Starting phenix.real_space_refine (version: dev) on Sat Feb 18 00:15:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8v_31493/02_2023/7f8v_31493_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8v_31493/02_2023/7f8v_31493.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/7f8v_31493/02_2023/7f8v_31493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8v_31493/02_2023/7f8v_31493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8v_31493/02_2023/7f8v_31493_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8v_31493/02_2023/7f8v_31493_updated.pdb" } resolution = 3.3 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= 0.003 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 "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6601 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 1 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2347 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 300} Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 133 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2128 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 236 " occ=0.00 Time building chain proxies: 4.24, per 1000 atoms: 0.64 Number of scatterers: 6601 At special positions: 0 Unit cell: (110.77, 117.04, 81.51, 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 53 16.00 O 1197 8.00 N 1127 7.00 C 4224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.04 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 9 sheets defined 38.8% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 281 removed outlier: 5.208A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'R' and resid 57 through 80 removed outlier: 4.475A pdb=" N ASN R 72 " --> pdb=" O SER R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 106 Processing helix chain 'R' and resid 108 through 116 removed outlier: 3.612A pdb=" N LEU R 113 " --> pdb=" O PRO R 109 " (cutoff:3.500A) Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 124 through 156 Processing helix chain 'R' and resid 159 through 165 Processing helix chain 'R' and resid 168 through 191 Proline residue: R 188 - end of helix Processing helix chain 'R' and resid 212 through 226 Processing helix chain 'R' and resid 228 through 247 Processing helix chain 'R' and resid 328 through 359 removed outlier: 4.132A pdb=" N ARG R 333 " --> pdb=" O LYS R 329 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET R 334 " --> pdb=" O ARG R 330 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE R 342 " --> pdb=" O ILE R 338 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 363 through 366 No H-bonds generated for 'chain 'R' and resid 363 through 366' Processing helix chain 'R' and resid 369 through 390 removed outlier: 4.837A pdb=" N HIS R 376 " --> pdb=" O SER R 373 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN R 386 " --> pdb=" O ALA R 383 " (cutoff:3.500A) Proline residue: R 387 - end of helix removed outlier: 4.409A pdb=" N TYR R 390 " --> pdb=" O PRO R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 404 Processing sheet with id= A, first strand: chain 'A' and resid 187 through 192 Processing sheet with id= B, first strand: chain 'A' and resid 221 through 227 removed outlier: 7.093A pdb=" N SER A 264 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE A 224 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 266 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 226 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 268 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.939A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.385A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.688A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.965A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.790A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.453A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1238 1.33 - 1.45: 1708 1.45 - 1.57: 3720 1.57 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 6743 Sorted by residual: bond pdb=" N LEU A 284 " pdb=" CA LEU A 284 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.37e-02 5.33e+03 9.10e+00 bond pdb=" C ALA R 370 " pdb=" N PRO R 371 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.42e+00 bond pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.48e+00 bond pdb=" C TYR R 189 " pdb=" N PRO R 190 " ideal model delta sigma weight residual 1.336 1.352 -0.016 9.80e-03 1.04e+04 2.83e+00 ... (remaining 6738 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.45: 163 106.45 - 113.42: 3699 113.42 - 120.39: 2592 120.39 - 127.36: 2617 127.36 - 134.33: 79 Bond angle restraints: 9150 Sorted by residual: angle pdb=" N PCA E 1 " pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 110.50 102.21 8.29 1.70e+00 3.46e-01 2.38e+01 angle pdb=" N PRO E 3 " pdb=" CA PRO E 3 " pdb=" C PRO E 3 " ideal model delta sigma weight residual 112.47 104.67 7.80 2.06e+00 2.36e-01 1.43e+01 angle pdb=" CB MET A 18 " pdb=" CG MET A 18 " pdb=" SD MET A 18 " ideal model delta sigma weight residual 112.70 122.52 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C MET R 134 " pdb=" CA MET R 134 " pdb=" CB MET R 134 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.02e+01 