Starting phenix.real_space_refine on Tue Mar 3 17:55:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l0q_23100/03_2026/7l0q_23100_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l0q_23100/03_2026/7l0q_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/cci-nas-00/data/ceres_data/7l0q_23100/03_2026/7l0q_23100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2026/7l0q_23100.map" model { file = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2026/7l0q_23100_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l0q_23100/03_2026/7l0q_23100_neut.cif" } resolution = 4.3 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 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 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: 1.86, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 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: 0.55 Conformation dependent library (CDL) restraints added in 389.3 milliseconds 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: 0.30 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: 1.26 Time building geometry restraints manager: 0.77 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: 0.00 - 1.97: 10232 1.97 - 3.93: 572 3.93 - 5.90: 64 5.90 - 7.87: 19 7.87 - 9.84: 19 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 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.297 3.040 nonbonded pdb=" OG SER B 277 " pdb=" O LEU B 318 " model vdw 2.298 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.990 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- 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 8048 Z= 0.373 Angle : 1.072 9.835 10908 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 : 7.70 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.012 0.001 ARG A 176 TYR 0.019 0.003 TYR A 167 PHE 0.022 0.003 PHE A 189 TRP 0.019 0.003 TRP C 135 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 8047) covalent geometry : angle 1.07157 (10906) SS BOND : bond 0.00792 ( 1) SS BOND : angle 1.36555 ( 2) hydrogen bonds : bond 0.14281 ( 426) hydrogen bonds : angle 7.23301 ( 1219) *********************** 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 to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.227 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: 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: 0.6181 (ttt180) REVERT: C 216 ASP cc_start: 0.5743 (p0) cc_final: 0.4796 (t0) REVERT: C 224 VAL cc_start: 0.7884 (m) cc_final: 0.7596 (m) REVERT: C 329 LEU cc_start: 0.8133 (mm) cc_final: 0.7571 (tt) REVERT: C 350 PHE cc_start: 0.8390 (t80) cc_final: 0.8131 (t80) REVERT: C 359 TYR cc_start: 0.7755 (m-10) cc_final: 0.6905 (m-80) REVERT: A 28 GLU cc_start: 0.7573 (tt0) cc_final: 0.7250 (tt0) REVERT: A 188 HIS cc_start: 0.8697 (m90) cc_final: 0.8022 (t70) REVERT: A 195 HIS cc_start: 0.7560 (t70) cc_final: 0.6559 (t70) REVERT: A 304 GLN cc_start: 0.8656 (tt0) cc_final: 0.8278 (tt0) REVERT: A 305 CYS cc_start: 0.8437 (m) cc_final: 0.7878 (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: 0.8384 (p) REVERT: B 222 PHE cc_start: 0.8500 (m-80) cc_final: 0.8172 (m-80) REVERT: B 234 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7800 (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: 0.0951 time to fit residues: 34.6587 Evaluate side-chains 186 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122105 restraints weight = 58461.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124362 restraints weight = 51136.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127894 restraints weight = 14966.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129778 restraints weight = 6234.