.37), residues: 202 sheet: 0.57 (0.51), residues: 103 loop : -1.25 (0.34), residues: 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.653 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 81 average time/residue: 1.2787 time to fit residues: 107.9874 Evaluate side-chains 77 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1469 time to fit residues: 1.5704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5319 Z= 0.204 Angle : 0.531 5.557 7149 Z= 0.285 Chirality : 0.041 0.140 781 Planarity : 0.004 0.054 909 Dihedral : 4.759 23.002 675 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.33), residues: 620 helix: 0.20 (0.37), residues: 196 sheet: 0.50 (0.55), residues: 93 loop : -1.24 (0.34), residues: 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.612 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 1.2519 time to fit residues: 111.0233 Evaluate side-chains 87 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 6 average time/residue: 0.2813 time to fit residues: 2.8685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5319 Z= 0.162 Angle : 0.508 6.153 7149 Z= 0.273 Chirality : 0.040 0.133 781 Planarity : 0.004 0.053 909 Dihedral : 4.590 23.740 675 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.33), residues: 620 helix: 0.26 (0.37), residues: 196 sheet: 0.77 (0.53), residues: 98 loop : -1.10 (0.34), residues: 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.562 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 83 average time/residue: 1.2158 time to fit residues: 105.3315 Evaluate side-chains 80 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1372 time to fit residues: 1.3658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5319 Z= 0.249 Angle : 0.579 7.926 7149 Z= 0.308 Chirality : 0.042 0.146 781 Planarity : 0.004 0.054 909 Dihedral : 4.850 22.788 675 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.33), residues: 620 helix: 0.13 (0.37), residues: 197 sheet: 0.50 (0.53), residues: 93 loop : -1.20 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.655 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 84 average time/residue: 1.3419 time to fit residues: 117.4651 Evaluate side-chains 84 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1155 time to fit residues: 1.1004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5319 Z= 0.207 Angle : 0.547 7.526 7149 Z= 0.292 Chirality : 0.041 0.138 781 Planarity : 0.004 0.053 909 Dihedral : 4.764 23.838 675 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.33), residues: 620 helix: 0.15 (0.37), residues: 197 sheet: 0.61 (0.55), residues: 93 loop : -1.18 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.663 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 81 average time/residue: 1.3771 time to fit residues: 116.1360 Evaluate side-chains 79 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1314 time to fit residues: 1.5919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 5319 Z= 0.202 Angle : 0.572 10.359 7149 Z= 0.301 Chirality : 0.041 0.138 781 Planarity : 0.004 0.053 909 Dihedral : 4.718 23.651 675 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.33), residues: 620 helix: 0.16 (0.37), residues: 197 sheet: 0.62 (0.54), residues: 93 loop : -1.18 (0.34), residues: 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.651 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 1.2005 time to fit residues: 90.6289 Evaluate side-chains 74 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.4845 time to fit residues: 2.4544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 161 GLN B 244 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 5319 Z= 0.287 Angle : 0.624 9.298 7149 Z= 0.331 Chirality : 0.043 0.172 781 Planarity : 0.004 0.054 909 Dihedral : 5.028 22.172 675 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.33), residues: 620 helix: 0.05 (0.37), residues: 197 sheet: 0.48 (0.53), residues: 92 loop : -1.21 (0.34), residues: 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.638 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 1.3157 time to fit residues: 105.6137 Evaluate side-chains 73 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.0856 time to fit residues: 1.2036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 244 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.194097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155350 restraints weight = 5884.988| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.75 r_work: 0.3776 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 5319 Z= 0.151 Angle : 0.535 10.489 7149 Z= 0.284 Chirality : 0.040 0.147 781 Planarity : 0.004 0.052 909 Dihedral : 4.580 24.099 675 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.34), residues: 620 helix: 0.27 (0.38), residues: 196 sheet: 0.70 (0.55), residues: 91 loop : -1.09 (0.34), residues: 333 =============================================================================== Job complete usr+sys time: 2473.55 seconds wall clock time: 44 minutes 45.48 seconds (2685.48 seconds total)