Starting phenix.real_space_refine on Mon Mar 11 09:36:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0q_23100/03_2024/7l0q_23100_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0q_23100/03_2024/7l0q_23100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0q_23100/03_2024/7l0q_23100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0q_23100/03_2024/7l0q_23100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0q_23100/03_2024/7l0q_23100_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0q_23100/03_2024/7l0q_23100_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5026 2.51 5 N 1340 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 8": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7891 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2409 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 2729 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2694 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 4, 'TRANS': 332} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 337, 2694 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 4, 'TRANS': 332} Chain breaks: 3 bond proxies already assigned to first conformer: 2697 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2385 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 310 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASP A 97 " occ=0.56 ... (14 atoms not shown) pdb=" OD2BASP A 97 " occ=0.44 residue: pdb=" N AARG A 105 " occ=0.68 ... (20 atoms not shown) pdb=" NH2BARG A 105 " occ=0.32 residue: pdb=" N AASP A 158 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP A 158 " occ=0.49 residue: pdb=" N AASP A 160 " occ=0.44 ... (14 atoms not shown) pdb=" OD2BASP A 160 " occ=0.56 Time building chain proxies: 5.82, per 1000 atoms: 0.74 Number of scatterers: 7891 At special positions: 0 Unit cell: (91.575, 113.025, 124.575, 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 56 16.00 O 1469 8.00 N 1340 7.00 C 5026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 225 " 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: 2.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 47.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'C' and resid 60 through 90 Processing helix chain 'C' and resid 102 through 128 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 138 through 172 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 182 through 206 Proline residue: C 203 - end of helix Processing helix chain 'C' and resid 230 through 269 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 298 through 334 removed outlier: 3.791A pdb=" N VAL C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Proline residue: C 323 - end of helix removed outlier: 3.602A pdb=" N ILE C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 371 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'A' and resid 4 through 7 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.572A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 68 Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.598A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.851A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.540A pdb=" N AASP A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 200 through 204 removed outlier: 4.064A pdb=" N GLY A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.605A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 4.755A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 48 Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222 removed outlier: 6.222A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 222 removed outlier: 6.222A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.631A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.597A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.523A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.760A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 235 removed outlier: 4.573A pdb=" N ALA B 240 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.427A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1219 