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129866 restraints weight = 3716.349| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8048 Z= 0.182 Angle : 0.697 11.105 10908 Z= 0.367 Chirality : 0.044 0.189 1252 Planarity : 0.005 0.083 1381 Dihedral : 5.886 79.398 1092 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.68 % Favored : 95.11 % Rotamer: Outliers : 0.23 % Allowed : 3.39 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.25), residues: 993 helix: -0.26 (0.23), residues: 460 sheet: -2.00 (0.37), residues: 167 loop : -2.32 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.033 0.002 TYR C 71 PHE 0.017 0.002 PHE C 189 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8047) covalent geometry : angle 0.69552 (10906) SS BOND : bond 0.00890 ( 1) SS BOND : angle 2.84527 ( 2) hydrogen bonds : bond 0.04686 ( 426) hydrogen bonds : angle 5.59914 ( 1219) *********************** 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 238 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.311 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: 0.7664 (tpt) cc_final: 0.6110 (tpt) REVERT: C 167 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7053 (ttt180) REVERT: C 216 ASP cc_start: 0.5927 (p0) cc_final: 0.5022 (t0) REVERT: C 260 ILE cc_start: 0.8685 (tt) cc_final: 0.8454 (mt) REVERT: C 329 LEU cc_start: 0.8168 (mm) cc_final: 0.7912 (tt) REVERT: C 359 TYR cc_start: 0.7355 (m-10) cc_final: 0.6697 (m-80) REVERT: A 15 ARG cc_start: 0.8310 (tpm170) cc_final: 0.8089 (ttm-80) REVERT: A 36 LEU cc_start: 0.9355 (mt) cc_final: 0.9064 (mp) REVERT: A 155 TYR cc_start: 0.5795 (m-80) cc_final: 0.5535 (m-80) REVERT: A 164 GLN cc_start: 0.6502 (tm-30) cc_final: 0.6265 (tm-30) REVERT: A 304 GLN cc_start: 0.8899 (tt0) cc_final: 0.8546 (tt0) REVERT: A 305 CYS cc_start: 0.8185 (m) cc_final: 0.7625 (t) REVERT: A 321 THR cc_start: 0.8874 (t) cc_final: 0.8160 (t) REVERT: A 325 CYS cc_start: 0.8168 (p) cc_final: 0.7887 (p) REVERT: B 82 TRP cc_start: 0.9142 (m100) cc_final: 0.8664 (m100) REVERT: B 108 SER cc_start: 0.8898 (m) cc_final: 0.8594 (p) REVERT: B 180 PHE cc_start: 0.7998 (m-80) cc_final: 0.7630 (m-10) REVERT: B 211 TRP cc_start: 0.8022 (m100) cc_final: 0.7770 (m100) REVERT: B 222 PHE cc_start: 0.8432 (m-80) cc_final: 0.8180 (m-80) REVERT: B 225 HIS cc_start: 0.7667 (m-70) cc_final: 0.7228 (m-70) REVERT: B 255 LEU cc_start: 0.8259 (mt) cc_final: 0.7979 (pt) REVERT: B 303 ASP cc_start: 0.7279 (m-30) cc_final: 0.6959 (m-30) REVERT: B 339 TRP cc_start: 0.8830 (m100) cc_final: 0.8290 (m100) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0754 time to fit residues: 25.0290 Evaluate side-chains 182 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 164 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.147611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113665 restraints weight = 62104.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116773 restraints weight = 48694.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120245 restraints weight = 21474.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120380 restraints weight = 14285.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121341 restraints weight = 11960.735| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8048 Z= 0.145 Angle : 0.645 10.875 10908 Z= 0.336 Chirality : 0.043 0.181 1252 Planarity : 0.005 0.079 1381 Dihedral : 5.500 77.098 1092 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 0.23 % Allowed : 4.44 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.26), residues: 993 helix: 0.32 (0.24), residues: 461 sheet: -1.93 (0.37), residues: 167 loop : -1.89 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.012 0.001 TYR B 59 PHE 0.025 0.002 PHE B 235 TRP 0.023 0.002 TRP B 339 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8047) covalent geometry : angle 0.64509 (10906) SS BOND : bond 0.00572 ( 1) SS BOND : angle 1.71867 ( 2) hydrogen bonds : bond 0.04100 ( 426) hydrogen bonds : angle 5.26107 ( 1219) *********************** 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 236 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.259 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: 0.7497 (tpt) cc_final: 0.6202 (tpt) REVERT: C 216 ASP cc_start: 0.5902 (p0) cc_final: 0.5117 (t0) REVERT: C 235 LYS cc_start: 0.6402 (mttt) cc_final: 0.6104 (mmmm) REVERT: C 267 MET cc_start: 0.7596 (ttt) cc_final: 0.7211 (ttp) REVERT: C 325 HIS cc_start: 0.8813 (m-70) cc_final: 0.8542 (m-70) REVERT: C 359 TYR cc_start: 0.7273 (m-10) cc_final: 0.6602 (m-80) REVERT: A 188 HIS cc_start: 0.8455 (m-70) cc_final: 0.8019 (m-70) REVERT: A 195 HIS cc_start: 0.6098 (t70) cc_final: 0.5868 (t-170) REVERT: A 304 GLN cc_start: 0.8848 (tt0) cc_final: 0.8436 (tt0) REVERT: A 305 CYS cc_start: 0.8411 (m) cc_final: 0.7805 (t) REVERT: B 82 TRP cc_start: 0.9079 (m100) cc_final: 0.8572 (m100) REVERT: B 89 LYS cc_start: 0.8835 (mttp) cc_final: 0.7989 (mttp) REVERT: B 108 SER cc_start: 0.8879 (m) cc_final: 0.8678 (p) REVERT: B 180 PHE cc_start: 0.8159 (m-80) cc_final: 0.7351 (m-10) REVERT: B 251 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6832 (tpp80) REVERT: B 311 HIS cc_start: 0.8567 (m-70) cc_final: 0.8362 (m170) outliers start: 1 outliers final: 1 residues processed: 235 average time/residue: 0.0731 time to fit residues: 24.0916 Evaluate side-chains 178 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 0.3980 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 164 GLN A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126336 restraints weight = 47862.