angle pdb=" CA MET R 108 " pdb=" CB MET R 108 " pdb=" CG MET R 108 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.14e+00 ... (remaining 9145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3600 17.86 - 35.72: 308 35.72 - 53.58: 61 53.58 - 71.44: 9 71.44 - 89.30: 6 Dihedral angle restraints: 3984 sinusoidal: 1526 harmonic: 2458 Sorted by residual: dihedral pdb=" CB CYS R 127 " pdb=" SG CYS R 127 " pdb=" SG CYS R 205 " pdb=" CB CYS R 205 " ideal model delta sinusoidal sigma weight residual 93.00 175.61 -82.61 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CA CYS R 107 " pdb=" C CYS R 107 " pdb=" N MET R 108 " pdb=" CA MET R 108 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA MET R 186 " pdb=" C MET R 186 " pdb=" N VAL R 187 " pdb=" CA VAL R 187 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 3981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 779 0.054 - 0.108: 218 0.108 - 0.161: 52 0.161 - 0.215: 4 0.215 - 0.269: 4 Chirality restraints: 1057 Sorted by residual: chirality pdb=" CA MET R 108 " pdb=" N MET R 108 " pdb=" C MET R 108 " pdb=" CB MET R 108 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA MET R 134 " pdb=" N MET R 134 " pdb=" C MET R 134 " pdb=" CB MET R 134 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR R 178 " pdb=" CA THR R 178 " pdb=" OG1 THR R 178 " pdb=" CG2 THR R 178 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1054 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA E 1 " -0.136 2.00e-02 2.50e+03 9.12e-02 1.04e+02 pdb=" CA PCA E 1 " 0.115 2.00e-02 2.50e+03 pdb=" CG PCA E 1 " -0.042 2.00e-02 2.50e+03 pdb=" CD PCA E 1 " -0.024 2.00e-02 2.50e+03 pdb=" OE PCA E 1 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 288 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO A 289 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO C 53 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.036 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1377 2.78 - 3.31: 6312 3.31 - 3.84: 11218 3.84 - 4.37: 13272 4.37 - 4.90: 22827 Nonbonded interactions: 55006 Sorted by model distance: nonbonded pdb=" O HIS R 364 " pdb=" OG SER R 368 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.290 2.440 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.307 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.308 2.440 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.310 2.520 ... (remaining 55001 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 53 5.16 5 C 4224 2.51 5 N 1127 2.21 5 O 1197 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=0.00 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: 0.910 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: 4.180 Check model and map are aligned: 0.100 Process input model: 20.810 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 0.068 6743 Z= 0.329 Angle : 0.873 9.912 9150 Z= 0.467 Chirality : 0.054 0.269 1057 Planarity : 0.007 0.091 1147 Dihedral : 14.097 89.299 2389 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: -1.49 (0.26), residues: 832 helix: -0.08 (0.27), residues: 331 sheet: -1.03 (0.41), residues: 131 loop : -1.78 (0.28), residues: 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.759 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1806 time to fit residues: 29.7366 Evaluate side-chains 99 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 ASN R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6743 Z= 0.216 Angle : 0.581 8.483 9150 Z= 0.305 Chirality : 0.042 0.167 1057 Planarity : 0.005 0.049 1147 Dihedral : 4.736 17.799 915 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.40 % 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: -1.02 (0.27), residues: 832 helix: 0.54 (0.28), residues: 332 sheet: -0.99 (0.42), residues: 131 loop : -1.67 (0.28), residues: 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 109 average time/residue: 0.1838 time to fit residues: 27.1909 Evaluate side-chains 105 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0674 time to fit residues: 1.9867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS R 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6743 Z= 0.182 Angle : 0.537 7.450 9150 Z= 0.284 Chirality : 0.041 0.148 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.517 17.574 915 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.54 % 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: -0.83 (0.28), residues: 832 helix: 0.81 (0.28), residues: 332 sheet: -1.01 (0.41), residues: 131 loop : -1.63 (0.29), residues: 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 110 average time/residue: 0.1800 time to fit residues: 26.9833 Evaluate side-chains 96 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0849 time to fit residues: 1.4538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6743 Z= 0.221 Angle : 0.553 7.359 9150 Z= 0.290 Chirality : 0.042 0.148 1057 Planarity : 0.004 0.039 1147 Dihedral : 4.562 17.326 915 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.83 % 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: -0.87 (0.28), residues: 832 helix: 0.82 (0.28), residues: 334 sheet: -1.33 (0.41), residues: 137 loop : -1.59 (0.29), residues: 