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: 2.27 Time building geometry restraints manager: 3.21 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: 1712 1.33 - 1.45: 1960 1.45 - 1.58: 4293 1.58 - 1.70: 1 1.70 - 1.83: 81 Bond restraints: 8047 Sorted by residual: bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.08e-02 8.57e+03 1.16e+01 bond pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 1.469 1.508 -0.039 1.28e-02 6.10e+03 9.45e+00 bond pdb=" N CYS B 233 " pdb=" CA CYS B 233 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" CA GLU B 138 " pdb=" C GLU B 138 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.32e-02 5.74e+03 6.78e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.21e+00 ... (remaining 8042 not shown) Histogram of bond angle deviations from ideal: 96.25 - 103.96: 74 103.96 - 111.66: 3509 111.66 - 119.37: 3170 119.37 - 127.08: 4063 127.08 - 134.79: 90 Bond angle restraints: 10906 Sorted by residual: angle pdb=" N PRO C 297 " pdb=" CA PRO C 297 " pdb=" CB PRO C 297 " ideal model delta sigma weight residual 103.25 111.61 -8.36 1.05e+00 9.07e-01 6.34e+01 angle pdb=" C PHE B 235 " pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 119.84 127.37 -7.53 1.25e+00 6.40e-01 3.63e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.08 129.12 -7.04 1.47e+00 4.63e-01 2.29e+01 angle pdb=" C SER C 335 " pdb=" N ASP C 336 " pdb=" CA ASP C 336 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.26e+01 angle pdb=" CA ASN B 268 " pdb=" CB ASN B 268 " pdb=" CG ASN B 268 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.00e+00 1.00e+00 2.20e+01 ... (remaining 10901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 4121 16.04 - 32.07: 496 32.07 - 48.10: 126 48.10 - 64.14: 26 64.14 - 80.17: 6 Dihedral angle restraints: 4775 sinusoidal: 1845 harmonic: 2930 Sorted by residual: dihedral pdb=" CA SER B 160 " pdb=" C SER B 160 " pdb=" N SER B 161 " pdb=" CA SER B 161 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA LEU B 192 " pdb=" C LEU B 192 " pdb=" N ALA B 193 " pdb=" CA ALA B 193 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE C 248 " pdb=" C PHE C 248 " pdb=" N PRO C 249 " pdb=" CA PRO C 249 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 885 0.060 - 0.119: 290 0.119 - 0.179: 57 0.179 - 0.239: 16 0.239 - 0.298: 4 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA PRO C 297 " pdb=" N PRO C 297 " pdb=" C PRO C 297 " pdb=" CB PRO C 297 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA HIS C 133 " pdb=" N HIS C 133 " pdb=" C HIS C 133 " pdb=" CB HIS C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1249 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 248 " -0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 249 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 4 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C THR A 4 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 4 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 5 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C THR A 340 " 0.055 2.00e-02 2.50e+03 pdb=" O THR A 340 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 341 " -0.018 2.00e-02 2.50e+03 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 713 2.74 - 3.28: 7947 3.28 - 3.82: 13494 3.82 - 4.36: 15647 4.36 - 4.90: 26762 Nonbonded interactions: 64563 Sorted by model distance: nonbonded pdb=" NZ LYS A 128 " pdb=" OD1AASP A 160 " model vdw 2.196 2.520 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.297 2.440 nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.298 2.440 ... (remaining 64558 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 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 : 0.007 0.093 8047 Z= 0.461 Angle : 1.072 9.835 10906 Z= 0.628 Chirality : 0.063 0.298 1252 Planarity : 0.007 0.094 1381 Dihedral : 14.952 80.175 2880 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.21 % Favored : 93.48 % Rotamer: Outliers : 0.70 % Allowed : 12.75 % Favored : 86.55 % Cbeta Deviations : 0.11 % 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: -3.51 (0.22), residues: 993 helix: -1.99 (0.19), residues: 453 sheet: -2.14 (0.39), residues: 151 loop : -2.63 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 135 HIS 0.005 0.001 HIS A 195 PHE 0.022 0.003 PHE A 189 TYR 0.019 0.003 TYR A 167 ARG 0.012 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7480 (tpt) cc_final: 0.6103 (tpt) REVERT: C 167 ARG cc_start: 0.6957 (mtt180) cc_final: 0.6171 (ttt180) REVERT: C 216 ASP cc_start: 0.5743 (p0) cc_final: 0.4798 (t0) REVERT: C 224 VAL cc_start: 0.7884 (m) cc_final: 0.7594 (m) REVERT: C 329 LEU cc_start: 0.8133 (mm) cc_final: 0.7572 (tt) REVERT: C 350 PHE cc_start: 0.8391 (t80) cc_final: 0.8136 (t80) REVERT: C 359 TYR cc_start: 0.7755 (m-10) cc_final: 0.6904 (m-80) REVERT: A 28 GLU cc_start: 0.7573 (tt0) cc_final: 0.7226 (tt0) REVERT: A 188 HIS cc_start: 0.8697 (m90) cc_final: 0.8032 (t70) REVERT: A 195 HIS cc_start: 0.7560 (t70) cc_final: 0.6543 (t70) REVERT: A 304 GLN cc_start: 0.8656 (tt0) cc_final: 0.8277 (tt0) REVERT: A 305 CYS cc_start: 0.8437 (m) cc_final: 0.7881 (t) REVERT: B 47 THR cc_start: 0.8969 (m) cc_final: 0.8346 (p) REVERT: B 108 SER cc_start: 0.8585 (m) cc_final: 0.8381 (p) REVERT: B 222 PHE cc_start: 0.8500 (m-80) cc_final: 0.8173 (m-80) REVERT: B 234 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 339 TRP cc_start: 0.8894 (m100) cc_final: 0.8453 (m100) outliers start: 5 outliers final: 1 residues processed: 279 average time/residue: 0.2219 time to fit residues: 80.3190 Evaluate side-chains 184 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 159 ASN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN A 52 GLN A 188 HIS A 269 ASN A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8047 Z= 0.265 Angle : 0.682 11.557 10906 Z= 0.359 Chirality : 0.044 0.182 1252 Planarity : 0.005 0.082 1381 Dihedral : 5.873 80.183 1092 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 0.23 % Allowed : 4.91 % Favored : 94.85 % 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: -1.91 (0.25), residues: 993 helix: -0.08 (0.23), residues: 458 sheet: -1.97 (0.37), residues: 165 loop : -2.35 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.002 HIS C 325 PHE 0.016 0.002 PHE A 334 TYR 0.033 0.002 TYR C 71 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7721 (tpt) cc_final: 0.6098 (tpt) REVERT: C 167 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6352 (ttt180) REVERT: C 216 ASP cc_start: 0.6078 (p0) cc_final: 0.5044 (t0) REVERT: C 267 MET cc_start: 0.7270 (ttt) cc_final: 0.7025 (ttp) REVERT: C 329 LEU cc_start: 0.7959 (mm) cc_final: 0.7645 (tt) REVERT: C 359 TYR cc_start: 0.7641 (m-10) cc_final: 0.6824 (m-80) REVERT: A 15 ARG cc_start: 0.8345 (tpm170) cc_final: 0.8118 (ttm-80) REVERT: A 36 LEU cc_start: 0.9366 (mt) cc_final: 0.9104 (mp) REVERT: A 248 LYS cc_start: 0.9333 (mttt) cc_final: 0.9124 (mppt) REVERT: A 304 GLN cc_start: 0.8679 (tt0) cc_final: 0.8352 (tt0) REVERT: A 305 CYS cc_start: 0.8631 (m) cc_final: 0.8002 (t) REVERT: A 318 GLU cc_start: 0.8695 (pt0) cc_final: 0.8454 (pm20) REVERT: B 44 GLN cc_start: 0.8537 (pt0) cc_final: 0.8256 (pm20) REVERT: B 51 LEU cc_start: 0.9015 (mp) cc_final: 0.8729 (mp) REVERT: B 57 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8457 (mtmm) REVERT: B 82 TRP cc_start: 0.9182 (m100) cc_final: 0.8685 (m100) REVERT: B 108 SER cc_start: 0.9016 (m) cc_final: 0.8740 (p) REVERT: B 180 PHE cc_start: 0.7724 (m-80) cc_final: 0.7010 (m-10) REVERT: B 251 ARG cc_start: 0.7454 (mtt90) cc_final: 0.7103 (mtt90) REVERT: B 289 TYR cc_start: 0.8570 (m-10) cc_final: 0.8000 (m-10) REVERT: B 339 TRP cc_start: 0.8906 (m100) cc_final: 0.8321 (m100) REVERT: G 39 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8746 (mt-10) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1752 time to fit residues: 56.3326 Evaluate side-chains 171 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS A 52 