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128250 restraints weight = 49941.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130999 restraints weight = 15476.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132990 restraints weight = 8084.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133335 restraints weight = 4712.441| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8048 Z= 0.134 Angle : 0.658 11.428 10908 Z= 0.340 Chirality : 0.043 0.179 1252 Planarity : 0.004 0.076 1381 Dihedral : 5.095 47.855 1092 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 0.23 % Allowed : 2.22 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 993 helix: 0.46 (0.23), residues: 462 sheet: -1.62 (0.36), residues: 182 loop : -1.73 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 328 TYR 0.025 0.001 TYR B 264 PHE 0.023 0.002 PHE A 199 TRP 0.026 0.002 TRP B 339 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8047) covalent geometry : angle 0.65768 (10906) SS BOND : bond 0.00362 ( 1) SS BOND : angle 1.39014 ( 2) hydrogen bonds : bond 0.04093 ( 426) hydrogen bonds : angle 5.07917 ( 1219) *********************** 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 229 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.354 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 88 THR cc_start: 0.7627 (p) cc_final: 0.7280 (p) REVERT: C 121 MET cc_start: 0.7525 (tpt) cc_final: 0.6445 (tpt) REVERT: C 166 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 167 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7006 (ttt180) REVERT: C 216 ASP cc_start: 0.5721 (p0) cc_final: 0.4966 (t0) REVERT: C 267 MET cc_start: 0.7491 (ttt) cc_final: 0.7147 (ttp) REVERT: C 345 ASP cc_start: 0.8147 (m-30) cc_final: 0.7527 (m-30) REVERT: C 359 TYR cc_start: 0.7204 (m-10) cc_final: 0.6651 (m-80) REVERT: A 28 GLU cc_start: 0.6778 (tt0) cc_final: 0.6421 (tt0) REVERT: A 304 GLN cc_start: 0.8874 (tt0) cc_final: 0.8546 (tt0) REVERT: A 305 CYS cc_start: 0.8344 (m) cc_final: 0.7709 (t) REVERT: B 55 LEU cc_start: 0.8990 (mm) cc_final: 0.8593 (mm) REVERT: B 82 TRP cc_start: 0.8881 (m100) cc_final: 0.8389 (m100) REVERT: B 89 LYS cc_start: 0.8863 (mttp) cc_final: 0.7999 (mttp) REVERT: B 172 GLU cc_start: 0.6815 (mp0) cc_final: 0.6453 (mp0) REVERT: B 303 ASP cc_start: 0.7277 (m-30) cc_final: 0.7062 (m-30) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.0896 time to fit residues: 27.8066 Evaluate side-chains 168 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 81 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN A 188 HIS A 331 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 311 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.150734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128356 restraints weight = 54263.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130765 restraints weight = 48449.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133595 restraints weight = 14019.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136363 restraints weight = 6601.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135828 restraints weight = 4032.092| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8048 Z= 0.127 Angle : 0.633 11.563 10908 Z= 0.326 Chirality : 0.043 0.172 1252 Planarity : 0.004 0.075 1381 Dihedral : 4.689 21.205 1092 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 0.23 % Allowed : 2.