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.1779 time to fit residues: 25.9784 Evaluate side-chains 100 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0709 time to fit residues: 2.0902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 196 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6743 Z= 0.196 Angle : 0.542 7.016 9150 Z= 0.282 Chirality : 0.041 0.148 1057 Planarity : 0.004 0.040 1147 Dihedral : 4.505 17.639 915 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.98 % 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: -0.79 (0.28), residues: 832 helix: 0.89 (0.28), residues: 340 sheet: -1.41 (0.41), residues: 137 loop : -1.53 (0.29), residues: 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 0.1731 time to fit residues: 25.2863 Evaluate side-chains 97 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0762 time to fit residues: 1.3446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 6743 Z= 0.342 Angle : 0.643 11.089 9150 Z= 0.335 Chirality : 0.045 0.188 1057 Planarity : 0.005 0.040 1147 Dihedral : 4.933 21.102 915 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 1.26 % 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: -1.20 (0.27), residues: 832 helix: 0.57 (0.28), residues: 334 sheet: -1.50 (0.38), residues: 149 loop : -1.79 (0.29), residues: 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 109 average time/residue: 0.1835 time to fit residues: 27.2723 Evaluate side-chains 105 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0720 time to fit residues: 2.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS A 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6743 Z= 0.211 Angle : 0.585 9.690 9150 Z= 0.304 Chirality : 0.042 0.182 1057 Planarity : 0.004 0.041 1147 Dihedral : 4.721 17.850 915 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.28 % 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: -0.93 (0.28), residues: 832 helix: 0.83 (0.29), residues: 333 sheet: -1.48 (0.39), residues: 147 loop : -1.62 (0.30), residues: 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1818 time to fit residues: 26.4840 Evaluate side-chains 98 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0615 time to fit residues: 1.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6743 Z= 0.170 Angle : 0.558 9.267 9150 Z= 0.287 Chirality : 0.042 0.152 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.486 20.772 915 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 1.12 % 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: -0.72 (0.28), residues: 832 helix: 0.98 (0.29), residues: 339 sheet: -1.38 (0.39), residues: 147 loop : -1.50 (0.30), residues: 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 0.1862 time to fit residues: 28.0411 Evaluate side-chains 113 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0894 time to fit residues: 2.0244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 66 optimal weight: 0.0770 chunk 69 optimal weight: 0.0970 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.0852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 6743 Z= 0.147 Angle : 0.539 8.951 9150 Z= 0.278 Chirality : 0.041 0.184 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.255 18.680 915 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -0.55 (0.28), residues: 832 helix: 1.16 (0.29), residues: 337 sheet: -1.26 (0.41), residues: 131 loop : -1.47 (0.29), residues: 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1851 time to fit residues: 29.0806 Evaluate side-chains 99 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 19 optimal weight: 0.1980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6743 Z= 0.212 Angle : 0.602 9.619 9150 Z= 0.307 Chirality : 0.043 0.183 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.405 19.540 915 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.14 % 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 (0.28), residues: 832 helix: 1.03 (0.29), residues: 336 sheet: -1.46 (0.41), residues: 137 loop : -1.48 (0.29), residues: 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.772 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.1849 time to fit residues: 24.7533 Evaluate side-chains 96 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0982 time to fit residues: 1.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 18 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.194276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.164214 restraints weight = 6759.951| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.17 r_work: 0.4092 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6743 Z= 0.208 Angle : 0.593 9.150 9150 Z= 0.306 Chirality : 0.043 0.179 1057 Planarity : 0.004 0.042 1147 Dihedral : 4.491 19.174 915 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.28 % 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: -0.73 (0.28), residues: 832 helix: 0.95 (0.29), residues: 336 sheet: -1.31 (0.39), residues: 147 loop : -1.49 (0.30), residues: 349 =============================================================================== Job complete usr+sys time: 1753.00 seconds wall clock time: 32 minutes 42.61 seconds (1962.61 seconds total)