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8047 Z= 0.180 Angle : 0.616 7.098 10906 Z= 0.322 Chirality : 0.042 0.174 1252 Planarity : 0.005 0.076 1381 Dihedral : 5.484 74.905 1092 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 0.12 % Allowed : 3.39 % Favored : 96.49 % 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: -1.24 (0.26), residues: 993 helix: 0.48 (0.24), residues: 457 sheet: -1.63 (0.38), residues: 170 loop : -2.03 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.004 0.001 HIS C 325 PHE 0.023 0.002 PHE B 235 TYR 0.031 0.001 TYR C 71 ARG 0.005 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7627 (tpt) cc_final: 0.6316 (tpt) REVERT: C 216 ASP cc_start: 0.6097 (p0) cc_final: 0.5110 (t0) REVERT: C 267 MET cc_start: 0.7265 (ttt) cc_final: 0.7000 (ttp) REVERT: C 359 TYR cc_start: 0.7710 (m-10) cc_final: 0.6868 (m-80) REVERT: A 188 HIS cc_start: 0.8767 (m-70) cc_final: 0.8502 (m-70) REVERT: A 304 GLN cc_start: 0.8637 (tt0) cc_final: 0.8327 (tt0) REVERT: A 305 CYS cc_start: 0.8702 (m) cc_final: 0.8029 (t) REVERT: B 44 GLN cc_start: 0.8621 (pt0) cc_final: 0.8234 (mp10) REVERT: B 57 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8552 (mtmm) REVERT: B 61 MET cc_start: 0.8501 (ppp) cc_final: 0.8275 (ppp) REVERT: B 172 GLU cc_start: 0.7593 (mp0) cc_final: 0.7086 (mp0) REVERT: B 222 PHE cc_start: 0.8578 (m-80) cc_final: 0.8178 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1841 time to fit residues: 56.1351 Evaluate side-chains 164 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8047 Z= 0.194 Angle : 0.617 6.893 10906 Z= 0.323 Chirality : 0.043 0.171 1252 Planarity : 0.004 0.077 1381 Dihedral : 5.239 70.176 1092 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 0.23 % Allowed : 3.04 % Favored : 96.73 % 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: -0.98 (0.27), residues: 993 helix: 0.65 (0.24), residues: 458 sheet: -1.58 (0.37), residues: 180 loop : -1.77 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.003 0.001 HIS C 133 PHE 0.014 0.002 PHE B 292 TYR 0.021 0.002 TYR B 264 ARG 0.004 0.000 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7470 (tpt) cc_final: 0.6403 (tpt) REVERT: C 166 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8815 (tm-30) REVERT: C 167 ARG cc_start: 0.7007 (mtt180) cc_final: 0.6499 (ttt180) REVERT: C 216 ASP cc_start: 0.6168 (p0) cc_final: 0.5235 (t0) REVERT: C 267 MET cc_start: 0.7267 (ttt) cc_final: 0.7035 (ttp) REVERT: C 359 TYR cc_start: 0.7713 (m-10) cc_final: 0.6954 (m-80) REVERT: A 188 HIS cc_start: 0.8761 (m-70) cc_final: 0.8354 (m-70) REVERT: A 304 GLN cc_start: 0.8645 (tt0) cc_final: 0.8294 (tt0) REVERT: A 305 CYS cc_start: 0.8733 (m) cc_final: 0.8098 (t) REVERT: A 321 THR cc_start: 0.8896 (t) cc_final: 0.7893 (t) REVERT: B 44 GLN cc_start: 0.8624 (pt0) cc_final: 0.8203 (mp10) REVERT: B 57 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8609 (mtmm) REVERT: B 89 LYS cc_start: 0.8678 (mttp) cc_final: 0.8068 (mtpt) REVERT: B 172 GLU cc_start: 0.7664 (mp0) cc_final: 0.7123 (mp0) REVERT: B 222 PHE cc_start: 0.8645 (m-80) cc_final: 0.8155 (m-80) REVERT: B 225 HIS cc_start: 0.7020 (m-70) cc_final: 0.6786 (m-70) REVERT: B 251 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6691 (tpp80) REVERT: B 311 HIS cc_start: 0.8800 (m-70) cc_final: 0.8561 (m-70) REVERT: G 35 LYS cc_start: 0.9090 (pttt) cc_final: 0.8373 (pttm) REVERT: G 39 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8477 (pp20) REVERT: G 42 ASP cc_start: 0.8917 (p0) cc_final: 0.8659 (p0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1840 time to fit residues: 54.2426 Evaluate side-chains 160 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 127 ASN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8047 Z= 0.199 Angle : 0.620 7.762 10906 Z= 0.323 Chirality : 0.043 0.172 1252 Planarity : 0.004 0.076 1381 Dihedral : 5.029 65.032 1092 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 0.12 % Allowed : 1.75 % Favored : 98.13 % 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: -0.77 (0.27), residues: 993 helix: 0.88 (0.24), residues: 457 sheet: -1.56 (0.37), residues: 185 loop : -1.69 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.003 0.001 HIS A 213 PHE 0.023 0.002 PHE B 234 TYR 0.020 0.001 TYR C 71 ARG 0.003 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7684 (tpt) cc_final: 0.6581 (tpt) REVERT: C 166 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8814 (tm-30) REVERT: C 216 ASP cc_start: 0.6185 (p0) cc_final: 0.5234 (t0) REVERT: C 267 MET cc_start: 0.7215 (ttt) cc_final: 0.6944 (ttp) REVERT: C 359 TYR cc_start: 0.7729 (m-10) cc_final: 0.7161 (m-80) REVERT: A 305 CYS cc_start: 0.8776 (m) cc_final: 0.8050 (t) REVERT: B 44 GLN cc_start: 0.8616 (pt0) cc_final: 0.7598 (pm20) REVERT: B 57 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8572 (mtmm) REVERT: B 172 GLU cc_start: 0.7646 (mp0) cc_final: 0.7129 (mp0) REVERT: B 222 PHE cc_start: 0.8580 (m-80) cc_final: 0.8215 (m-80) REVERT: B 225 HIS cc_start: 0.7070 (m-70) cc_final: 0.6780 (m-70) REVERT: B 251 ARG cc_start: 0.7181 (mtt90) cc_final: 0.6815 (mtt90) REVERT: B 311 HIS cc_start: 0.8822 (m-70) cc_final: 0.8595 (m170) REVERT: G 31 MET cc_start: 0.4411 (mmt) cc_final: 0.4152 (ttm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1789 time to fit residues: 54.6533 Evaluate side-chains 161 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 0.0470 chunk 90 optimal weight: 10.0000 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8047 Z= 0.295 Angle : 0.675 6.924 10906 Z= 0.353 Chirality : 0.044 0.174 1252 Planarity : 0.004 0.079 1381 Dihedral : 5.255 64.777 1092 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.31 % Favored : 93.58 % Rotamer: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.31 % 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: -0.85 (0.27), residues: 993 helix: 0.82 (0.24), residues: 458 sheet: -1.59 (0.37), residues: 185 loop : -1.75 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 297 HIS 0.008 0.002 HIS A 213 PHE 0.016 0.002 PHE C 206 TYR 0.027 0.002 TYR C 71 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7700 (tpt) cc_final: 0.6149 (tpt) REVERT: C 166 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8813 (tm-30) REVERT: C 167 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6815 (ttt180) REVERT: C 216 ASP cc_start: 0.6358 (p0) cc_final: 0.5460 (t0) REVERT: C 267 MET cc_start: 0.7292 (ttt) cc_final: 0.7006 (ttp) REVERT: C 359 TYR cc_start: 0.7963 (m-10) cc_final: 0.6850 (m-80) REVERT: A 26 ASP cc_start: 0.8198 (t0) cc_final: 0.7833 (t0) REVERT: A 197 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8756 (ttmt) REVERT: A 200 ASP cc_start: 0.7697 (t0) cc_final: 0.7496 (t0) REVERT: A 305 CYS cc_start: 0.8741 (m) cc_final: 0.8062 (t) REVERT: A 339 VAL cc_start: 0.8635 (t) cc_final: 0.8374 (t) REVERT: B 44 GLN cc_start: 0.8424 (pt0) cc_final: 0.7971 (pm20) REVERT: B 57 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8608 (mtmm) REVERT: B 222 PHE cc_start: 0.8642 (m-80) cc_final: 0.8378 (m-80) REVERT: B 225 HIS cc_start: 0.7149 (m-70) cc_final: 0.6661 (m-70) REVERT: B 311 HIS cc_start: 0.8879 (m-70) cc_final: 0.8546 (m170) REVERT: G 31 MET cc_start: 0.4577 (mmt) cc_final: 0.4122 (ttm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1623 time to fit residues: 47.5691 Evaluate side-chains 159 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8047 Z= 0.329 Angle : 0.715 6.887 10906 Z= 0.375 Chirality : 0.046 0.182 1252 Planarity : 0.005 0.080 1381 Dihedral : 5.617 77.552 1092 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 0.12 % Allowed : 2.22 % Favored : 97.66 % 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: -0.94 (0.27), residues: 993 helix: 0.66 (0.24), residues: 458 sheet: -1.56 (0.38), residues: 179 loop : -1.72 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 297 HIS 0.008 0.002 HIS A 213 PHE 0.019 0.002 PHE C 206 TYR 0.029 0.002 TYR C 71 ARG 0.004 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7766 (tpt) cc_final: 