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.27), residues: 993 helix: 0.79 (0.24), residues: 462 sheet: -1.54 (0.36), residues: 180 loop : -1.57 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 327 TYR 0.014 0.001 TYR C 349 PHE 0.024 0.002 PHE B 234 TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8047) covalent geometry : angle 0.63246 (10906) SS BOND : bond 0.00872 ( 1) SS BOND : angle 2.72865 ( 2) hydrogen bonds : bond 0.03843 ( 426) hydrogen bonds : angle 4.89150 ( 1219) *********************** 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 218 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 THR cc_start: 0.7607 (p) cc_final: 0.7403 (p) REVERT: C 121 MET cc_start: 0.7436 (tpt) cc_final: 0.6456 (tpt) REVERT: C 166 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8690 (tm-30) REVERT: C 167 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7052 (ttt180) REVERT: C 216 ASP cc_start: 0.5928 (p0) cc_final: 0.5214 (t0) REVERT: C 244 MET cc_start: 0.7119 (mmm) cc_final: 0.6899 (tpt) REVERT: C 267 MET cc_start: 0.7341 (ttt) cc_final: 0.7091 (ttp) REVERT: C 345 ASP cc_start: 0.8307 (m-30) cc_final: 0.7922 (m-30) REVERT: C 359 TYR cc_start: 0.7005 (m-10) cc_final: 0.6512 (m-80) REVERT: A 28 GLU cc_start: 0.6716 (tt0) cc_final: 0.6451 (tt0) REVERT: A 197 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8532 (ttmt) REVERT: A 198 MET cc_start: 0.8819 (tpp) cc_final: 0.8558 (mmm) REVERT: A 304 GLN cc_start: 0.8829 (tt0) cc_final: 0.8504 (tt0) REVERT: A 305 CYS cc_start: 0.8394 (m) cc_final: 0.7683 (t) REVERT: B 45 MET cc_start: 0.8051 (mmt) cc_final: 0.7815 (mmm) REVERT: B 89 LYS cc_start: 0.8775 (mttp) cc_final: 0.8306 (mtpt) REVERT: B 172 GLU cc_start: 0.6823 (mp0) cc_final: 0.6454 (mp0) REVERT: B 180 PHE cc_start: 0.8009 (m-80) cc_final: 0.7428 (m-10) REVERT: B 211 TRP cc_start: 0.7867 (m100) cc_final: 0.7652 (m100) REVERT: B 303 ASP cc_start: 0.7292 (m-30) cc_final: 0.7088 (m-30) REVERT: G 66 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6842 (tm-30) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.0870 time to fit residues: 26.0512 Evaluate side-chains 161 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS A 164 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.121334 restraints weight = 62133.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124330 restraints weight = 51991.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126310 restraints weight = 17627.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128973 restraints weight = 11009.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129072 restraints weight = 7326.673| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8048 Z= 0.147 Angle : 0.645 10.211 10908 Z= 0.336 Chirality : 0.043 0.171 1252 Planarity : 0.004 0.074 1381 Dihedral : 4.706 25.794 1092 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 0.35 % Allowed : 2.46 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 993 helix: 0.81 (0.24), residues: 461 sheet: -1.50 (0.37), residues: 182 loop : -1.49 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 47 TYR 0.019 0.001 TYR B 264 PHE 0.017 0.002 PHE B 180 TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8047) covalent geometry : angle 0.64425 (10906) SS BOND : bond 0.00477 ( 1) SS BOND : angle 1.86607 ( 2) hydrogen bonds : bond 0.03994 ( 426) hydrogen bonds : angle 4.87977 ( 1219) *********************** 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 210 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.287 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 88 THR cc_start: 0.7662 (p) cc_final: 0.7272 (p) REVERT: C 166 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8732 (tm-30) REVERT: C 167 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7100 (ttt180) REVERT: C 216 ASP cc_start: 0.6154 (p0) cc_final: 0.5437 (t0) REVERT: C 257 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7596 (t0) REVERT: C 267 MET cc_start: 0.7365 (ttt) cc_final: 0.7040 (ttp) REVERT: C 345 ASP cc_start: 0.8172 (m-30) cc_final: 0.7583 (m-30) REVERT: A 198 MET cc_start: 0.8800 (tpp) cc_final: 0.8502 (mmm) REVERT: A 304 GLN cc_start: 0.8826 (tt0) cc_final: 0.8600 (tt0) REVERT: A 305 CYS cc_start: 0.8427 (m) cc_final: 0.7703 (t) REVERT: B 45 MET cc_start: 0.8037 (mmt) cc_final: 0.7619 (mmt) REVERT: B 55 LEU cc_start: 0.8828 (mm) cc_final: 0.8408 (mm) REVERT: B 89 LYS cc_start: 0.8779 (mttp) cc_final: 0.8418 (mtmm) REVERT: B 172 GLU cc_start: 0.6838 (mp0) cc_final: 0.6494 (mp0) REVERT: B 180 PHE cc_start: 0.8136 (m-80) cc_final: 0.7512 (m-10) REVERT: B 211 TRP cc_start: 0.7959 (m100) cc_final: 0.7554 (m100) REVERT: B 225 HIS cc_start: 0.7364 (m-70) cc_final: 0.6962 (m-70) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.0825 time to fit residues: 23.9996 Evaluate side-chains 166 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS A 164 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.149721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126136 restraints weight = 59439.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128983 restraints weight = 48710.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132461 restraints weight = 14385.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133267 restraints weight = 6637.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133744 restraints weight = 4938.256| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8048 Z= 0.130 Angle : 0.643 12.347 10908 Z= 0.331 Chirality : 0.043 0.175 1252 Planarity : 0.004 0.072 1381 Dihedral : 4.695 22.917 1092 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 0.23 % Allowed : 1.52 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.27), residues: 993 helix: 0.82 (0.24), residues: 460 sheet: -1.40 (0.36), residues: 190 loop : -1.47 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.019 0.001 TYR C 359 PHE 0.014 0.002 PHE A 199 TRP 0.013 0.001 TRP B 297 HIS 0.006 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8047) covalent geometry : angle 0.64309 (10906) SS BOND : bond 0.00363 ( 1) SS BOND : angle 1.57190 ( 2) hydrogen bonds : bond 0.03896 ( 426) hydrogen bonds : angle 4.80841 ( 1219) *********************** 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 211 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.213 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 88 THR cc_start: 0.7617 (p) cc_final: 0.7384 (p) REVERT: C 166 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8698 (tm-30) REVERT: C 167 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7020 (ttt180) REVERT: C 216 ASP cc_start: 0.6118 (p0) cc_final: 0.5434 (t0) REVERT: C 267 MET cc_start: 0.7457 (ttt) cc_final: 0.7073 (ttp) REVERT: A 197 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8317 (ttmt) REVERT: A 198 MET cc_start: 0.8919 (tpp) cc_final: 0.8621 (mmm) REVERT: A 304 GLN cc_start: 0.8817 (tt0) cc_final: 0.8491 (tt0) REVERT: A 305 CYS cc_start: 0.8456 (m) cc_final: 0.7759 (t) REVERT: B 45 MET cc_start: 0.8058 (mmt) cc_final: 0.7592 (mmt) REVERT: B 89 LYS cc_start: 0.8788 (mttp) cc_final: 0.8394 (mtmm) REVERT: B 172 GLU cc_start: 0.6841 (mp0) cc_final: 0.6508 (mp0) REVERT: B 180 PHE cc_start: 0.8181 (m-80) cc_final: 0.7555 (m-10) REVERT: B 211 TRP cc_start: 0.7958 (m100) cc_final: 0.7569 (m100) REVERT: B 251 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6969 (tpp80) REVERT: B 289 TYR cc_start: 0.7942 (m-80) cc_final: 0.7579 (m-80) REVERT: B 339 TRP cc_start: 0.8779 (m100) cc_final: 0.8312 (m100) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.0781 time to fit residues: 23.3469 Evaluate side-chains 157 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS A 164 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.145614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119662 restraints weight = 38113.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123134 restraints weight = 47100.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126378 restraints weight = 14421.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127283 restraints weight = 8384.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127639 restraints weight = 6114.145| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8048 Z= 0.164 Angle : 0.677 11.972 10908 Z= 0.355 Chirality : 0.044 0.175 1252 Planarity : 0.004 0.073 1381 Dihedral : 4.747 24.457 1092 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 0.23 % Allowed : 0.