0.6468 (tpt) REVERT: C 166 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8855 (tm-30) REVERT: C 216 ASP cc_start: 0.6721 (p0) cc_final: 0.5765 (t0) REVERT: C 267 MET cc_start: 0.7264 (ttt) cc_final: 0.6978 (ttp) REVERT: C 359 TYR cc_start: 0.8060 (m-10) cc_final: 0.7197 (m-80) REVERT: A 53 MET cc_start: 0.8328 (mmm) cc_final: 0.8031 (mpp) REVERT: A 305 CYS cc_start: 0.8744 (m) cc_final: 0.8144 (t) REVERT: A 339 VAL cc_start: 0.8621 (t) cc_final: 0.8345 (t) REVERT: B 44 GLN cc_start: 0.8470 (pt0) cc_final: 0.7777 (pm20) REVERT: B 45 MET cc_start: 0.7969 (mmm) cc_final: 0.7417 (mmm) REVERT: B 57 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8594 (mtmm) REVERT: B 225 HIS cc_start: 0.6947 (m-70) cc_final: 0.6373 (m-70) REVERT: B 311 HIS cc_start: 0.8702 (m-70) cc_final: 0.8425 (m-70) REVERT: B 339 TRP cc_start: 0.8618 (m100) cc_final: 0.8184 (m100) REVERT: G 31 MET cc_start: 0.4502 (mmt) cc_final: 0.4094 (ttm) REVERT: G 35 LYS cc_start: 0.8878 (pttp) cc_final: 0.8673 (pptt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1647 time to fit residues: 45.4386 Evaluate side-chains 148 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8047 Z= 0.204 Angle : 0.648 7.523 10906 Z= 0.338 Chirality : 0.043 0.180 1252 Planarity : 0.004 0.077 1381 Dihedral : 5.399 76.653 1092 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 0.23 % Allowed : 0.82 % Favored : 98.95 % 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: -0.80 (0.27), residues: 993 helix: 0.78 (0.23), residues: 459 sheet: -1.46 (0.38), residues: 180 loop : -1.68 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 297 HIS 0.006 0.001 HIS A 213 PHE 0.016 0.002 PHE C 206 TYR 0.026 0.001 TYR C 71 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7650 (tpt) cc_final: 0.6467 (tpt) REVERT: C 139 ASP cc_start: 0.5555 (t0) cc_final: 0.5348 (t0) REVERT: C 166 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8793 (tm-30) REVERT: C 216 ASP cc_start: 0.6723 (p0) cc_final: 0.5789 (t0) REVERT: C 267 MET cc_start: 0.7317 (ttt) cc_final: 0.7066 (ttp) REVERT: C 359 TYR cc_start: 0.7981 (m-10) cc_final: 0.6869 (m-80) REVERT: A 26 ASP cc_start: 0.8215 (t0) cc_final: 0.7920 (t0) REVERT: A 53 MET cc_start: 0.8300 (mmm) cc_final: 0.8060 (mpp) REVERT: A 197 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8735 (ttmt) REVERT: A 304 GLN cc_start: 0.8468 (tt0) cc_final: 0.8224 (tt0) REVERT: A 305 CYS cc_start: 0.8642 (m) cc_final: 0.8117 (t) REVERT: A 339 VAL cc_start: 0.8709 (t) cc_final: 0.8457 (t) REVERT: B 44 GLN cc_start: 0.8554 (pt0) cc_final: 0.7878 (pm20) REVERT: B 45 MET cc_start: 0.7877 (mmm) cc_final: 0.7665 (mmm) REVERT: B 57 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8568 (mtmm) REVERT: B 225 HIS cc_start: 0.6792 (m-70) cc_final: 0.6382 (m-70) REVERT: B 264 TYR cc_start: 0.6015 (m-80) cc_final: 0.4775 (m-80) REVERT: B 289 TYR cc_start: 0.8233 (m-10) cc_final: 0.7982 (m-80) REVERT: B 311 HIS cc_start: 0.8588 (m-70) cc_final: 0.8214 (m-70) REVERT: B 339 TRP cc_start: 0.8386 (m100) cc_final: 0.8084 (m100) REVERT: G 39 GLU cc_start: 0.8834 (pp20) cc_final: 0.8619 (pp20) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.1572 time to fit residues: 46.6928 Evaluate side-chains 165 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8047 Z= 0.189 Angle : 0.648 8.387 10906 Z= 0.340 Chirality : 0.044 0.222 1252 Planarity : 0.004 0.075 1381 Dihedral : 5.169 72.694 1092 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % 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: -0.61 (0.27), residues: 993 helix: 0.87 (0.24), residues: 464 sheet: -1.23 (0.37), residues: 185 loop : -1.60 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.013 0.002 HIS C 269 PHE 0.016 0.001 PHE C 206 TYR 0.026 0.001 TYR C 71 ARG 0.005 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7589 (tpt) cc_final: 0.6571 (tpt) REVERT: C 166 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8869 (tm-30) REVERT: C 216 ASP cc_start: 0.6456 (p0) cc_final: 0.5535 (t0) REVERT: C 267 MET cc_start: 0.7275 (ttt) cc_final: 0.7028 (ttp) REVERT: C 359 TYR cc_start: 0.7924 (m-10) cc_final: 0.6700 (m-80) REVERT: A 26 ASP cc_start: 0.8151 (t0) cc_final: 0.7888 (t0) REVERT: A 53 MET cc_start: 0.8240 (mmm) cc_final: 0.8014 (mpp) REVERT: A 305 CYS cc_start: 0.8602 (m) cc_final: 0.8078 (t) REVERT: A 339 VAL cc_start: 0.8666 (t) cc_final: 0.8371 (t) REVERT: B 44 GLN cc_start: 0.8659 (pt0) cc_final: 0.8204 (pm20) REVERT: B 45 MET cc_start: 0.7954 (mmm) cc_final: 0.7405 (mmm) REVERT: B 57 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8551 (mtmm) REVERT: B 225 HIS cc_start: 0.6767 (m-70) cc_final: 0.6295 (m-70) REVERT: B 289 TYR cc_start: 0.8229 (m-10) cc_final: 0.7794 (m-80) REVERT: B 311 HIS cc_start: 0.8582 (m-70) cc_final: 0.8298 (m-70) REVERT: G 39 GLU cc_start: 0.8846 (pp20) cc_final: 0.8597 (pp20) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1705 time to fit residues: 49.7216 Evaluate side-chains 166 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 269 HIS ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8047 Z= 0.186 Angle : 0.637 6.812 10906 Z= 0.333 Chirality : 0.043 0.171 1252 Planarity : 0.004 0.074 1381 Dihedral : 5.317 85.889 1092 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % 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 (0.27), residues: 993 helix: 0.95 (0.24), residues: 464 sheet: -1.20 (0.37), residues: 180 loop : -1.63 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 339 HIS 0.005 0.001 HIS A 213 PHE 0.033 0.002 PHE A 189 TYR 0.027 0.001 TYR C 71 ARG 0.003 0.000 ARG A 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.7512 (tpt) cc_final: 0.6719 (tpt) REVERT: C 150 ASP cc_start: 0.7747 (t70) cc_final: 0.7310 (t70) REVERT: C 166 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8845 (tm-30) REVERT: C 167 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6585 (ttt180) REVERT: C 216 ASP cc_start: 0.6408 (p0) cc_final: 0.5494 (t0) REVERT: C 267 MET cc_start: 0.7238 (ttt) cc_final: 0.6995 (ttp) REVERT: C 359 TYR cc_start: 0.7868 (m-10) cc_final: 0.7010 (m-80) REVERT: A 26 ASP cc_start: 0.8124 (t0) cc_final: 0.7840 (t0) REVERT: A 53 MET cc_start: 0.8171 (mmm) cc_final: 0.7929 (mpp) REVERT: A 305 CYS cc_start: 0.8543 (m) cc_final: 0.8014 (t) REVERT: A 339 VAL cc_start: 0.8668 (t) cc_final: 0.8333 (t) REVERT: B 44 GLN cc_start: 0.8571 (pt0) cc_final: 0.8114 (pm20) REVERT: B 45 MET cc_start: 0.7819 (mmm) cc_final: 0.7503 (mmm) REVERT: B 57 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8674 (mtpt) REVERT: B 251 ARG cc_start: 0.7054 (mtt90) cc_final: 0.6697 (tpp80) REVERT: G 31 MET cc_start: 0.5620 (ttm) cc_final: 0.4995 (ttm) REVERT: G 39 GLU cc_start: 0.8810 (pp20) cc_final: 0.8599 (pp20) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1646 time to fit residues: 47.1761 Evaluate side-chains 162 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN C 241 ASN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 188 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.146957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124642 restraints weight = 59804.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.126789 restraints weight = 47087.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129912 restraints weight = 13983.390| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8047 Z= 0.203 Angle : 0.643 8.363 10906 Z= 0.337 Chirality : 0.044 0.205 1252 Planarity : 0.004 0.074 1381 Dihedral : 5.277 85.294 1092 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 0.12 % Allowed : 0.58 % Favored : 99.30 % 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: -0.54 (0.27), residues: 993 helix: 1.00 (0.24), residues: 462 sheet: -1.10 (0.36), residues: 192 loop : -1.75 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.006 0.001 HIS A 213 PHE 0.030 0.002 PHE A 189 TYR 0.025 0.002 TYR C 71 ARG 0.003 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.13 seconds wall clock time: 38 minutes 49.25 seconds (2329.25 seconds total)