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 993 helix: 0.79 (0.24), residues: 462 sheet: -1.41 (0.36), residues: 192 loop : -1.48 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.026 0.002 TYR C 359 PHE 0.016 0.002 PHE C 206 TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8047) covalent geometry : angle 0.67653 (10906) SS BOND : bond 0.00285 ( 1) SS BOND : angle 1.59200 ( 2) hydrogen bonds : bond 0.04097 ( 426) hydrogen bonds : angle 4.91771 ( 1219) *********************** 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 208 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.294 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: symmetry clash REVERT: C 88 THR cc_start: 0.7767 (p) cc_final: 0.7265 (p) REVERT: C 166 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8760 (tm-30) REVERT: C 167 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7083 (ttt180) REVERT: C 216 ASP cc_start: 0.6105 (p0) cc_final: 0.5420 (t0) REVERT: C 345 ASP cc_start: 0.8263 (m-30) cc_final: 0.7374 (m-30) REVERT: C 359 TYR cc_start: 0.6706 (m-80) cc_final: 0.6377 (m-80) REVERT: A 304 GLN cc_start: 0.8826 (tt0) cc_final: 0.8614 (tt0) REVERT: A 305 CYS cc_start: 0.8466 (m) cc_final: 0.7721 (t) REVERT: B 45 MET cc_start: 0.8024 (mmt) cc_final: 0.7593 (mmt) REVERT: B 55 LEU cc_start: 0.8912 (mm) cc_final: 0.8489 (mm) REVERT: B 71 VAL cc_start: 0.9477 (t) cc_final: 0.9273 (p) REVERT: B 89 LYS cc_start: 0.8798 (mttp) cc_final: 0.8470 (mtmm) REVERT: B 180 PHE cc_start: 0.8222 (m-80) cc_final: 0.7565 (m-10) REVERT: B 211 TRP cc_start: 0.8101 (m100) cc_final: 0.7692 (m100) REVERT: B 289 TYR cc_start: 0.8133 (m-80) cc_final: 0.7722 (m-80) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.0734 time to fit residues: 21.5018 Evaluate side-chains 156 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 90 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 92 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 164 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.146559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124821 restraints weight = 54487.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127222 restraints weight = 50457.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130542 restraints weight = 14077.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132461 restraints weight = 6002.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132307 restraints weight = 3965.345| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3732 r_free = 0.3732 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8048 Z= 0.142 Angle : 0.658 11.605 10908 Z= 0.341 Chirality : 0.044 0.171 1252 Planarity : 0.004 0.073 1381 Dihedral : 4.722 22.005 1092 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 0.23 % Allowed : 0.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 993 helix: 0.87 (0.24), residues: 461 sheet: -1.35 (0.36), residues: 192 loop : -1.46 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 327 TYR 0.029 0.002 TYR B 264 PHE 0.016 0.002 PHE C 206 TRP 0.016 0.002 TRP B 297 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8047) covalent geometry : angle 0.65753 (10906) SS BOND : bond 0.00254 ( 1) SS BOND : angle 1.59218 ( 2) hydrogen bonds : bond 0.03970 ( 426) hydrogen bonds : angle 4.90657 ( 1219) *********************** 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 202 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.311 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 71 TYR cc_start: 0.6511 (m-80) cc_final: 0.4726 (m-80) REVERT: C 88 THR cc_start: 0.7583 (p) cc_final: 0.7233 (p) REVERT: C 129 ILE cc_start: 0.8149 (mp) cc_final: 0.7860 (mp) REVERT: C 166 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8735 (tm-30) REVERT: C 167 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7165 (ttt180) REVERT: C 216 ASP cc_start: 0.6095 (p0) cc_final: 0.5410 (t0) REVERT: C 359 TYR cc_start: 0.6800 (m-80) cc_final: 0.6420 (m-80) REVERT: A 197 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8355 (ttmt) REVERT: A 198 MET cc_start: 0.8911 (tpp) cc_final: 0.8659 (mmm) REVERT: A 305 CYS cc_start: 0.8411 (m) cc_final: 0.7670 (t) REVERT: B 45 MET cc_start: 0.8026 (mmt) cc_final: 0.7503 (mmt) REVERT: B 55 LEU cc_start: 0.8935 (mm) cc_final: 0.8522 (mm) REVERT: B 89 LYS cc_start: 0.8778 (mttp) cc_final: 0.8405 (mtmm) REVERT: B 172 GLU cc_start: 0.6962 (mp0) cc_final: 0.6673 (mp0) REVERT: B 180 PHE cc_start: 0.8208 (m-80) cc_final: 0.7496 (m-10) REVERT: B 211 TRP cc_start: 0.8011 (m100) cc_final: 0.7536 (m100) REVERT: B 251 ARG cc_start: 0.7227 (mtt90) cc_final: 0.6872 (tpp80) REVERT: B 289 TYR cc_start: 0.8016 (m-80) cc_final: 0.7647 (m-80) REVERT: B 339 TRP cc_start: 0.8755 (m100) cc_final: 0.8259 (m100) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.0801 time to fit residues: 22.7079 Evaluate side-chains 161 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 95 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 164 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122966 restraints weight = 51421.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125121 restraints weight = 52661.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.128880 restraints weight = 16551.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130619 restraints weight = 7843.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130598 restraints weight = 5411.698| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8048 Z= 0.147 Angle : 0.665 11.635 10908 Z= 0.346 Chirality : 0.044 0.176 1252 Planarity : 0.004 0.073 1381 Dihedral : 4.748 21.808 1092 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 0.23 % Allowed : 0.35 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.27), residues: 993 helix: 0.78 (0.24), residues: 463 sheet: -1.19 (0.36), residues: 187 loop : -1.52 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 327 TYR 0.026 0.002 TYR B 264 PHE 0.016 0.002 PHE C 206 TRP 0.017 0.002 TRP B 297 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8047) covalent geometry : angle 0.66439 (10906) SS BOND : bond 0.00291 ( 1) SS BOND : angle 1.49918 ( 2) hydrogen bonds : bond 0.03998 ( 426) hydrogen bonds : angle 4.86499 ( 1219) ********************** 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 199 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.308 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: symmetry clash revert: symmetry clash REVERT: C 88 THR cc_start: 0.7653 (p) cc_final: 0.7302 (p) REVERT: C 166 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 167 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7027 (ttt180) REVERT: C 216 ASP cc_start: 0.6029 (p0) cc_final: 0.5432 (t0) REVERT: C 349 TYR cc_start: 0.6969 (m-80) cc_final: 0.6633 (m-80) REVERT: C 359 TYR cc_start: 0.6875 (m-80) cc_final: 0.6502 (m-80) REVERT: A 197 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8540 (ttmt) REVERT: A 305 CYS cc_start: 0.8379 (m) cc_final: 0.7718 (t) REVERT: B 45 MET cc_start: 0.8064 (mmt) cc_final: 0.7533 (mmt) REVERT: B 55 LEU cc_start: 0.8900 (mm) cc_final: 0.8466 (mm) REVERT: B 172 GLU cc_start: 0.7026 (mp0) cc_final: 0.6741 (mp0) REVERT: B 180 PHE cc_start: 0.8248 (m-80) cc_final: 0.7481 (m-10) REVERT: B 211 TRP cc_start: 0.8110 (m100) cc_final: 0.7727 (m100) REVERT: B 289 TYR cc_start: 0.8114 (m-80) cc_final: 0.7770 (m-80) REVERT: B 339 TRP cc_start: 0.8722 (m100) cc_final: 0.8302 (m100) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.0797 time to fit residues: 22.2112 Evaluate side-chains 159 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 90 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.150104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123131 restraints weight = 63980.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125958 restraints weight = 49885.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129819 restraints weight = 19534.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129825 restraints weight = 12677.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130648 restraints weight = 8842.715| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8048 Z= 0.128 Angle : 0.663 11.789 10908 Z= 0.344 Chirality : 0.044 0.188 1252 Planarity : 0.004 0.072 1381 Dihedral : 4.722 20.552 1092 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 0.23 % Allowed : 0.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.27), residues: 993 helix: 0.78 (0.24), residues: 462 sheet: -1.12 (0.37), residues: 187 loop : -1.50 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 327 TYR 0.034 0.002 TYR C 71 PHE 0.015 0.001 PHE C 206 TRP 0.017 0.002 TRP C 321 HIS 0.014 0.002 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8047) covalent geometry : angle 0.66288 (10906) SS BOND : bond 0.00261 ( 1) SS BOND : angle 1.38314 ( 2) hydrogen bonds : bond 0.03977 ( 426) hydrogen bonds : angle 4.86072 ( 1219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.74 seconds wall clock time: 26 minutes 17.96 seconds (1577.96 seconds total)